Talk:DEC Berlin Meeting 2017: Difference between revisions

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==Contact Details==
==Contact Details==
===Dr Mark Hill===
Head of Embryology, School of Medical Sciences
Room 221, level 2, Wallace Wurth West
UNSW AUSTRALIA
UNSW SYDNEY NSW 2052 AUSTRALIA
T: +61 (2) 9385 2477
F: +61 (2) 9385 2866
E: m.hill@unsw.edu.au
W: medicalsciences.med.unsw.edu.au
===Prof Beate Brand-Saberi===
Abteilung für Anatomie und Molekulare Embryologie
Institut für Anatomie
Ruhr-Universität Bochum
Universitätsstraße 150
MA 5 Süd/161
44801 Bochum
Tel: 0234/3224556
===Prof Rosa Mirapeix===
Anatomy and Embryology Unit
Morphological Science Department
Universitat Autònoma de Barcelona
email: rosa.mirapeix@uab.cat


===Prof Wouter H Lamers===
===Prof Wouter H Lamers===
Line 16: Line 44:
E-mail: shyamada@cac.med.kyoto-u.ac.jp (office) shyamada@mac.com (home)
E-mail: shyamada@cac.med.kyoto-u.ac.jp (office) shyamada@mac.com (home)
Phone (+81) 75-753-4345  Fax (+81) 75-753-4621
Phone (+81) 75-753-4345  Fax (+81) 75-753-4621
===Dr Thorsten Heupel===
Product Manager
Technology Center Software & Digital Solutions
Microscopy Business Group
Carl Zeiss Microscopy GmbH
ZEISS Group
Kistlerhofstr. 75
81379 München, Germany
Phone: +49 89 90 9000-881
Mobile: +49 171 2246860
Fax: +49 89 90 9000-820
thorsten.heupel@zeiss.com
www.zeiss.com


===Dr. Peter Giere===
===Dr. Peter Giere===
Line 35: Line 79:
Sprecher der AG Kuratoren der Gesellschaft für Biologische Systematik (GfBS)  
Sprecher der AG Kuratoren der Gesellschaft für Biologische Systematik (GfBS)  
Speaker of the Curators' Group within the Society of Biological Systematics (GfBS, Germany)
Speaker of the Curators' Group within the Society of Biological Systematics (GfBS, Germany)
===Dr Steven Lisgo===
HDBR Resource Manager
Email: steven.lisgo@ncl.ac.uk
Telephone: +44 (0) 191 241 8646
Fax: +44 (0) 191 241 8666
Address: Institute of Genetic Medicine
Newcastle University
International Centre for Life
Central Parkway
Newcastle upon Tyne
NE1 3BZ


===Bernhard Schurian===
===Bernhard Schurian===
Line 47: Line 104:
10115 Berlin
10115 Berlin
Deutschland
Deutschland
===Elizabeth Lockett===
National Museum of Health and Medicine


==Links==
==Links==


* [[Media:DEC-OMERO-training-manual-2017.pdf|DEC OMERO training manual]]
* [[Media:DEC-OMERO-training-manual-2017.pdf|DEC OMERO training manual]]
==Introduction==
==2. DEC Beginnings==
===2013===
{|
|-bgcolor="FAF5FF"
! colspan=2|Research and Presentations
|-
| [[File:Hill Viebahn Blechschmidt Collection.jpg|300px|link=https://human-embryology.org/wiki/Blechschmidt_Collection]]
| [[File:Giere_Hill_-_Hill_Collection.jpg|300px|link=Hubrecht Collection)]]
|-
| [[Anatomy and Embryology Goettingen - 2013_Seminar|Goettingen Anatomy and Embryology Seminar]]
| [[Museum_of_Natural_History_Berlin - 2013_Seminar|Museum of Natural History Embryology Seminar]]
|}
===2014===
Establish the DEC.
{|
|-bgcolor="FAF5FF"
! colspan=2| [[Kyoto Collection|Kyoto Collection Research]] 
|-
| width=420px|<html5media height="600" width="450">File:Stage20 MRI S05.mp4</html5media>
| width=420px|<html5media height="600" width="400">File:Stage20 MRI S02.mp4</html5media>
|}
{|
| width=520px|[[File:Kohei Shiota-Mark Hill-Shigehito Yamada-Mineo Yasuda.jpg|500px|alt=Prof. Kohei Shiota, Dr Mark Hill, Prof. Shigehito Yamada and Prof. Mineo Yasuda]]
Prof. Kohei Shiota, Dr Mark Hill, Prof. Shigehito Yamada and Prof. Mineo Yasuda
|
{|
! Kyoto Collection iBook
|-
| (Published 2016)
<br>
[[File:Kyoto Embryo Collection - cover.jpg|200px|link=http://itunes.apple.com/us/book/id1143922693]]
<br><br>
[[File:AvailableBook.png|150px|link=https://itunes.apple.com/au/book/kyoto-embryo-collection/id1143922693?mt=11]]
|}
|}
===2015===
Planned with partners the digitization project.
{|
|-bgcolor="FAF5FF"
! colspan=2|Presentations
|-
! Kyoto (Nov 2015)
! Washington (Dec 2015)
|-
| [[File:Kyoto2015symposium40 slide02.jpg|link=Media:Developing the Digital Kyoto Collection in Education and Research Nov 2015.pdf|400px]]
| [[File:Washinton2015seminar slide01.jpg|link=Media:Digital Embryology Consortium Dec 2015.pdf|400px]]
|-
| <br>
|-bgcolor="FAF5FF"
! colspan=2|Purchased slide scanner
|-
| [[File:Axio-Scan Z1.png|400px|link=https://www.zeiss.com/microscopy/int/products/imaging-systems/axio-scan-z1.html]]
| [[File:UNSW Foundation donation plaque.jpg|400px|link=http://www.giving.unsw.edu.au/unsw-foundation-limited]]
|-
| [https://www.zeiss.com/microscopy/en_de/products/imaging-systems/axio-scan-z1.html Zeiss] [https://human-embryology.org/wiki/Slide_Scanning Axioscan.Z1]
| [http://www.giving.unsw.edu.au/unsw-foundation-limited UNSW Foundation] donation plaque
|}
<br>
[[Blechschmidt Collection]] scanning commences.
===2016===
{|
|-bgcolor="FAF5FF"
! colspan=2|Slide Scanning
|-
| [[File:Mark and Embryo.jpg|400px]]
|-
| [[Blechschmidt Collection]] slide scanning completed.
|}
<br>
{|
|-bgcolor="FAF5FF"
! colspan=2|New collections join DEC
|-
| width=260px|[[File:Hill Mirapeix Domenech-Mateu Collection.jpg|250px]]
Prof. Rosa Mirapeix
|
[https://human-embryology.org/wiki/Domenech-Mateu_Collection Domenech-Mateu Collection] – Universitat Autònoma de Barcelona.
<br><br>
[https://human-embryology.org/index.php?title=HDBR_and_HuDSeN Collection HDBR and HuDSeN Collection] – Newcastle University.
<br><br>
[https://human-embryology.org/index.php?title=Amsterdam_Collection Amsterdam Collection] - Amsterdam University, Academic Medical Center
<br><br>
<pubmed>27884980</pubmed>
<br>
[[Media:ANZSCDB-Poster-MH-Apr2016.pdf|ANZSCDB Meeting presentation]]
|}
<br>
{|
|-bgcolor="FAF5FF"
! colspan=2|Image Server
|-
| [[File:OmeroWeb.png|500px]]
|-
| [[File:Ome-logo-400.png|200px|link=https://www.openmicroscopy.org|left]] Testing of online server [https://www.openmicroscopy.org/site The Open Microscopy Environment] [http://help.openmicroscopy.org OME Help] [http://help.openmicroscopy.org/web-client.html Using OMERO.web]
<br>
OMERO [http://glencoesoftware.com/2016-08-30-glencoe-software-zeiss-partner-open-source-file-reader-whole-slide.html development of JPG XR compatibility] in Bioformats and for server.
|}
<br>
===Summary===
Between 2013 to 2016 following presentations, collection visits, and research the consortium was established.
{| class="wikitable mw-collapsible mw-collapsed"
! Summary - DEC Beginnings&nbsp;
|-
| '''Slide Scanner'''
A key to the project was to evaluate the slide scanning options.
* Many of the collections have historic (irreplaceable) slides and most modern slide scanners are primarily designed for pathology labs where the slide preservation is not crucial.
* Many of the collections have slides of non-standard historic dimensions.
* The scanner requires easy transport and set up at each new location.
<br>
The [https://www.zeiss.com/microscopy/int/products/imaging-systems/axio-scan-z1.html Zeiss axioscan] met all the above criteria.
* Slides are never mechanically handled once loaded onto a carrier rack.
* Slide racks can be manufactured to deal with non-standard slide sizes.
* A scanner carrier case is available for ease of transport.
|-
| '''Online Database Software'''
A well supported and freely available software was required for this large image database.
* Zeiss provides [https://www.zeiss.com/microscopy/int/products/microscope-software/zen.html Zen] software, that is licensed and requires ongoing subscription as well as expensive for storage space.
* Glencoe provides [http://www.openmicroscopy.org/site/products/omero OMERO] software that is widely used internationally by research institutes, labs and journals (J Cell Biology).
|}
==3. DEC Current==
===2017===
{|
|-bgcolor="FAF5FF"
! colspan=2|Slide Scanning
|-
| [[Hinrichsen Collection]] commences (1200 slides scanned to date)
|-
| [[File:Hinrichsen Collection Hill Brand-Saberi.jpg|300px]]
Prof. Beate Brand-Saberi
| [[File:ME54 001.jpg|250px]]
ME 54 [[Carnegie stage 21]], CRL 22.5 mm<br>8 weeks, female,  frontal, {{HE}}
|-
|}
<br>
[https://human-embryology.org/wiki/Embryo_Collections Current DEC Collections]
{|
| width=210px|[[File:Ome-logo-400.png|200px|link=https://www.openmicroscopy.org/community/viewtopic.php?f=11&t=8284]]
|
* OMERO updated to version 5.3 now JPG XR compatible.
* Server - Quad-Core Intel Xeon E5 Processor Speed - 3.7 GHz
* Storage - 2 x Areca ARC-5028T2, Thunderbolt 2, 6-Bay RAID 5 - 72 TB
|}
===Summary===
2017 completed first collection scanning and testing of the updated online database software.
{| class="wikitable mw-collapsible mw-collapsed"
! Summary - DEC Current&nbsp;
|-
| '''Scanned Slide Files'''
* The original - The HDD containing the scanned slides files are held as an archive by the original collection curator.
* The DEC copy - The files are then converted from CZI format ( 1-4 GB each) to a compressed JPGXR format (200-400 MB each) onto a separate DEC HDD.
** These second HDDs are stored in Australia.
* The online version - The compressed images are then batch uploaded onto the DEC server.
** DEC server database is protected in a RAID 5 storage system.
This means there are always at least 3 separate copies of the original data in 3 different locations.
|-
| '''Online Database'''
* 2016 - Server was run continuously with sample uncompressed images to test stability.
* Mar 2017 - software updated to import the JPGXR format files.
* Server is currently being tested for remote uploading of files from international locations.
|}
==4. DEC Online==
Below is a link to the Online Image database - a single section on a slide from the Blechschmidt collection.
{| class="wikitable mw-collapsible mw-collapsed"
! Online Image Database - Access &nbsp;
|-
| Please note that only registered users who have agreed to the DEC usage conditions can access the database images.
Therefore for non-registered viewers, the links below will show only a link to the OMERO log-in page.
|}
{|
| [[File:Embryo-1951-09-01-Slide-60.jpg|300px]]
|
* [[Blechschmidt Collection]] - [http://149.171.80.223:8080/webclient/?show=image-1987 Embryo 1951 09 01 Slide 60]
** there are 12 serial sections on this single slide (76 slides in this embryo series).
* [http://149.171.80.223:8080/webclient/?show=image-1995 Slide 60] - [http://149.171.80.223:8080/webclient/img_detail/1995/?c=1|0:255$FF0000,2|0:255$00FF00,3|0:255$0000FF&m=c&p=normal&ia=0&q=0.9&t=1&z=1&zm=1.5603469238874927&x=12337&y=25443.05974025974 Scene 11]
** This single section pixel size is 24674H x 50841W
*** Image is as wide as more than 26 full HD TV screens (1920W×1080H)
** Pixels Size (XYZ) (µm): 0.22 x 0.22
** Acquisition Date: 2015-07-01 20:49:32
|}
<br>
The images below are screenshots from the [http://149.171.80.223:8080/ DEC online database].
<br>
{{Embryo1951-09-01-Slide60 gallery}}
<br>
{{Embryo1951-09-01-Slide60 links}}

Latest revision as of 17:15, 9 December 2017

Contact Details

Dr Mark Hill

Head of Embryology, School of Medical Sciences Room 221, level 2, Wallace Wurth West UNSW AUSTRALIA UNSW SYDNEY NSW 2052 AUSTRALIA T: +61 (2) 9385 2477 F: +61 (2) 9385 2866 E: m.hill@unsw.edu.au W: medicalsciences.med.unsw.edu.au


Prof Beate Brand-Saberi

Abteilung für Anatomie und Molekulare Embryologie Institut für Anatomie Ruhr-Universität Bochum Universitätsstraße 150 MA 5 Süd/161 44801 Bochum Tel: 0234/3224556

Prof Rosa Mirapeix

Anatomy and Embryology Unit Morphological Science Department Universitat Autònoma de Barcelona email: rosa.mirapeix@uab.cat

Prof Wouter H Lamers

Tytgat Institute for Liver and Intestinal Research Academic Medical Center, University of Amsterdam Meibergdreef 69-71, 1105 BK Amsterdam, The Netherlands T: +31205665948 (secr) F: +31205669190

Prof Shigehito Yamada

Congenital Anomaly Research Center, Kyoto University Graduate School of Medicine, Kyoto, Japan. E-mail: shyamada@cac.med.kyoto-u.ac.jp (office) shyamada@mac.com (home) Phone (+81) 75-753-4345 Fax (+81) 75-753-4621

Dr Thorsten Heupel

Product Manager Technology Center Software & Digital Solutions Microscopy Business Group

Carl Zeiss Microscopy GmbH ZEISS Group Kistlerhofstr. 75 81379 München, Germany

Phone: +49 89 90 9000-881 Mobile: +49 171 2246860 Fax: +49 89 90 9000-820 thorsten.heupel@zeiss.com www.zeiss.com

Dr. Peter Giere

Head, Centre of Collections Curator of the Embryological Collection Museum für Naturkunde Leibniz Institute for Evolution and Biodiversity Science

phone: +49-(0)30-2093-8703 fax: +49-(0)30-2093-8868 e-mail: peter.giere(at)mfn-berlin.de Postal Address: Museum für Naturkunde Berlin Leibniz Institute for Evolution and Biodiversity Science Dr. Peter Giere Invalidenstr. 43 10115 Berlin Germany Sprecher der AG Kuratoren der Gesellschaft für Biologische Systematik (GfBS) Speaker of the Curators' Group within the Society of Biological Systematics (GfBS, Germany)

Dr Steven Lisgo

HDBR Resource Manager

Email: steven.lisgo@ncl.ac.uk Telephone: +44 (0) 191 241 8646 Fax: +44 (0) 191 241 8666 Address: Institute of Genetic Medicine Newcastle University International Centre for Life Central Parkway Newcastle upon Tyne NE1 3BZ

Bernhard Schurian

Museum für Naturkunde

Email: bernhard.schurian@mfn-berlin.de Tel: +49 (0)30 2093 - 8422 Fax: +49 (0)30 2093 - 8868

Leibniz-Institut für Evolutions- und Biodiversitätsforschung Invalidenstraße 43 10115 Berlin Deutschland

Elizabeth Lockett

National Museum of Health and Medicine

Links

Introduction

2. DEC Beginnings

2013

Research and Presentations
File:Hill Viebahn Blechschmidt Collection.jpg File:Giere Hill - Hill Collection.jpg
Goettingen Anatomy and Embryology Seminar Museum of Natural History Embryology Seminar

2014

Establish the DEC.

Kyoto Collection Research 
<html5media height="600" width="450">File:Stage20 MRI S05.mp4</html5media> <html5media height="600" width="400">File:Stage20 MRI S02.mp4</html5media>
File:Kohei Shiota-Mark Hill-Shigehito Yamada-Mineo Yasuda.jpg

Prof. Kohei Shiota, Dr Mark Hill, Prof. Shigehito Yamada and Prof. Mineo Yasuda

Kyoto Collection iBook
(Published 2016)


File:Kyoto Embryo Collection - cover.jpg

File:AvailableBook.png

2015

Planned with partners the digitization project.

Presentations
Kyoto (Nov 2015) Washington (Dec 2015)
File:Kyoto2015symposium40 slide02.jpg File:Washinton2015seminar slide01.jpg

Purchased slide scanner
Axio-Scan Z1.png UNSW Foundation donation plaque.jpg
Zeiss Axioscan.Z1 UNSW Foundation donation plaque


Blechschmidt Collection scanning commences.

2016

Slide Scanning
File:Mark and Embryo.jpg
Blechschmidt Collection slide scanning completed.


New collections join DEC
File:Hill Mirapeix Domenech-Mateu Collection.jpg

Prof. Rosa Mirapeix

Domenech-Mateu Collection – Universitat Autònoma de Barcelona.

Collection HDBR and HuDSeN Collection – Newcastle University.

Amsterdam Collection - Amsterdam University, Academic Medical Center

<pubmed>27884980</pubmed>
ANZSCDB Meeting presentation



Image Server
OmeroWeb.png
Ome-logo-400.png
Testing of online server The Open Microscopy Environment OME Help Using OMERO.web


OMERO development of JPG XR compatibility in Bioformats and for server.


Summary

Between 2013 to 2016 following presentations, collection visits, and research the consortium was established.

Summary - DEC Beginnings 
Slide Scanner

A key to the project was to evaluate the slide scanning options.

  • Many of the collections have historic (irreplaceable) slides and most modern slide scanners are primarily designed for pathology labs where the slide preservation is not crucial.
  • Many of the collections have slides of non-standard historic dimensions.
  • The scanner requires easy transport and set up at each new location.


The Zeiss axioscan met all the above criteria.

  • Slides are never mechanically handled once loaded onto a carrier rack.
  • Slide racks can be manufactured to deal with non-standard slide sizes.
  • A scanner carrier case is available for ease of transport.
Online Database Software

A well supported and freely available software was required for this large image database.

  • Zeiss provides Zen software, that is licensed and requires ongoing subscription as well as expensive for storage space.
  • Glencoe provides OMERO software that is widely used internationally by research institutes, labs and journals (J Cell Biology).

3. DEC Current

2017

Slide Scanning
Hinrichsen Collection commences (1200 slides scanned to date)
Hinrichsen Collection Hill Brand-Saberi.jpg

Prof. Beate Brand-Saberi

File:ME54 001.jpg

ME 54 Carnegie stage 21, CRL 22.5 mm
8 weeks, female, frontal, HE


Current DEC Collections

Ome-logo-400.png
  • OMERO updated to version 5.3 now JPG XR compatible.
  • Server - Quad-Core Intel Xeon E5 Processor Speed - 3.7 GHz
  • Storage - 2 x Areca ARC-5028T2, Thunderbolt 2, 6-Bay RAID 5 - 72 TB

Summary

2017 completed first collection scanning and testing of the updated online database software.

Summary - DEC Current 
Scanned Slide Files
  • The original - The HDD containing the scanned slides files are held as an archive by the original collection curator.
  • The DEC copy - The files are then converted from CZI format ( 1-4 GB each) to a compressed JPGXR format (200-400 MB each) onto a separate DEC HDD.
    • These second HDDs are stored in Australia.
  • The online version - The compressed images are then batch uploaded onto the DEC server.
    • DEC server database is protected in a RAID 5 storage system.

This means there are always at least 3 separate copies of the original data in 3 different locations.

Online Database
  • 2016 - Server was run continuously with sample uncompressed images to test stability.
  • Mar 2017 - software updated to import the JPGXR format files.
  • Server is currently being tested for remote uploading of files from international locations.

4. DEC Online

Below is a link to the Online Image database - a single section on a slide from the Blechschmidt collection.

Online Image Database - Access  
Please note that only registered users who have agreed to the DEC usage conditions can access the database images.

Therefore for non-registered viewers, the links below will show only a link to the OMERO log-in page.

File:Embryo-1951-09-01-Slide-60.jpg
  • Blechschmidt Collection - Embryo 1951 09 01 Slide 60
    • there are 12 serial sections on this single slide (76 slides in this embryo series).
  • Slide 60 - Scene 11
    • This single section pixel size is 24674H x 50841W
      • Image is as wide as more than 26 full HD TV screens (1920W×1080H)
    • Pixels Size (XYZ) (µm): 0.22 x 0.22
    • Acquisition Date: 2015-07-01 20:49:32


The images below are screenshots from the DEC online database.
Template:Embryo1951-09-01-Slide60 gallery


Template:Embryo1951-09-01-Slide60 links

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