Berlin Meeting 2017 - Digital Embryology Consortium: Difference between revisions

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http://tiny.cc/DEC-Berlin_2017
http://tiny.cc/DEC-Berlin_2017
==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 links}}


{{Footer}}
{{Footer}}

Revision as of 18:31, 9 December 2017

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2017 Berlin - Digital Embryology Consortium

See also the online page - DEC - Meetings

QR-DEC-Berlin 2017.png


http://tiny.cc/DEC-Berlin_2017

Introduction

2. DEC Beginnings

2013

Research and Presentations
Hill Viebahn Blechschmidt Collection.jpg 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>
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)


Kyoto Embryo Collection - cover.jpg

AvailableBook.png

2015

Planned with partners the digitization project.

Presentations
Kyoto (Nov 2015) Washington (Dec 2015)
Kyoto2015symposium40 slide02.jpg 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
Mark and Embryo.jpg
Blechschmidt Collection slide scanning completed.


New collections join DEC
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

ME54 001.jpg

ME 54 Carnegie stage 21, CRL 22.5 mm
8 weeks, female, frontal, (Stain - Haematoxylin Eosin)


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.

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.

Embryo 1951-01-09 CRL 11 mm - Week 6 stage 16 stage 17

Slide 60 Links: Slide menu | Slide sections | Slide label | Scene 11 | Zoom x0.6 | Zoom x1.25 | Zoom x2.5 | Zoom x5 | Zoom x10 | Zoom x20 | Zoom x40 | Zoom x80


Embryo 1951-09-01 Slide 60 Information 

OMERO Blechschmidt Collection - Embryo 1951 09 01 Slide 60

Note these are only screenshots of the OMERO image database.


Acquisition Date: 2015-07-01 20:49:32

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


Cite this page: Hill, M.A. (2024, March 28) Embryology Berlin Meeting 2017 - Digital Embryology Consortium. Retrieved from https://embryology.med.unsw.edu.au/embryology/index.php/Berlin_Meeting_2017_-_Digital_Embryology_Consortium

What Links Here?
© Dr Mark Hill 2024, UNSW Embryology ISBN: 978 0 7334 2609 4 - UNSW CRICOS Provider Code No. 00098G