Human Embryology - User contributions [en]

Domenech-Mateu Collection Embryos

2021-08-02T11:29:45Z

AnnaUAB: /* F061 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-E58-033 and UAB-E58-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F052===

Crown-Rump Length: 70mm

Scanned one out of two slides from 01-260 and correlative slides from 506-529 (upper limb) Two scans of each slide were taken in this case.

On march 18, 19, 22, 2021 and may 07, 10, 11 and 12 2021.

Some ROIs were not in order, check with the screenshots

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F059===

Crown-Rump Length: 76mm

Scanned one out of two slides from 294-529

On march 23, 24, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

LOWER LIMB: Slides from 530-556.Two scans of each slide were taken

Scann1: june 8th 2021.

Scann2: june 9th and 11th 2021

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F061===

Crown-Rump Length: 82mm

Scanned one out of three slides from 01-209. On april 06, 07, 08, 09 and 12 2021. Some ROIs are upside down

Correlative slides scanned from 229-428. on may 26, 27, 28, 29, 31th and june 1, 2 and 3 2021

Scanned one out of three slides from 429-796

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F069===

Crown-Rump Length: 95mm

Non correlative slides were scanned from 01-387

On april 22, 23, 26, and 27 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F070===

Crown-Rump Length: 100mm. Upper limb.

Two scans of correlative slides were made from 01-55

On may 14, 15, and 17 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F070-B===

Crown-Rump Length: 100mm

Body part: Hand and wrist

Correlative slides were scanned from 64-87. Two scans of each slide were taken. On scan2 ROIs are upside down.

On may 07, 10 and 11 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F071===

Crown-Rump Length: 105mm

Non correlative slides scanned from 19-769.

On april 27, 28, 29, 30 and may 03, 04, and 05 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F072===

Crown-Rump Length: 108mm

Non correlative slides were scanned from 23-229

On may 05 and 06 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F076===

Crown-Rump Length: 130mm

Non correlative slides were scanned from 401-1449

On may 11, 12, 13, 14, 17, 18 and 19 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F077===

Crown-Rump Length: 132mm

Non correlative slides were scanned from 26-352

On may 19, 20, 21 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F079===

Crown-Rump Length: 150mm

Upper limb

two scans of each slide were taken. Slides from 219-245

On april 09, 13 and may 06, 07 2021.

ROIs from scan 2 are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F081===

Crown-Rump Length: 160mm

Non correlative slides were scanned from 1052-1328

On may 21, 25, 26 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-08-02T11:25:27Z

AnnaUAB: /* F069 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-E58-033 and UAB-E58-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F052===

Crown-Rump Length: 70mm

Scanned one out of two slides from 01-260 and correlative slides from 506-529 (upper limb) Two scans of each slide were taken in this case.

On march 18, 19, 22, 2021 and may 07, 10, 11 and 12 2021.

Some ROIs were not in order, check with the screenshots

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F059===

Crown-Rump Length: 76mm

Scanned one out of two slides from 294-529

On march 23, 24, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

LOWER LIMB: Slides from 530-556.Two scans of each slide were taken

Scann1: june 8th 2021.

Scann2: june 9th and 11th 2021

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F061===

Crown-Rump Length: 82mm

Scanned one out of three slides from 01-209. On april 06, 07, 08, 09 and 12 2021. Some ROIs are upside down

Correlative slides scanned from 244-428. on may 27, 28, 29, 31th and june 1, 2 and 3 2021

Scanned one out of three slides from 429-796

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F069===

Crown-Rump Length: 95mm

Non correlative slides were scanned from 01-387

On april 22, 23, 26, and 27 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F070===

Crown-Rump Length: 100mm. Upper limb.

Two scans of correlative slides were made from 01-55

On may 14, 15, and 17 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F070-B===

Crown-Rump Length: 100mm

Body part: Hand and wrist

Correlative slides were scanned from 64-87. Two scans of each slide were taken. On scan2 ROIs are upside down.

On may 07, 10 and 11 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F071===

Crown-Rump Length: 105mm

Non correlative slides scanned from 19-769.

On april 27, 28, 29, 30 and may 03, 04, and 05 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F072===

Crown-Rump Length: 108mm

Non correlative slides were scanned from 23-229

On may 05 and 06 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F076===

Crown-Rump Length: 130mm

Non correlative slides were scanned from 401-1449

On may 11, 12, 13, 14, 17, 18 and 19 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F077===

Crown-Rump Length: 132mm

Non correlative slides were scanned from 26-352

On may 19, 20, 21 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F079===

Crown-Rump Length: 150mm

Upper limb

two scans of each slide were taken. Slides from 219-245

On april 09, 13 and may 06, 07 2021.

ROIs from scan 2 are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F081===

Crown-Rump Length: 160mm

Non correlative slides were scanned from 1052-1328

On may 21, 25, 26 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-08-02T11:17:14Z

AnnaUAB: /* F061 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-E58-033 and UAB-E58-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F052===

Crown-Rump Length: 70mm

Scanned one out of two slides from 01-260 and correlative slides from 506-529 (upper limb) Two scans of each slide were taken in this case.

On march 18, 19, 22, 2021 and may 07, 10, 11 and 12 2021.

Some ROIs were not in order, check with the screenshots

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F059===

Crown-Rump Length: 76mm

Scanned one out of two slides from 294-529

On march 23, 24, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

LOWER LIMB: Slides from 530-556.Two scans of each slide were taken

Scann1: june 8th 2021.

Scann2: june 9th and 11th 2021

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F061===

Crown-Rump Length: 82mm

Scanned one out of three slides from 01-209. On april 06, 07, 08, 09 and 12 2021. Some ROIs are upside down

Correlative slides scanned from 244-428. on may 27, 28, 29, 31th and june 1, 2 and 3 2021

Scanned one out of three slides from 429-796

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F069===

Crown-Rump Length: 95mm

Non correlative slides were scanned from 01-387

On april 22, 23, 26, and 27 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F070-B===

Crown-Rump Length: 100mm

Body part: Hand and wrist

Correlative slides were scanned from 64-87. Two scans of each slide were taken. On scan2 ROIs are upside down.

On may 07, 10 and 11 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F071===

Crown-Rump Length: 105mm

Non correlative slides scanned from 19-769.

On april 27, 28, 29, 30 and may 03, 04, and 05 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F072===

Crown-Rump Length: 108mm

Non correlative slides were scanned from 23-229

On may 05 and 06 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F076===

Crown-Rump Length: 130mm

Non correlative slides were scanned from 401-1449

On may 11, 12, 13, 14, 17, 18 and 19 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F077===

Crown-Rump Length: 132mm

Non correlative slides were scanned from 26-352

On may 19, 20, 21 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F079===

Crown-Rump Length: 150mm

Upper limb

two scans of each slide were taken. Slides from 219-245

On april 09, 13 and may 06, 07 2021.

ROIs from scan 2 are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F081===

Crown-Rump Length: 160mm

Non correlative slides were scanned from 1052-1328

On may 21, 25, 26 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-08-02T11:09:26Z

AnnaUAB: /* F059 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-E58-033 and UAB-E58-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F052===

Crown-Rump Length: 70mm

Scanned one out of two slides from 01-260 and correlative slides from 506-529 (upper limb) Two scans of each slide were taken in this case.

On march 18, 19, 22, 2021 and may 07, 10, 11 and 12 2021.

Some ROIs were not in order, check with the screenshots

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F059===

Crown-Rump Length: 76mm

Scanned one out of two slides from 294-529

On march 23, 24, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

LOWER LIMB: Slides from 530-556.Two scans of each slide were taken

Scann1: june 8th 2021.

Scann2: june 9th and 11th 2021

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F061===

Crown-Rump Length: 82mm

Scanned one out of three slides from 01-796

On april 06, 07, 08, 09 and 12 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F069===

Crown-Rump Length: 95mm

Non correlative slides were scanned from 01-387

On april 22, 23, 26, and 27 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F070-B===

Crown-Rump Length: 100mm

Body part: Hand and wrist

Correlative slides were scanned from 64-87. Two scans of each slide were taken. On scan2 ROIs are upside down.

On may 07, 10 and 11 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F071===

Crown-Rump Length: 105mm

Non correlative slides scanned from 19-769.

On april 27, 28, 29, 30 and may 03, 04, and 05 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F072===

Crown-Rump Length: 108mm

Non correlative slides were scanned from 23-229

On may 05 and 06 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F076===

Crown-Rump Length: 130mm

Non correlative slides were scanned from 401-1449

On may 11, 12, 13, 14, 17, 18 and 19 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F077===

Crown-Rump Length: 132mm

Non correlative slides were scanned from 26-352

On may 19, 20, 21 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F079===

Crown-Rump Length: 150mm

Upper limb

two scans of each slide were taken. Slides from 219-245

On april 09, 13 and may 06, 07 2021.

ROIs from scan 2 are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F081===

Crown-Rump Length: 160mm

Non correlative slides were scanned from 1052-1328

On may 21, 25, 26 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-08-02T11:07:00Z

AnnaUAB:

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-E58-033 and UAB-E58-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F052===

Crown-Rump Length: 70mm

Scanned one out of two slides from 01-260 and correlative slides from 506-529 (upper limb) Two scans of each slide were taken in this case.

On march 18, 19, 22, 2021 and may 07, 10, 11 and 12 2021.

Some ROIs were not in order, check with the screenshots

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F059===

Crown-Rump Length: 76mm

Scanned one out of two slides from 294-529

On march 23, 24, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F061===

Crown-Rump Length: 82mm

Scanned one out of three slides from 01-796

On april 06, 07, 08, 09 and 12 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F069===

Crown-Rump Length: 95mm

Non correlative slides were scanned from 01-387

On april 22, 23, 26, and 27 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F070-B===

Crown-Rump Length: 100mm

Body part: Hand and wrist

Correlative slides were scanned from 64-87. Two scans of each slide were taken. On scan2 ROIs are upside down.

On may 07, 10 and 11 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F071===

Crown-Rump Length: 105mm

Non correlative slides scanned from 19-769.

On april 27, 28, 29, 30 and may 03, 04, and 05 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F072===

Crown-Rump Length: 108mm

Non correlative slides were scanned from 23-229

On may 05 and 06 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F076===

Crown-Rump Length: 130mm

Non correlative slides were scanned from 401-1449

On may 11, 12, 13, 14, 17, 18 and 19 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F077===

Crown-Rump Length: 132mm

Non correlative slides were scanned from 26-352

On may 19, 20, 21 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F079===

Crown-Rump Length: 150mm

Upper limb

two scans of each slide were taken. Slides from 219-245

On april 09, 13 and may 06, 07 2021.

ROIs from scan 2 are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F081===

Crown-Rump Length: 160mm

Non correlative slides were scanned from 1052-1328

On may 21, 25, 26 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-08-02T11:06:38Z

AnnaUAB: /* E058 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-E58-033 and UAB-E58-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E059===

Lower limb. two scans of each slide were taken

Scann1: june 8th 2021.

Scann2: june 9th and 11th 2021

Slides from F59-530 to F59-556

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F052===

Crown-Rump Length: 70mm

Scanned one out of two slides from 01-260 and correlative slides from 506-529 (upper limb) Two scans of each slide were taken in this case.

On march 18, 19, 22, 2021 and may 07, 10, 11 and 12 2021.

Some ROIs were not in order, check with the screenshots

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F059===

Crown-Rump Length: 76mm

Scanned one out of two slides from 294-529

On march 23, 24, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F061===

Crown-Rump Length: 82mm

Scanned one out of three slides from 01-796

On april 06, 07, 08, 09 and 12 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F069===

Crown-Rump Length: 95mm

Non correlative slides were scanned from 01-387

On april 22, 23, 26, and 27 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F070-B===

Crown-Rump Length: 100mm

Body part: Hand and wrist

Correlative slides were scanned from 64-87. Two scans of each slide were taken. On scan2 ROIs are upside down.

On may 07, 10 and 11 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F071===

Crown-Rump Length: 105mm

Non correlative slides scanned from 19-769.

On april 27, 28, 29, 30 and may 03, 04, and 05 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F072===

Crown-Rump Length: 108mm

Non correlative slides were scanned from 23-229

On may 05 and 06 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F076===

Crown-Rump Length: 130mm

Non correlative slides were scanned from 401-1449

On may 11, 12, 13, 14, 17, 18 and 19 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F077===

Crown-Rump Length: 132mm

Non correlative slides were scanned from 26-352

On may 19, 20, 21 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F079===

Crown-Rump Length: 150mm

Upper limb

two scans of each slide were taken. Slides from 219-245

On april 09, 13 and may 06, 07 2021.

ROIs from scan 2 are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F081===

Crown-Rump Length: 160mm

Non correlative slides were scanned from 1052-1328

On may 21, 25, 26 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-08-02T11:04:34Z

AnnaUAB: /* E058 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-F58-033 and UAB-F58-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E059===

Lower limb. two scans of each slide were taken

Scann1: june 8th 2021.

Scann2: june 9th and 11th 2021

Slides from F59-530 to F59-556

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F052===

Crown-Rump Length: 70mm

Scanned one out of two slides from 01-260 and correlative slides from 506-529 (upper limb) Two scans of each slide were taken in this case.

On march 18, 19, 22, 2021 and may 07, 10, 11 and 12 2021.

Some ROIs were not in order, check with the screenshots

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F059===

Crown-Rump Length: 76mm

Scanned one out of two slides from 294-529

On march 23, 24, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F061===

Crown-Rump Length: 82mm

Scanned one out of three slides from 01-796

On april 06, 07, 08, 09 and 12 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F069===

Crown-Rump Length: 95mm

Non correlative slides were scanned from 01-387

On april 22, 23, 26, and 27 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F070-B===

Crown-Rump Length: 100mm

Body part: Hand and wrist

Correlative slides were scanned from 64-87. Two scans of each slide were taken. On scan2 ROIs are upside down.

On may 07, 10 and 11 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F071===

Crown-Rump Length: 105mm

Non correlative slides scanned from 19-769.

On april 27, 28, 29, 30 and may 03, 04, and 05 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F072===

Crown-Rump Length: 108mm

Non correlative slides were scanned from 23-229

On may 05 and 06 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F076===

Crown-Rump Length: 130mm

Non correlative slides were scanned from 401-1449

On may 11, 12, 13, 14, 17, 18 and 19 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F077===

Crown-Rump Length: 132mm

Non correlative slides were scanned from 26-352

On may 19, 20, 21 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F079===

Crown-Rump Length: 150mm

Upper limb

two scans of each slide were taken. Slides from 219-245

On april 09, 13 and may 06, 07 2021.

ROIs from scan 2 are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F081===

Crown-Rump Length: 160mm

Non correlative slides were scanned from 1052-1328

On may 21, 25, 26 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-26T13:38:39Z

AnnaUAB: /* F077 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F052===

Crown-Rump Length: 70mm

Scanned one out of two slides from 01-260 and correlative slides from 506-529 (upper limb) Two scans of each slide were taken in this case.

On march 18, 19, 22, 2021 and may 07, 10, 11 and 12 2021.

Some ROIs were not in order, check with the screenshots

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F059===

Crown-Rump Length: 76mm

Scanned one out of two slides from 294-529

On march 23, 24, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F061===

Crown-Rump Length: 82mm

Scanned one out of three slides from 01-796

On april 06, 07, 08, 09 and 12 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F069===

Crown-Rump Length: 95mm

Non correlative slides were scanned from 01-387

On april 22, 23, 26, and 27 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F070-B===

Crown-Rump Length: 100mm

Body part: Hand and wrist

Correlative slides were scanned from 64-87. Two scans of each slide were taken. On scan2 ROIs are upside down.

On may 07, 10 and 11 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F071===

Crown-Rump Length: 105mm

Non correlative slides scanned from 19-769.

On april 27, 28, 29, 30 and may 03, 04, and 05 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F072===

Crown-Rump Length: 108mm

Non correlative slides were scanned from 23-229

On may 05 and 06 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F076===

Crown-Rump Length: 130mm

Non correlative slides were scanned from 401-1449

On may 11, 12, 13, 14, 17, 18 and 19 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F077===

Crown-Rump Length: 132mm

Non correlative slides were scanned from 26-352

On may 19, 20, 21 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F079===

Crown-Rump Length: 150mm

Upper limb

two scans of each slide were taken. Slides from 219-245

On april 09, 13 and may 06, 07 2021.

ROIs from scan 2 are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F081===

Crown-Rump Length: 160mm

Non correlative slides were scanned from 1052-1328

On may 21, 25, 26 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-26T13:37:23Z

AnnaUAB: /* F079 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F052===

Crown-Rump Length: 70mm

Scanned one out of two slides from 01-260 and correlative slides from 506-529 (upper limb) Two scans of each slide were taken in this case.

On march 18, 19, 22, 2021 and may 07, 10, 11 and 12 2021.

Some ROIs were not in order, check with the screenshots

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F059===

Crown-Rump Length: 76mm

Scanned one out of two slides from 294-529

On march 23, 24, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F061===

Crown-Rump Length: 82mm

Scanned one out of three slides from 01-796

On april 06, 07, 08, 09 and 12 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F069===

Crown-Rump Length: 95mm

Non correlative slides were scanned from 01-387

On april 22, 23, 26, and 27 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F070-B===

Crown-Rump Length: 100mm

Body part: Hand and wrist

Correlative slides were scanned from 64-87. Two scans of each slide were taken. On scan2 ROIs are upside down.

On may 07, 10 and 11 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F071===

Crown-Rump Length: 105mm

Non correlative slides scanned from 19-769.

On april 27, 28, 29, 30 and may 03, 04, and 05 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F072===

Crown-Rump Length: 108mm

Non correlative slides were scanned from 23-229

On may 05 and 06 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F076===

Crown-Rump Length: 130mm

Non correlative slides were scanned from 401-1449

On may 11, 12, 13, 14, 17, 18 and 19 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F077===

Crown-Rump Length: 132mm

Non correlative slides were scanned from 26-352

On may 19, 20, 13, 21 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F079===

Crown-Rump Length: 150mm

Upper limb

two scans of each slide were taken. Slides from 219-245

On april 09, 13 and may 06, 07 2021.

ROIs from scan 2 are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F081===

Crown-Rump Length: 160mm

Non correlative slides were scanned from 1052-1328

On may 21, 25, 26 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-26T13:33:47Z

AnnaUAB: /* F050 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F052===

Crown-Rump Length: 70mm

Scanned one out of two slides from 01-260 and correlative slides from 506-529 (upper limb) Two scans of each slide were taken in this case.

On march 18, 19, 22, 2021 and may 07, 10, 11 and 12 2021.

Some ROIs were not in order, check with the screenshots

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F059===

Crown-Rump Length: 76mm

Scanned one out of two slides from 294-529

On march 23, 24, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F061===

Crown-Rump Length: 82mm

Scanned one out of three slides from 01-796

On april 06, 07, 08, 09 and 12 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F069===

Crown-Rump Length: 95mm

Non correlative slides were scanned from 01-387

On april 22, 23, 26, and 27 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F070-B===

Crown-Rump Length: 100mm

Body part: Hand and wrist

Correlative slides were scanned from 64-87. Two scans of each slide were taken. On scan2 ROIs are upside down.

On may 07, 10 and 11 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F071===

Crown-Rump Length: 105mm

Non correlative slides scanned from 19-769.

On april 27, 28, 29, 30 and may 03, 04, and 05 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F072===

Crown-Rump Length: 108mm

Non correlative slides were scanned from 23-229

On may 05 and 06 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F076===

Crown-Rump Length: 130mm

Non correlative slides were scanned from 401-1449

On may 11, 12, 13, 14, 17, 18 and 19 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F077===

Crown-Rump Length: 132mm

Non correlative slides were scanned from 26-352

On may 19, 20, 13, 21 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F079===

Crown-Rump Length: 150mm

Upper limb

two scans of each slide were taken. Slides from 219-245

On april 09, 13 and may 06, 07 2021.

ROIs from scan 2 are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-26T13:33:27Z

AnnaUAB: /* F052 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F059===

Crown-Rump Length: 76mm

Scanned one out of two slides from 294-529

On march 23, 24, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F061===

Crown-Rump Length: 82mm

Scanned one out of three slides from 01-796

On april 06, 07, 08, 09 and 12 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F069===

Crown-Rump Length: 95mm

Non correlative slides were scanned from 01-387

On april 22, 23, 26, and 27 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F070-B===

Crown-Rump Length: 100mm

Body part: Hand and wrist

Correlative slides were scanned from 64-87. Two scans of each slide were taken. On scan2 ROIs are upside down.

On may 07, 10 and 11 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F071===

Crown-Rump Length: 105mm

Non correlative slides scanned from 19-769.

On april 27, 28, 29, 30 and may 03, 04, and 05 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F072===

Crown-Rump Length: 108mm

Non correlative slides were scanned from 23-229

On may 05 and 06 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F076===

Crown-Rump Length: 130mm

Non correlative slides were scanned from 401-1449

On may 11, 12, 13, 14, 17, 18 and 19 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F077===

Crown-Rump Length: 132mm

Non correlative slides were scanned from 26-352

On may 19, 20, 13, 21 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F079===

Crown-Rump Length: 150mm

Upper limb

two scans of each slide were taken. Slides from 219-245

On april 09, 13 and may 06, 07 2021.

ROIs from scan 2 are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-26T13:31:57Z

AnnaUAB: /* F076 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F052===

Crown-Rump Length: 70mm

Scanned one out of two slides from 01-260 and correlative slides from 506-529 (upper limb) Two scans of each slide were taken in this case.

On march 18, 19, 22, 2021 and may 07, 10, 11 and 12 2021.

Some ROIs were not in order, check with the screenshots

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F059===

Crown-Rump Length: 76mm

Scanned one out of two slides from 294-529

On march 23, 24, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F061===

Crown-Rump Length: 82mm

Scanned one out of three slides from 01-796

On april 06, 07, 08, 09 and 12 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F069===

Crown-Rump Length: 95mm

Non correlative slides were scanned from 01-387

On april 22, 23, 26, and 27 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F070-B===

Crown-Rump Length: 100mm

Body part: Hand and wrist

Correlative slides were scanned from 64-87. Two scans of each slide were taken. On scan2 ROIs are upside down.

On may 07, 10 and 11 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F071===

Crown-Rump Length: 105mm

Non correlative slides scanned from 19-769.

On april 27, 28, 29, 30 and may 03, 04, and 05 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F072===

Crown-Rump Length: 108mm

Non correlative slides were scanned from 23-229

On may 05 and 06 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F076===

Crown-Rump Length: 130mm

Non correlative slides were scanned from 401-1449

On may 11, 12, 13, 14, 17, 18 and 19 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F077===

Crown-Rump Length: 132mm

Non correlative slides were scanned from 26-352

On may 19, 20, 13, 21 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F079===

Crown-Rump Length: 150mm

Upper limb

two scans of each slide were taken. Slides from 219-245

On april 09, 13 and may 06, 07 2021.

ROIs from scan 2 are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-26T11:08:38Z

AnnaUAB: /* F069 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F052===

Crown-Rump Length: 70mm

Scanned one out of two slides from 01-260 and correlative slides from 506-529 (upper limb) Two scans of each slide were taken in this case.

On march 18, 19, 22, 2021 and may 07, 10, 11 and 12 2021.

Some ROIs were not in order, check with the screenshots

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F059===

Crown-Rump Length: 76mm

Scanned one out of two slides from 294-529

On march 23, 24, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F061===

Crown-Rump Length: 82mm

Scanned one out of three slides from 01-796

On april 06, 07, 08, 09 and 12 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F069===

Crown-Rump Length: 95mm

Non correlative slides were scanned from 01-387

On april 22, 23, 26, and 27 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F070-B===

Crown-Rump Length: 100mm

Body part: Hand and wrist

Correlative slides were scanned from 64-87. Two scans of each slide were taken. On scan2 ROIs are upside down.

On may 07, 10 and 11 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F071===

Crown-Rump Length: 105mm

Non correlative slides scanned from 19-769.

On april 27, 28, 29, 30 and may 03, 04, and 05 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F072===

Crown-Rump Length: 108mm

Non correlative slides were scanned from 23-229

On may 05 and 06 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F076===

Crown-Rump Length: 130mm

Non correlative slides were scanned from 401-1449

On may 11, 12, 13, 14, 17, 18 and 19 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F079===

Crown-Rump Length: 150mm

Upper limb

two scans of each slide were taken. Slides from 219-245

On april 09, 13 and may 06, 07 2021.

ROIs from scan 2 are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-26T10:44:38Z

AnnaUAB: /* F050 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F052===

Crown-Rump Length: 70mm

Scanned one out of two slides from 01-260 and correlative slides from 506-529 (upper limb) Two scans of each slide were taken in this case.

On march 18, 19, 22, 2021 and may 07, 10, 11 and 12 2021.

Some ROIs were not in order, check with the screenshots

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F059===

Crown-Rump Length: 76mm

Scanned one out of two slides from 294-529

On march 23, 24, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F061===

Crown-Rump Length: 82mm

Scanned one out of three slides from 01-796

On april 06, 07, 08, 09 and 12 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F069===

Crown-Rump Length: 95mm

Non correlative slides were scanned from 01-387

On april 22, 23, 26, and 27 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F071===

Crown-Rump Length: 105mm

Non correlative slides scanned from 19-769.

On april 27, 28, 29, 30 and may 03, 04, and 05 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F072===

Crown-Rump Length: 108mm

Non correlative slides were scanned from 23-229

On may 05 and 06 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F076===

Crown-Rump Length: 130mm

Non correlative slides were scanned from 401-1449

On may 11, 12, 13, 14, 17, 18 and 19 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F079===

Crown-Rump Length: 150mm

Upper limb

two scans of each slide were taken. Slides from 219-245

On april 09, 13 and may 06, 07 2021.

ROIs from scan 2 are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-26T10:30:49Z

AnnaUAB: /* F062 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F059===

Crown-Rump Length: 76mm

Scanned one out of two slides from 294-529

On march 23, 24, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F061===

Crown-Rump Length: 82mm

Scanned one out of three slides from 01-796

On april 06, 07, 08, 09 and 12 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F069===

Crown-Rump Length: 95mm

Non correlative slides were scanned from 01-387

On april 22, 23, 26, and 27 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F071===

Crown-Rump Length: 105mm

Non correlative slides scanned from 19-769.

On april 27, 28, 29, 30 and may 03, 04, and 05 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F072===

Crown-Rump Length: 108mm

Non correlative slides were scanned from 23-229

On may 05 and 06 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F076===

Crown-Rump Length: 130mm

Non correlative slides were scanned from 401-1449

On may 11, 12, 13, 14, 17, 18 and 19 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F079===

Crown-Rump Length: 150mm

Upper limb

two scans of each slide were taken. Slides from 219-245

On april 09, 13 and may 06, 07 2021.

ROIs from scan 2 are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-26T10:26:21Z

AnnaUAB: /* F055 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F059===

Crown-Rump Length: 76mm

Scanned one out of two slides from 294-529

On march 23, 24, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F069===

Crown-Rump Length: 95mm

Non correlative slides were scanned from 01-387

On april 22, 23, 26, and 27 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F071===

Crown-Rump Length: 105mm

Non correlative slides scanned from 19-769.

On april 27, 28, 29, 30 and may 03, 04, and 05 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F072===

Crown-Rump Length: 108mm

Non correlative slides were scanned from 23-229

On may 05 and 06 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F076===

Crown-Rump Length: 130mm

Non correlative slides were scanned from 401-1449

On may 11, 12, 13, 14, 17, 18 and 19 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F079===

Crown-Rump Length: 150mm

Upper limb

two scans of each slide were taken. Slides from 219-245

On april 09, 13 and may 06, 07 2021.

ROIs from scan 2 are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-26T10:19:47Z

AnnaUAB: /* F079 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F069===

Crown-Rump Length: 95mm

Non correlative slides were scanned from 01-387

On april 22, 23, 26, and 27 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F071===

Crown-Rump Length: 105mm

Non correlative slides scanned from 19-769.

On april 27, 28, 29, 30 and may 03, 04, and 05 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F072===

Crown-Rump Length: 108mm

Non correlative slides were scanned from 23-229

On may 05 and 06 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F076===

Crown-Rump Length: 130mm

Non correlative slides were scanned from 401-1449

On may 11, 12, 13, 14, 17, 18 and 19 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F079===

Crown-Rump Length: 150mm

Upper limb

two scans of each slide were taken. Slides from 219-245

On april 09, 13 and may 06, 07 2021.

ROIs from scan 2 are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-26T10:19:16Z

AnnaUAB: /* F071 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F069===

Crown-Rump Length: 95mm

Non correlative slides were scanned from 01-387

On april 22, 23, 26, and 27 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F071===

Crown-Rump Length: 105mm

Non correlative slides scanned from 19-769.

On april 27, 28, 29, 30 and may 03, 04, and 05 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F072===

Crown-Rump Length: 108mm

Non correlative slides were scanned from 23-229

On may 05 and 06 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F076===

Crown-Rump Length: 130mm

Non correlative slides were scanned from 401-1449

On may 11, 12, 13, 14, 17, 18 and 19 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F079===

Crown-Rump Length: 150mm

Upper limb

two scans of each slide were taken. Slides from 219-245

On april 09, 13 and march 06, 07 2021.

ROIs from scan 2 are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-26T10:17:39Z

AnnaUAB: /* F072 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F069===

Crown-Rump Length: 95mm

Non correlative slides were scanned from 01-387

On april 22, 23, 26, and 27 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F071===

Crown-Rump Length: 105mm

Non correlative slides scanned from 19-769.

On april 27, 28, 29, 30 and march 03, 04, and 05 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F072===

Crown-Rump Length: 108mm

Non correlative slides were scanned from 23-229

On may 05 and 06 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F076===

Crown-Rump Length: 130mm

Non correlative slides were scanned from 401-1449

On may 11, 12, 13, 14, 17, 18 and 19 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F079===

Crown-Rump Length: 150mm

Upper limb

two scans of each slide were taken. Slides from 219-245

On april 09, 13 and march 06, 07 2021.

ROIs from scan 2 are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-26T10:12:49Z

AnnaUAB: /* F079 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F069===

Crown-Rump Length: 95mm

Non correlative slides were scanned from 01-387

On april 22, 23, 26, and 27 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F071===

Crown-Rump Length: 105mm

Non correlative slides scanned from 19-769.

On april 27, 28, 29, 30 and march 03, 04, and 05 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F072===

Crown-Rump Length: 108mm

Non correlative slides were scanned from 23-229

On march 05 and 06 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F079===

Crown-Rump Length: 150mm

Upper limb

two scans of each slide were taken. Slides from 219-245

On april 09, 13 and march 06, 07 2021.

ROIs from scan 2 are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-26T10:10:42Z

AnnaUAB: /* F070-B */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F069===

Crown-Rump Length: 95mm

Non correlative slides were scanned from 01-387

On april 22, 23, 26, and 27 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F079===

Crown-Rump Length: 150mm

Slides scanned from 219-245. Scan 1 and scan 2 were made for every slide, in order to scan all the samples. Images on Scan 2 are upside down.

Body zone: Hand and wrist

On april 09 and 13 and march 06 and 07 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F071===

Crown-Rump Length: 105mm

Non correlative slides scanned from 19-769.

On april 27, 28, 29, 30 and march 03, 04, and 05 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F072===

Crown-Rump Length: 108mm

Non correlative slides were scanned from 23-229

On march 05 and 06 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F079===

Crown-Rump Length: 150mm

Upper limb

two scans of each slide were taken. Slides from 219-245

On april 09, 13 and march 06, 07 2021.

ROIs from scan 2 are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-26T10:06:04Z

AnnaUAB: /* F070-B */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F069===

Crown-Rump Length: 95mm

Non correlative slides were scanned from 01-387

On april 22, 23, 26, and 27 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F070-B===

Crown-Rump Length: 100mm

Slides scanned from 64-87. Scan 1 and scan 2 were made for every slide, in order to scan all the samples. Images on Scan 2 are upside down.

Body zone: Hand and wrist

On march 07, 10, and 11 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F071===

Crown-Rump Length: 105mm

Non correlative slides scanned from 19-769.

On april 27, 28, 29, 30 and march 03, 04, and 05 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F072===

Crown-Rump Length: 108mm

Non correlative slides were scanned from 23-229

On march 05 and 06 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F079===

Crown-Rump Length: 150mm

Upper limb

two scans of each slide were taken. Slides from 219-245

On april 09, 13 and march 06, 07 2021.

ROIs from scan 2 are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-26T10:01:33Z

AnnaUAB: /* F070-B */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F069===

Crown-Rump Length: 95mm

Non correlative slides were scanned from 01-387

On april 22, 23, 26, and 27 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F070-B===

Crown-Rump Length: 100mm

Slides scanned from 64-87. Scan 1 and scan 2 were made for every slide, in order to scan all the samples. Images on Scan 2 are upside down.

Body zone: Hand and wrist

On march 07, 10, and 11 2021.

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F072===

Crown-Rump Length: 108mm

Non correlative slides were scanned from 23-229

On march 05 and 06 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F079===

Crown-Rump Length: 150mm

Upper limb

two scans of each slide were taken. Slides from 219-245

On april 09, 13 and march 06, 07 2021.

ROIs from scan 2 are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-26T09:53:56Z

AnnaUAB: /* F070-B */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F069===

Crown-Rump Length: 95mm

Non correlative slides were scanned from 01-387

On april 22, 23, 26, and 27 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F070-B===

Crown-Rump Length: 100mm

Slides scanned from 64-87. Scan 1 and scan 2 were made for every slide, in order to scan all the samples. Images on Scan 2 are upside down.

Body zone: Hand and wrist

On march 07, 10, and 11 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F079===

Crown-Rump Length: 150mm

Upper limb

two scans of each slide were taken. Slides from 219-245

On april 09, 13 and march 06, 07 2021.

ROIs from scan 2 are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-26T09:49:05Z

AnnaUAB: /* F065 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F069===

Crown-Rump Length: 95mm

Non correlative slides were scanned from 01-387

On april 22, 23, 26, and 27 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F070-B===

Crown-Rump Length: 100mm

Slides scanned from 64-87

Body zone: Hand and wrist

On march 07, 10, and 11 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F079===

Crown-Rump Length: 150mm

Upper limb

two scans of each slide were taken. Slides from 219-245

On april 09, 13 and march 06, 07 2021.

ROIs from scan 2 are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-18T09:39:24Z

AnnaUAB: /* F065 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F079===

Crown-Rump Length: 150mm

Upper limb

two scans of each slide were taken. Slides from 219-245

On april 09, 13 and march 06, 07 2021.

ROIs from scan 2 are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-14T13:33:25Z

AnnaUAB: /* F042 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-14T13:33:01Z

AnnaUAB: /* F041 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Crown-Rump Length: 60mm.

Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-14T13:31:34Z

AnnaUAB: /* F039 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Crown-Rump Length: 60mm.
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-14T13:31:07Z

AnnaUAB: /* F030 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Crown-Rump Length: 54mm.

Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-14T13:28:52Z

AnnaUAB: /* F029 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Crown-Rump Length: 50mm.

Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-14T13:27:01Z

AnnaUAB: /* F027 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Crown-Rump Length: 47mm.

Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-14T13:26:06Z

AnnaUAB: /* F024 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Crown-Rump Length: 45m.

Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-14T13:25:33Z

AnnaUAB: /* F023 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Crown-Rump Length: 45mm.

Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-14T13:24:26Z

AnnaUAB: /* F021 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Crown-Rump Length: 643mm

Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}

Domenech-Mateu Collection Embryos

2021-05-14T13:24:01Z

AnnaUAB: /* F017 */

==Introduction==

Please note that this current page is working page, designed to aid the collection scanning process and will be simplified at a later date to contain only the catalogue with direct links to the online DEC database.

'''DEC Users''' in the tables below clicking the embryo number will take you to the embryo template folder in the DEC database.

[[Domenech-Mateu Collection]]

* Full Collection = 203 Specimens Total Slides = 9100 Total Sections = 114425
** Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
** Total Fetuses (Approximate) = 89 Total Number of Slides = 5290 Total number of Sections = 10353

==General Scanning Notes==
'''Tray 7''' - Do Not Use this Tray
* not loading correctly, if slides loaded in this tray, scanner will potentially jam.
'''Tray 3,4,5''' - did not detect both slides, yet worked the next day? Appears to not be trays but slide holder marked with red sticker.

===Image Coding===

Full Collection = '''203''' Specimens Total Slides = '''9100''' Total Sections = '''114425'''

Embryo image file example: UAB-E25-003-2

* '''UAB''' - identifies collection location
* '''E25''' - identifies New Embryo Reference
* '''E25B''' - identifies New Embryo Reference if there is a "B" series.
* '''003''' - identifies Slide number (note 3 digit coding could be used if more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

Fetus image file example: UAB-F25-003-2

* '''UAB''' - identifies collection location
* '''F25''' - identifies New Fetus Reference
* '''003''' - identifies Slide number (note 3 digit coding as these contain more than 100 slides)
* '''2''' - used only if the slide needs scanning to capture sections in label region (close to slide holder).

* Sections should be scanned in the correct serial sequence
** This will be "upside down" compared to photocopied slide images.

===Histology Staining===

HE/TA/ identified in table below. Still need to identify V (VOF) and B stain?

{| class="wikitable" border="1"
|-
! colspan="6" |[[Histology Stains]] - Common Stains and Their Reactions
|-
| <center>'''Stain'''</center>
| <center>'''Nucleus'''</center>
| <center>'''Cytoplasm'''</center>
| <center>'''Collagen'''</center>
| <center>'''RBCs'''</center>
| <center>'''Other'''</center>

|-
| [[Histology_Stains#Haematoxylin|'''H'''aematoxylin]]
| <center>blue</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| mucins - light blue

|-
| [[Histology_Stains#Eosin|'''E'''osin]]
| <center>-</center>
| <center>pink</center>
| <center>pale pink</center>
| <center>bright red</center>
| colloid - pink muscle - red

|-
| '''T'''richrome '''A'''zan (Heidenhain's Azan)
| <center>red</center>
| <center>purple/red</center>
| <center>deep blue</center>
| <center>red</center>
| muscle - red

|-
| '''B'''ielschowsky stain (Bielschowsky's silver stain)
| <center>-</center>
| <center>-</center>
| <center>-</center>
| <center>-</center>
| nerve fibers - black

|}<noinclude>[[Category:Histology]][[Category:Template]]</noinclude>

===Step by Step===

====1. In the Collection Room====
[[File:UAB-Slide photocopy 1.jpg|thumb|200px|Slide Photocopy Folder]]
# '''Choose''' from the printed catalogue or the online catalogue the [[Template:Domenech-Mateu Collection Embryos table2|Embryo]] or [[Template:Domenech-Mateu Collection Embryos table5|Fetus]] and find the slide boxes.
## Start with the '''green''' then do the '''orange''' and finally the '''red'''.
# '''Find''' the photocopy of the embryo or fetus slides in the folder.
## Remember to first use this photocopy "upside down" when using with the scanner for section numbering.
# '''Use''' the "New Reference" number for the embryo or fetus in all scanning and online notes.
## Never use the original reference for scanning.

Now take printed catalogue, slide boxes and photocopy folder to the scanning lab.

====2. In the Scanning Lab====
[[File:Domenech-Mateu Collection-Scanner2019-06.jpg|thumb|47 mm Slide holder]]
'''Slide Preparation'''
# Cleaning - should be cleaned with microfibre cloth and/or alcohol swabs.
# Label - the slides with a round sticker identifying embryo. For example embryo E26 slide 1 is labelled ("E26") and slide number ("1"). Do not cover any section with the label.
# Tray - clip the slide carefully in the tray with lobe towards the clip end. Then place in the numbered box on the bench.
# Scan Log - Fill in the scan log with: Embryo number, Scan Date, and Slide Number for each tray before loading scanner. Add any special information to this log (sections out of order, broken slide, faded stain, sections near edge).
# Slide Photocopy - the slides are first mounted in the holders "upside down" (rotate 180 degrees) compared to photocopy sheets (see the images below). Turn the Slide photocopy catalogue upside down to get correct Scan Direction

{|
! Slide photocopy
! Slide photocopy (rotate 180 degrees)
|-
| [[File:UAB-Slide photocopy 1.jpg|300px]]
| [[File:UAB-Slide photocopy 2.jpg|300px]]
|-
| Red Arrow shows embryo number.
| Red C shows how the slide is mounted in the scan holder.
|}

Scan Direction codes:
* RLTB - Right to Left, then Top to Bottom
* LRTB - Left to Right, then Top to Bottom
* TBRL - Top to Bottom, then Right to Left
* TBLR - Top to Bottom, then Left to Right

'''Scanning'''
# '''Find''' Anna's "how to scan" notes and read all the written procedure BEFORE scanning.

{|
! Turn on the scanner
! Turn on the computer
|-
| [[File:Domenech-Mateu Collection-Scanner2019-03.jpg|300px]]
| [[File:Domenech-Mateu Collection-Scanner2019-04.jpg|300px]]
|-
|}

====3. Selecting Regions of Interest (ROIs)====

Resetting full slide region:
* After "Preview" open the Slide using "Advanced"
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs.
** Danger of Crush - Do not extend beyond the slide clip region.
* Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan".

ROI's numbering:
* Turn off "Live Update"
* check the numbering sequence as not always correct.
* all ROIs can be renumbered by double clicking the number.
** you cannot use a number greater than the number of regions on the slide.

====4. Making Two Copies====
'''Transfer''' the completed embryo scan folder from Drive D to external HDD.
# Copy to the external UAB HDD (UAB-DMC 1, 2, 3....).
# Copy to the external DEC HDD (UAB-DMC 1, 2, 3....).
# Confirm by opening sample images using ZEN that these copies are OK.
# Only then can the embryo scan folder be deleted from Drive D.

====5. Uploading to Database====
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]

'''Upload''' scans from embryo folder to the DEC Database.
# Use OMERO.insight - ([https://www.openmicroscopy.org/omero/downloads/ download page]) also see help page [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight]
# All collection uploads require database ADMIN access to upload as the User - Rosa Mirapiex.
# Make a new (blue) Project folder in user Rosa Mirapiex for each embryo/fetus (there are examples in the database).
## For correct sorting of folders, numbering should have 3 digits, for example E76 becomes E076.
# Within the Project folder, make a new (green) Dataset folder for each slide. Details - Add Embryo/Fetus information from collection spreadsheet to the folder Dataset Details.

''Table below requires correction.''

{|
! User - Rosa Mirapiex
! Dataset Details
|-
| [[File:UAB-Uploading to Database 1.jpg|450px]]
| [[File:UAB-Uploading to Database 2.jpg|450px]]
|}

Note - Embryo '''Folder name''' and '''Dataset Details''' should not be changed by other users.

'''User Comments''' - If other users want to add a comment there is a separate section for this shown by the red arrow below. Note that you will be identified as the author of the comment and it will be date stamped.

[[File:UAB-Uploading to Database 3.jpg|450px]]

====6. Image Analysis====

The simplest form of analysis is to find your region of interest (ROI) add a scale bar and export that image to your computer for analysis.

The best form of image analysis uses the direct interaction between FIJI and OMERO database ([https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO])

* [https://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] - This covers all OMERO versions from 5.1.0 and newer and assumes you have never installed ImageJ or Fiji before.
* [https://imagej.net/Fiji FIJI Download] - Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

==Embryos==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072

===E001===
Slide 1 broken and repaired (there's a crack)
07 october Scan1
08 October Scan2

Screenshots were taken

Photocopy picture was attached

===E002===
04 October Scan1
07 October Scan2

Screenshots were taken

Photocopy picture was attached

===E003===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Red (Color refering to the histological quality)

===E004===
Couldn't be scanned because the slides doesn't match with the holder. Anyway it was Orange (Color refering to the histological quality)

===E005===
07 October Scan1

08 October scan2
The Sacnner was not detecting tray number 10

Screenshots of every slide were taken

Photocopy picture in the folder

===E006===
07 October Scan1

08 October Scan2

Screenshots of every slide were taken

Photocopy picture in the folder

===E007===
04 october Scan1
07 october Scan2

Slide1, Sections not in order within the slide because of the curved clumn. screenshot taken
Slide4, Sections not in order. Screenshot taken
Slide5, Sections not in order. Secreenshot taken

Photocopy picture in the folder

===E008===
09 october Scan1 / 10 october Scan2

Slide UAB-E008-001 broken and repaidred with adhesive tape. Scan1 and Scan2 Screenshots were taken. photocpy picture added.

===E009===
09 october Scan1 / 10 october Scan2
Scan2 of UAB-E009-001, 002 and 003 was made on october the 14th
When doing the second scanning I opened to clean one slide. After closing the door it didn't detect tray number 13. I didn't dare to open and close it again in case it didn't detect other trays and lost all the previews and the selection of ROIs. So I scanned the slides on that tray the day after.

Screenshots of slide 7 were taken. Photocopy picture added.

===E010===
09 october Scan1 / 10 october Scan2

Scan 2 of Slides 3 and 4 was made on October the 14Th because tray 18 was not detected when doing the second scanning. I scanned the slides on that tray the day after.

screenshots were taken of slides 3 and 5 (scan1 and scan2)

Photocopy picture in the folder

===E011===
09 october Scan1 / 10 october Scan2
screenshots were taken of slide 4 (scan1 and scan2)

Photocopy picture in the folder

===E012===
Scan1 14 october 2019
Scan2 16 october 2019
Screenshots of slides number 5 and 6 were taken

Photocopy picture in the folder

===E013===
Scan1 14 october 2019

Scan2 16 october 2019

Screenshots of slides number 4 and 6 were taken. Slide 4 had a wide focus range

Photocopy picture in the folder

===E014===
Slides from number 1 to 18:
Scan1 14 october 2019
Scan2 16 october 2019

Screenshots of slides number 4 and 5 were taken
Slides 7 and eleven had air between the slide and the coverslide

Slides from number 19 to 29:
Scan1: 17 october 2019
Scan2: 21 october 2019
Screenshots of slides 20 and 21 were taken

NOTE:The scanning on October the 14th (embrios, 12,13 and 14. Total:36 slides) took almost 24h

Photocopy picture in the folder

===E015===
Scan1: 24 october / Scan2: 28 october
Screenshots of Scan1 and 2 taken for every slide except UAB-E015-002
NOTE:UAB-E015-004, several ROIs(regions of interest) are not in order. Check with the screenshot and the photocopy picture.
UAB-E015-005 needed a wide focus range (400)

===E016===
Scanned during 4 days from novebmer the 04th to 07th. Columns on the slides were messed (very messed) not only within the slide. So i scanned groups of columns and create a sort of virtual slide in order to put all the columns in the right order. Check screenshots and photocopy picture.
1e, 3b and 5b "have mirror effect". in 2d, 7a, 7b and 10b ROIs are not in order due to the curved cloumn of samples.

===E017===
Couldn't be scanned because of the slide size (it doesn't fit the holder)

===E018===
Several time consuming issues realted to slide detection in both scan 1 and 2. I can't relate the problem to an especific tray or holder. Seems quite random so far. I lost half the work done, because i opened the scan door to clean again one slide. when closing it didn't detect all the slides (the ROI detection was already made and got lost)

Scan1 was made on nebember 08th ans 13th

Scan2 was made in nobember the 15th

*Slide UAB-E018-010-2 ROIs not in order due to the curved column

Screenshots of every slide were taken

Photocopy picture in the folder

===E019===
Slide detection issues again

Scan1: november 19th / Scan2: november 20th

Screenshots of every slide were taken

Photocopy picture in the folder

===E020===
Slide detection issues. And software issues too (screenshot stopped working-already fixed-. And also some problems with merging ROIs.

Scan1: nobember 21th / Scan2: november 22th

Slides number 3, 4, 5 and 12 have ROIs not in order in both scannings. See screnshots.

Screenshots of every slide were taken

Photocopy picture in the folder

===E021===
Nomvember 21th: Cloudn't be scanned -as scheduled- due to scan detection issues

November 22th: Only scan1 of slide 1 was made for the same reason: slide detection issues.

November 25th: Couldn't be scanned. Slide detection issues, plus slides jamming and even one jumped out of the holder. another one was broken inside the scanner.

Photocopy picture in the folder

Scanned on January 8th 2020 (Scan1) and January 13th (scan2)

Slide UAB-E021-004 is broken and fixed with adhesive tape affecting the tissue on scan1 (samples under the adhesive tape)

Scerrenshots of every slide were taken

Photocopy picture added on folder

===E022===

{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4056 '''E22''']
| {{CS16}}
| 10.0
| 37
| T/O
| 10
| {{HE}}
| Tot
| 2
| '''green'''-'''orange'''
| 12
| 622
| Palatal fissure. slide # 7-'''orange''' Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1-4, 7-12 scanned.

Photocopy picture in the folder

Screenshots were taken

===E023===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Comments
|-
|}
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken

===E024===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4054 '''E24''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 8
| 427
| Y
| slide 3 broken. Scanned 16-18 September.
|}

16-17 September - Embryo used for test scanning.
* Slides 1,2, 4-8 scanned.
* Slide 3 broken and repaired. Test damaged slide scan.

Screenshots were taken

Photocopy picture in the folder

===E025===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-451 '''E25''']
| {{CS16}}
| 10.0
| 37
| F
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 11
| 502
| Y
| slide 7 trencat. Very good. Scanned 16-18 September.
|}
[[File:Domenech-Mateu Collection-DEC-E25-slide001.jpg|thumb|DEC E25 [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1''']]]
30 September - [http://149.171.80.223:8080/webclient/?show=dataset-4052 '''Slide 1'''] uploaded to database.

17 September - Embryo test scanning of rotated slides.

* Slide 3,4,5,6,9 turned around and missing 2 columns scanned.
* Numbering UAB-E25-3-2.
** Last number indicates that this is the second rotated scan

16-17 September - Embryo used for test scanning.

* Slides 3-6, 8-11 scanned.
* Slide 7 broken - scanned OK included rotation scan.

16 September - Embryo used for test scanning.
* Slides 1 and 2 scanned in actual sectioning series.
** Slide 1 using modified autodetect sections. (total scan time 20 minutes)
** Slide 2 using Boxes. (total scan time 30 minutes)

16 September - Tray 7 loading problem again. Left empty for overnight scan.

===E026===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4055 '''E26''']
| {{CS16}}
| 10.0
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''orange'''
| 23
| 655
| Y
| Slide 18 broken. Some fading
|}

25-26 September - Scan slides.

===E027===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4057 '''E27''']
| {{CS16}}
| 10.0
| 37
| T/F
| 7
| {{HE}}
| Tot
| 1
| '''orange'''
| 22
| 1107
| Y
| En tesis talls F. Molt destenyit
|}
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns.

Scanned on November 28th, 29th and december the 2nd

There were some issues with the slides detection on tray number 6, and some software issues associated with ROI' selection and merging
*Slide UAB-E027-003 Scan1: ROIs not in order and there is air trapped between the slide and the coverslide
*Slide UAB-E027-004 Scan1: ROIs not in order
*Slide UAB-E027-005 Scan1: ROIs not in order
*Slide UAB-E027-006 Scan2: There's air inside
*Slide UAB-E027-007 Scan1: Tere's air inside
*Slide UAB-E027-011 ROIs not in order. i can't understand the reason why, because there are no curved cloumns
*Slide UAB-E027-012 Scan1: Air inside

Screenshots of every slide were taken

Photocopy picture in the folder

===E028===
Not Scanned. Slide size didn't fit the holders

===E029===
Detection issues with trays number 6 and 10

Scan1: December the 2nd

Scan2: December the 3rd

Screenshots of every slide were taken

Photocopy picture in the folder

===E030===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Boxes
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=project-463 '''E30''']
| {{CS16}}
| 10.3
| 37
| T
| 10
| {{HE}}
| Tot
| 1
| '''green'''
| 13
| 747
|
| Raquisquisis total. Neural tube well developed.
|}

1-2 October - scan 13 slides.
3 october- scan2 13 slides

===E031===
Detection problems with trays 1 and 3

Scan1: December the 3rd

Scan2: December the 4th

Screenshots of every slide were taken

Photocopy picture in the folder

===E032===
Detection problems with trays 10, 11, 13, 15, 16, 17 and 18

Scanned on 3rd, 4th and 5th of December 2019

*Slide UAB-E032-004-2 ROIs not in order

*Slide UAB-E032-009 ROIs not in oder

*Slide UAB-E032-010 wide focus range (400 microns)

*Slide UAB-E032-011 wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture in the folder

===E033===
Scan1:December the 4th 2019

Scann2:December the 5th 2019

*Slide UAB-E033-001 i UAB-E033-001-2. ROIs not in order due to curved columns

*Slide UAB-E033-002-12 ROIs not in order due to curved columns

*Slide UAB-E033-006-1 There's air inside and images 38, 39 and 40 are inverted

*Slide UAB-E033-009 ROIS not in oder dur to curved sample columns

Screenshots of every slide were taken

Photocopy picture added in the folder

===E034===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

Several detection issues with trays number 1, 3, 9, 10, 11, 12, 13 and 16

*Slide UAB-E034-013-1 there's air inside

*Slide UAB-E034-017 There's air inside

Screenshots of every slide were taken

Photocopy picture added in the folder

===E035===

Scann1: December the 11th 2019

Scann2: December the 12th 2019

*Slide UAB-E035-010 Wide focus range 8700 microns)

*Slide UAB-E035-014 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E036===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

Detection problems with trays number 1 and 2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E037===
Scann1: December the 13th 2019

Scann2: December the 16th 2019

*Slide UAB-E037-005 ROIs not in order

*Slide UAB-E037-007 ROIs not in order

*Slide UAB-E037-010-2 ROIs not in order

*Slide UAB-E037-011 ROIs not in order

Screenshots of every slide were taken

Photocpy picture added in the folder

===E038===
Scann1: December the 13th 2019

Scann2: December the 16th and 17th 2019

*Slide UAB-E038-007 ROIs not in order

*Slide UAB-E038-012 ROIs not in order

*Slide UAB-E038-013 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E040===

Scann1: january 20th 2020

Slides: UAB-E040-003, UAB-E040-011, UAB-E040-012, UAB-040-013 ROIs not in order

Scann2: January 22nd 2020. Detection problems with tray number 4. Was skipped.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E041===
Scann1: January 22nd and 23rd 2020
Detection problems with trays number 16 and 1. ON 22th scanner light went red, couldn't find the reason why. I rebooted both scanner and software.

Scann2: was made on january 23rd, 24th and 27th 2020.

Slides UAB-E041-005-2 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E042===

Scann1: January 24th and 27th 2020. Detection problems with one holder.

Scann2: January 28th 2020. Detection problems with tray 18. Tray 15 jammed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E047===

Scann1: October 1st 2020. Detection problems with one holder. Detection problems on trays 13 and 23

Scann2: October 1st and 5th 2020. Detection problems with tray 18. Trays 15 and 17 jammed.

Slide UAB-047-008 ROIs not in order due to curved ROI column

Slide UAB-047-018 was broken and repaired with tape. Doesn't focus where the tape was placed.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E050===

Scann1: September 29th 2020. Slide UAB-050-002 Rois not in order

Scann2: October 1st 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E051===

Scann1: January the 29th and 30 2020. Detection problems with tray 14

Slide UAB-E051-029 had a wide focus range (400 microns)

Screenshots of every slide were taken

Photocopy picture added in the folder

===E052===

Scann1: September 29th and Oct 1st 2020. Detection problems on tray 9. Slide UAB-052-018 ROIs not in order

Scann2: October 1st and Oct 5th 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===E055===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E057===

Scann1: February 4th 2020

Many tray detection problems. Very time consuming. it took one hour and a half and 26 attempts to get started

Scann2: February 6th and 7th 2020

Detection problems on several random trays

Screenshots of every slide were taken

Photocopy picture added in the folder

===E058===

Scann1: October 5th and 6th 2020. Detection problems on trays 1,2,3,10,12 and 21. Tray 10 was skipped

Scann2: October 6th and 7th 2020

Slides UAB-058-033 and UAB-058-36 ROIs not in order. Mirrorlike

Screenshots of every slide were taken

Photocopy picture added in the folder

===E060===

Scann1: October 7th 2020
Scann2: October 8th 2020

Slides UAB-060-008, UAB-060-009, UAB-060-011, UAB-060-012, UAB-060-013 and UAB-058-36 ROIs not in order

Screenshots of every slide were taken

Photocopy picture added in the folder

===E064===

Scann1: February 4th, 5th, 6th 2020 (Many detection problems) ROIs on slides UAB-E064-024 and UAB-E64-032, not in order

Scann2: Februray 7th and 10th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E068===

Scann1: February 10th, 11th 2020. Tray 15 jammed. There's air inside slide UAB-E068-022.

Scann2: February 11th 12th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E069===

Scann1: October 7th 2020. Detection problems on tray 14. Sticker on the slide was trimmed amn afterwards it worked properly

Scann2: October 8th 2020

Slide UAB-069-009 Broken coverslide. Samples in that coverslideless area were not scanned

Screenshots of every slide were taken

Photocopy picture added in the folder

===E074===

Scann1: October 9th 2020. Detection problems on tray 1

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E078===

Scann1: October 9th 2020. Detection problems on trays 18 and 19

Scann2: October 13th 2020

Screenshots of every slide were taken

Photocopy picture added in the folder

===E079===
{|
|-bgcolor="CEDFF2"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4060 '''E79''']
| {{CS20}}
| 21.0
| 51
| T
| 10
| {{HE}}
|
| 1
| '''green'''
| 45
| 1211
| Y
|}

27 September - All slides loaded. Scanned 4 of 5 columns. RLTB

===E079===

Scann1: February 13th, 14th, 17th 2020

Scann2: February 14th, 17th, 18th 2020. Air bubble on slide UAB-E079-037-2

Screenshots of every slide were taken

Photocopy picture added in the folder

===E090===

Scann1: March 10th, 2nd 2020. Detection problems on trays 14,15,18,21,22 and 24. Trays 14, 15 and 222 were skipped. The scanning took 24h

Slide UAB-E090-004. Rois not in order and flipped

Slide UAB-090-034 ROI 16, flipped in mirror effect

Scann2: March 4, 5 and 6th 2020. Many detection problems on trays 1,2,4,5,6,9,10,12,13,14,20,21,22.

Slide UAB-090-010-2, ROI 5,flipped, mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===E093===
On March 9th Scanning was aborted. We had many detection problems, several trays jammed amd one slide was broken

Scann1: October 14th 2020

Scann2: October 20th 2020. Detection problems on trays 14,18. looks like the sticker interfered. The sticker was trimmed

Screenshots of every slide were taken

Photocopy picture added in the folder

===E094===
Scann1: September 22nd 23rd 2020. Detection problems on tray2 12,19 and 23

Scann2: September 23rd 25th and 28th 2020. Detection problems on trays 2,5,12 and23. On 28th we had many detection problems

Slide UAB-094-012, one of the ROIs column was badly situated, it needed 3 scannings to put the samples in the right order (you can check that on the documents added in its folder)

Screenshots of every slide were taken

Photocopy picture added in the folder and info about slide UAB-094-012

===E099===
Scann1: October 16th, 19th and 23rd 2020. Detection problems on tray6

Scann2: October 19th and 26th 2020.

Slide UAB-099-036, Mirror like

Screenshots of every slide were taken

Photocopy picture added in the folder

===E106===
Scann1: October 22, 23 2020

Scann2: October 26, 27, 28, 29 2020. Many detection problems on trays 6, 9, 10, 11, 12, 13, 14, 18, 23, 25

Slide UAB-106-015-2. ROIs 9 and 10 not in ordera and upsidedown

Screenshots of every slide were taken

Photocopy picture added in the folder

===E104===
Scann1: October 23rd, 27th, 28th, 29th and 30th 2020. Many detection problems on several trays (every day). Trays 2 and 15 jammed

Scann2: October 26, 27, 28, 29, 30; November 02, 03, 04, 06 23rd 25th and 28th 2020. Many detection problems on several trays. Door got stucked. Some days it took 1h and a half to start working. System was rebooted

Slide UAB-E104-026: ROI nº9 upside down. Slide UAB-E104-012: ROIs 5 and 6 upside down

Screenshots of every slide were taken

Photocopy picture added in the folder

===E109===
{|
|-bgcolor="F5FAFF"
! Reference New
! Carnegie Stage
! Crown-Rump Length (mm)
! Age (days)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain ({{HE}}/T/A/AT/V/B)
! Part of the body
! Number of colours
! Histology ('''green'''/'''orange'''/'''red''')
! Slides
! Sections
! Thesis (Y)
! Comments
|-
| [http://149.171.80.223:8080/webclient/?show=dataset-4051 '''E109''']
| {{CS23}}
| 30.0
| 57
| T/S
| 10
| {{HE}}/B
| Body
| 1
| '''green'''
| 23
| 626
|
| "slide 9 broken. HEAD: Sag./Biels. BODY: Transv /HE-{{VOF}}. En el documento pone 23 slides en caja hay 42. Por el 23 se refiere al BI-1 C"
|}

[[File:Domenech-Mateu Collection-Scanner2019-02.jpg|thumb|Embryo E109]]
====First Test Scan====
12-13 September - Embryo used for test scanning.
* Slides 1-42 scanned. (more than 14 hours to scan)
* Bottom Top Left Right from late end. Not the that this is opposite to actual sectioning series.
* Position of sections means that not all sections were scanned
** Slides 33-40 - only half section of first column scanned.
** Slides 41,42 - end column of sections completely missing.
13 September - Tray 7 loading problem on second run, OK on first.

19-20 September -

Embryo E109 30 mm (Carnegie Stage {{CS23}})

Stage 23 Human Embryo (E109) 30 mm Abdomen (slide 1-17), thorax (slide 17-23), Original name - Bi-1

Slide 1-42

Additional slides Also a "B" series? slide 8 - 23 and 55?

==Embryo Catalogue==
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
 
{{Domenech-Mateu Collection Embryos table3}}

{{Domenech-Mateu Collection Embryos table2-sort-collapse}}
 
{{Carnegie_stage_table_1}}

==Fetuses==

===F010===
Crown-Rump Length: 39mm.

Scanned Slides from 1-41 and from 47-101

Scann1: December 05, 06, 09, 10, 11 and 12 2020.

Scann2: December 09, 10, 11 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F012===
Crown-Rump Length: 39mm.

Scanned Slides from 1-124

On November 11, 12, 16, 18, 23, 24 and 12 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F017===
Crown-Rump Length: 40mm.

Scanned Slides from 12-200

On November 24, 25, 26, 27, 30, 2020 and December 01, 02 2020.

Several detection issues

Screenshots of every slide were taken

Photocopy picture added in the folder

===F021===
Scanned Slides from 08-41

On December 01, 02, 03 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F023===
Scanned Slides from 18-129

On December 02, 03, 04, 09, 10 2020.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F024===
Scanned Slides from 46-100

On January 07, 08, 2021.

Slide UAB-F24-63 needed two scanns. The focus range was too wide. On slide UAB-F24-069 ROIS were not in order, upside down and with mirror effect.

Screenshots of every slide were taken

Photocopy picture added in the folder

===F027===
Scanned Slides from 26-62

On December 10, 11 2020.

ROIs 5, 6, 7 and 8 mirror effect

Screenshots of every slide were taken

Photocopy picture added in the folder

===F029===
Scanned Slides from 01-275

On December 11, 14, 16, 17, 18, 21, 22, 23, 2020.

ROIs 4, 5 and 6 mirror effect. Some slides were scanned upside down (as a scan 2)

Screenshots of every slide were taken

We finally found the reason why we had been experiencing detection issues: The slides were too thin. the problem was fixed attaching a piece of adhesive tape on the non dectected slide so the detection system was able to detect them.

Photocopy picture added in the folder

===F030===
Scanned Slides from 198-395

On January 11, 12, 13, 14, 15, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F039===
Scanned one out of two slides from 85-448

On January 19, 20, 21, 22, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F041===
Scanned one out of two slides from 01-157

On January 22, 25, 26, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F042===
Scanned one out of two slides from 10-88 and from 148-274

On January 26, 27, 28, 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape

Photocopy picture added in the folder

===F044===

Crown-Rump Length: 61mm. Section plane: Frontal.
Scanned one out of two slides from 04-243

On february 08, 10, 11, 15, 16 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken

Some detection usses fixed with adhesive tape.

Photocopy picture added in the folder

===F048===

Crown-Rump Length: 68mm

Scanned one out of two slides from 07-41 and from 135-326

On february 01, 02, 03, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape.

===F049===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-200

On february 18, 19, 22, 05, 08 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F050===

Crown-Rump Length: 70mm

Scanned one out of three slides from 01-198

On february 24, 25, 26 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

===F055===

Crown-Rump Length: 70mm

Scanned one out of three slides from 162-834

On february 26, march 01, 02, 10, 12, 15, 16, 17 2021.

Not all the ROIs are facing the same direction (check with screenshots or photocopy picture)

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F062===

Crown-Rump Length: 83mm

Scanned one out of two slides from 28-120

On april 12, 13, 14 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F065===

Crown-Rump Length: 85mm

Scanned one out of three slides from 01-799

On april 04, 14, 15, 16, 19, 20, 21, 22 2021.

Some ROIs are upside down

Screenshots of every slide were taken, photocopy picture added in the folder

Some detection usses fixed with adhesive tape

===F36===
17 September - Slides 101-122 (Box D)

18 September - Slides 101-122 (Box D) scanned rotated. (-2)

{|
|-bgcolor="F5FAFF"
! Fetus
! Box
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 36
| 137
| F36
| A
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 138
| F36
| B
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 85
|
|
|
|-
| 36
| 139
| F36
| C
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 100
|
|
|
|-bgcolor="F5FAFF"
| 36
| 140
| F36
| D
| 58.0
|
| T/S
| 10
|
|
| 1
| '''orange'''
| 22
|
|
| Scanned 17-18 September
|}

===F52===

CRL 70.0 mm, 10 micron, 7 Boxes A to G, Head and Body, 591 slides

{|
|-bgcolor="F5FAFF"
! New Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| F52
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|}

1 October - Slide 101 - 128, looks like HE stain?
3 October Scan2 slide 101-128

{| class="wikitable mw-collapsible mw-collapsed"
! colspan=10|Domenech-Mateu Collection Fetus F52  
|-bgcolor="CEDFF2"
! Fetus
! Box
! New Reference
! Old Reference
! Box ref
! Crown-Rump Length (mm)
! Age (fetuses-weeks)
! Section Plane {{transverse}} {{frontal}} {{sagittal}} oblique
! Thickness (μm)
! Stain (HE/T/A/AT/V/B)
! Part of the body
! (n° color)
! Histology ('''green'''/'''orange'''/'''red''')
! No of Slides
! No of sections
! Thesis (si/no)
! Comments
|-
| 52
| 216
| F52
| DF-3
| A
| 70.0
|
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 480
| si
|
|-bgcolor="F5FAFF"
| 52
| 217
| F52
| DF-3
| B
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 100
| 305
| si
| "slides 101, 133, 152 broken"
|-
| 52
| 218
| F52
| DF-3
| C
| 70.0
| 11
| S
| 10
| B
| Head
| 2
| '''green'''; '''red'''
| 61
| 267
| si
|
|-bgcolor="F5FAFF"
| 52
| 219
| F52
| DF-3
| D
| 70.0
| 11
| F
| 10
| B
| Body torax
| 2
| '''green'''; '''red'''
| 100
| 643
| si
|
|-
| 52
| 220
| F52
| DF-3
| E
| 70.0
| 11
| F
| 10
|
| Body
| 2
| '''green'''; '''red'''
| 42
| 292
|
| Slide 134 broken
|-bgcolor="F5FAFF"
| 52
| 221
| F52
| DF-3
| F
| 70.0
| 11
| T
| 10
| B
| Pelvis
| 2
| '''green'''; '''red'''
| 100
| 1001
| si
|
|-
| 52
| 222
| F52
| DF-3
| G
| 70.0
| 11
| Varis
| 10
| HE/TM
| Limbs
| 2
| '''green'''; '''red'''
| 88
| 3319
| si
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf
|}

===F72===
CanoScan 9000F Mark II [[Slide_Scanning#Flatbed_Scanner|flatbed scan]] of slide 200.

Original image size: 27.5 Mb, 9600 DPI, 7 x 4.24 cm, 26473 x 16022

Reduced to 1280 width for online (264 Kb).

[[File:UAB-F72-200.jpg|800px]]

Small region (W 3000 px) from original scan reduced in size (W 1280 px).

[[File:UAB-F72-200-1.jpg|800px]]

==Fetus Catalogue==
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353

{{Domenech-Mateu Collection Embryos table6}}

{{Domenech-Mateu Collection Embryos table5-sort-collapse}}

{{Footer}}