Domenech-Mateu Collection Embryos: Difference between revisions
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'''Tray 7''' - Do Not Use this Tray | '''Tray 7''' - Do Not Use this Tray | ||
* not loading correctly, if slides loaded in this tray, scanner will potentially jam. | * 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? | '''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=== | ===Image Coding=== | ||
Line 94: | Line 94: | ||
====1. In the Collection Room==== | ====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. | # '''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 <font color=green>'''green'''</font> then do the <font color=orange>'''orange'''</font> and finally the <font color=red>'''red'''</font>. | ## Start with the <font color=green>'''green'''</font> then do the <font color=orange>'''orange'''</font> and finally the <font color=red>'''red'''</font>. | ||
Line 105: | Line 105: | ||
====2. In 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 | |||
====Regions of Interest (ROIs)==== | '''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: | Resetting full slide region: | ||
Line 121: | Line 149: | ||
* Use "Back" to reset the full slide region (Red Box) that will be analysed for ROIs. | * 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. | ** Danger of Crush - Do not extend beyond the slide clip region. | ||
* Note this will also reset the "Preview Scan" for that slide, simply repeat. | * Note this will also reset the "Preview Scan" for that slide, simply repeat "Preview Scan". | ||
ROI's numbering: | ROI's numbering: | ||
Line 135: | Line 157: | ||
** you cannot use a number greater than the number of regions on the slide. | ** 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== | ==Embryos== | ||
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072 | 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=== | |||
{| | {| | ||
Line 184: | Line 416: | ||
* Slides 1-4, 7-12 scanned. | * Slides 1-4, 7-12 scanned. | ||
=== | Photocopy picture in the folder | ||
Screenshots were taken | |||
===E023=== | |||
{| | {| | ||
|-bgcolor="F5FAFF" | |-bgcolor="F5FAFF" | ||
Line 202: | Line 438: | ||
|- | |- | ||
|} | |} | ||
Scanned on November the 26th and 27th. screenshots taken of every slide. Photocoopy picture taken | |||
=== | ===E024=== | ||
{| | {| | ||
|-bgcolor="F5FAFF" | |-bgcolor="F5FAFF" | ||
Line 241: | Line 478: | ||
* Slide 3 broken and repaired. Test damaged slide scan. | * Slide 3 broken and repaired. Test damaged slide scan. | ||
=== | Screenshots were taken | ||
Photocopy picture in the folder | |||
===E025=== | |||
{| | {| | ||
|-bgcolor="F5FAFF" | |-bgcolor="F5FAFF" | ||
Line 259: | Line 500: | ||
! Comments | ! Comments | ||
|- | |- | ||
| [http://149.171.80.223:8080/webclient/?show= | | [http://149.171.80.223:8080/webclient/?show=project-451 '''E25'''] | ||
| {{CS16}} | | {{CS16}} | ||
| 10.0 | | 10.0 | ||
Line 274: | Line 515: | ||
| slide 7 trencat. Very good. Scanned 16-18 September. | | 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. | 17 September - Embryo test scanning of rotated slides. | ||
Line 294: | Line 537: | ||
16 September - Tray 7 loading problem again. Left empty for overnight scan. | 16 September - Tray 7 loading problem again. Left empty for overnight scan. | ||
=== | ===E026=== | ||
{| | {| | ||
|-bgcolor="F5FAFF" | |-bgcolor="F5FAFF" | ||
Line 330: | Line 573: | ||
25-26 September - Scan slides. | 25-26 September - Scan slides. | ||
=== | ===E027=== | ||
{| | {| | ||
|-bgcolor="F5FAFF" | |-bgcolor="F5FAFF" | ||
Line 365: | Line 608: | ||
25 September - Test scan slide 1 and 2. These sections are organised in rows not columns. | 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 (<font color=green>'''green'''</font>/<font color=orange>'''orange'''</font>/<font color=red>'''red'''</font>) | |||
! 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 | |||
| <font color=green>'''green'''</font> | |||
| 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" | |-bgcolor="CEDFF2" | ||
Line 400: | Line 1,017: | ||
27 September - All slides loaded. Scanned 4 of 5 columns. RLTB | 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=== | ===E109=== | ||
Line 457: | Line 1,159: | ||
==Embryo Catalogue== | ==Embryo Catalogue== | ||
Total Embryos = 114 Total Slides = 3810 Total Sections = 104072 | Total Embryos = 114 Total Slides = 3810 Total Sections = 104072 | ||
<br> | |||
{{Domenech-Mateu Collection Embryos table3}} | {{Domenech-Mateu Collection Embryos table3}} | ||
{{Domenech-Mateu Collection Embryos table2-sort-collapse}} | |||
<br> | |||
{{Carnegie_stage_table_1}} | {{Carnegie_stage_table_1}} | ||
==Fetuses== | ==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=== | ===F36=== | ||
Line 555: | Line 1,685: | ||
| | | | ||
| Scanned 17-18 September | | 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 (<font color=green>'''green'''</font>/<font color=orange>'''orange'''</font>/<font color=red>'''red'''</font>) | |||
! No of Slides | |||
! No of sections | |||
! Thesis (si/no) | |||
! Comments | |||
|- | |||
| F52 | |||
| E | |||
| 70.0 | |||
| 11 | |||
| F | |||
| 10 | |||
| | |||
| Body | |||
| 2 | |||
| <font color=green>'''green'''</font>; <font color=red>'''red'''</font> | |||
| 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 (<font color=green>'''green'''</font>/<font color=orange>'''orange'''</font>/<font color=red>'''red'''</font>) | |||
! No of Slides | |||
! No of sections | |||
! Thesis (si/no) | |||
! Comments | |||
|- | |||
| 52 | |||
| 216 | |||
| F52 | |||
| DF-3 | |||
| A | |||
| 70.0 | |||
| | |||
| S | |||
| 10 | |||
| B | |||
| Head | |||
| 2 | |||
| <font color=green>'''green'''</font>; <font color=red>'''red'''</font> | |||
| 100 | |||
| 480 | |||
| si | |||
| | |||
|-bgcolor="F5FAFF" | |||
| 52 | |||
| 217 | |||
| F52 | |||
| DF-3 | |||
| B | |||
| 70.0 | |||
| 11 | |||
| S | |||
| 10 | |||
| B | |||
| Head | |||
| 2 | |||
| <font color=green>'''green'''</font>; <font color=red>'''red'''</font> | |||
| 100 | |||
| 305 | |||
| si | |||
| "slides 101, 133, 152 broken" | |||
|- | |||
| 52 | |||
| 218 | |||
| F52 | |||
| DF-3 | |||
| C | |||
| 70.0 | |||
| 11 | |||
| S | |||
| 10 | |||
| B | |||
| Head | |||
| 2 | |||
| <font color=green>'''green'''</font>; <font color=red>'''red'''</font> | |||
| 61 | |||
| 267 | |||
| si | |||
| | |||
|-bgcolor="F5FAFF" | |||
| 52 | |||
| 219 | |||
| F52 | |||
| DF-3 | |||
| D | |||
| 70.0 | |||
| 11 | |||
| F | |||
| 10 | |||
| B | |||
| Body torax | |||
| 2 | |||
| <font color=green>'''green'''</font>; <font color=red>'''red'''</font> | |||
| 100 | |||
| 643 | |||
| si | |||
| | |||
|- | |||
| 52 | |||
| 220 | |||
| F52 | |||
| DF-3 | |||
| E | |||
| 70.0 | |||
| 11 | |||
| F | |||
| 10 | |||
| | |||
| Body | |||
| 2 | |||
| <font color=green>'''green'''</font>; <font color=red>'''red'''</font> | |||
| 42 | |||
| 292 | |||
| | |||
| Slide 134 broken | |||
|-bgcolor="F5FAFF" | |||
| 52 | |||
| 221 | |||
| F52 | |||
| DF-3 | |||
| F | |||
| 70.0 | |||
| 11 | |||
| T | |||
| 10 | |||
| B | |||
| Pelvis | |||
| 2 | |||
| <font color=green>'''green'''</font>; <font color=red>'''red'''</font> | |||
| 100 | |||
| 1001 | |||
| si | |||
| | |||
|- | |||
| 52 | |||
| 222 | |||
| F52 | |||
| DF-3 | |||
| G | |||
| 70.0 | |||
| 11 | |||
| Varis | |||
| 10 | |||
| HE/TM | |||
| Limbs | |||
| 2 | |||
| <font color=green>'''green'''</font>; <font color=red>'''red'''</font> | |||
| 88 | |||
| 3319 | |||
| si | |||
| 3 series: DF-3 B1 extremitat sup longitudinal; DF-3 B2 extremitat sup transversal; DF-3 P estremitat inf | |||
|} | |} | ||
Line 574: | Line 1,894: | ||
{{Domenech-Mateu Collection Embryos table6}} | {{Domenech-Mateu Collection Embryos table6}} | ||
{{Domenech-Mateu Collection Embryos table5-sort-collapse}} | |||
{{Footer}} | {{Footer}} |
Latest revision as of 21:29, 2 August 2021
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.
- 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?
Histology Stains - Common Stains and Their Reactions | |||||
---|---|---|---|---|---|
Haematoxylin | mucins - light blue | ||||
Eosin | colloid - pink muscle - red | ||||
Trichrome Azan (Heidenhain's Azan) | muscle - red | ||||
Bielschowsky stain (Bielschowsky's silver stain) | nerve fibers - black |
Step by Step
1. In the Collection Room
- Choose from the printed catalogue or the online catalogue the Embryo or 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
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) |
---|---|
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 |
---|---|
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
Upload scans from embryo folder to the DEC Database.
- Use OMERO.insight - (download page) also see help page 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 |
---|---|
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.
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 (Using ImageJ with OMERO)
- 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.
- 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
Reference New | Carnegie Stage | Crown-Rump Length (mm) | Age (days) | Section Plane 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|
E22 | 16 | 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
Reference New | Carnegie Stage | Crown-Rump Length (mm) | Age (days) | Section Plane 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
Reference New | Carnegie Stage | Crown-Rump Length (mm) | Age (days) | Section Plane 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
E24 | 16 | 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
Reference New | Carnegie Stage | Crown-Rump Length (mm) | Age (days) | Section Plane 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
E25 | 16 | 10.0 | 37 | F | 10 | HE | Tot | 1 | green | 11 | 502 | Y | slide 7 trencat. Very good. Scanned 16-18 September. |
30 September - 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
Reference New | Carnegie Stage | Crown-Rump Length (mm) | Age (days) | Section Plane 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
E26 | 16 | 10.0 | 37 | T | 10 | HE | Tot | 1 | orange | 23 | 655 | Y | Slide 18 broken. Some fading |
25-26 September - Scan slides.
E027
Reference New | Carnegie Stage | Crown-Rump Length (mm) | Age (days) | Section Plane 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
E27 | 16 | 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
Reference New | Carnegie Stage | Crown-Rump Length (mm) | Age (days) | Section Plane 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
E30 | 16 | 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
Reference New | Carnegie Stage | Crown-Rump Length (mm) | Age (days) | Section Plane 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
E79 | 20 | 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
Reference New | Carnegie Stage | Crown-Rump Length (mm) | Age (days) | Section Plane 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
E109 | 23 | 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" |
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 23)
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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Total Embryos = 114 Total Slides = 3810 Total Sections = 104072 DEC Links: D-M Collection Embryos | [Template:Domenech-Mateu Collection Embryos table2 D-M Collection Embryos (Catalan)] | Domenech-Mateu Collection Embryology Links: D-M Collection Embryos (Catalan) | D-M Collection Embryos (English) | Collection Domenech-Mateu Collection |
Domenech-Mateu Collection Embryos (sortable table) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Best to sort this table by Histology. Green Embryos = 60 Total Embryos = 114 Total Slides = 3810 Total Sections = 104072
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Total Embryos = 114 Total Slides = 3810 Total Sections = 104072 DEC Links: D-M Collection Embryos | [Template:Domenech-Mateu Collection Embryos table2 D-M Collection Embryos (Catalan)] | Domenech-Mateu Collection Embryology Links: D-M Collection Embryos (Catalan) | D-M Collection Embryos (English) | Collection Domenech-Mateu Collection |
Week: | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 |
Carnegie stage: | 1 2 3 4 | 5 6 | 7 8 9 | 10 11 12 13 | 14 15 | 16 17 | 18 19 | 20 21 22 23 |
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)
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 | ||||||
36 | 138 | F36 | B | 58.0 | T/S | 10 | 1 | orange | 85 | ||||||
36 | 139 | F36 | C | 58.0 | T/S | 10 | 1 | orange | 100 | ||||||
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
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
Domenech-Mateu Collection Fetus F52 | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | ||
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 | |
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 | ||
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 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).
Small region (W 3000 px) from original scan reduced in size (W 1280 px).
Fetus Catalogue
Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353
Domenech-Mateu Collection Fetuses | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353 |
Domenech-Mateu Collection Fetuses (sortable table) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Best to sort this table by Histology. Approximate Number of Fetuses = 89 Total Number of Slides = 5290 Total number of Sections = 10353
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