Berlin Meeting 2017 - Digital Embryology Consortium: Difference between revisions
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{| | |||
| colspan=2|Dr Mark Hill's two presentations from the [https://human-embryology.org/wiki/DEC_Berlin_Meeting_2017 '''December 2017 Berlin Meeting'''] | |||
|- | |||
| | |||
<br> | |||
# [[#Introduction|'''Introduction''']] | |||
# [[#Blechschmidt Collection|'''Blechschmidt Collection''']] | |||
<br> | |||
[https://human-embryology.org | [[File:DEC icons thumbnail.jpg|500px|link=https://human-embryology.org]] | ||
| valign=top|[[File:Mark Hill.jpg|150px]] | |||
Dr Mark Hill | |||
http://tiny.cc/DEC-Berlin_2017 | |||
[[File:QR-DEC-Berlin 2017.png|100px]] | |||
|} | |||
=Introduction= | |||
==DEC Beginnings== | |||
===2013=== | |||
{| | |||
|-bgcolor="FAF5FF" | |||
! colspan=2|Research and Presentations | |||
|- | |||
| [[File:Giere_Hill_-_Hill_Collection.jpg|300px|link=Hubrecht Collection)]] | |||
| [[File:Hill Viebahn Blechschmidt Collection.jpg|300px|link=https://human-embryology.org/wiki/Blechschmidt_Collection]] | |||
|- | |||
| [[Museum_of_Natural_History_Berlin - 2013_Seminar|Museum of Natural History Embryology Seminar]] | |||
| [[Anatomy and Embryology Goettingen - 2013_Seminar|Goettingen Anatomy and 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] | |||
(Described later in the meeting by Dr Thorsten Heupel) | |||
| [http://www.giving.unsw.edu.au/unsw-foundation-limited UNSW Foundation] donation plaque | |||
|} | |||
<br> | |||
<html5media width="480" height="360">https://www.youtube.com/embed/1RbeEqn9Rmo</html5media> | |||
[[Blechschmidt Collection]] scanning commences. | |||
===2016=== | |||
{| | |||
|-bgcolor="FAF5FF" | |||
! colspan=2|Slide Scanning | |||
|- | |||
| [[File:Mark and Embryo.jpg|400px]] | |||
|- | |||
| [[Blechschmidt Collection]] slide scanning completed. (described later in the Berlin meeting by Hannes Sydow ) | |||
|} | |||
[[Hinrichsen Collection]] slide scanning commences. (described later in the Berlin meeting by Dr Nenad Maricic.) | |||
<br> | |||
{| | |||
|-bgcolor="FAF5FF" | |||
! colspan=2|New collections join DEC | |||
|- | |||
| width=260px|[[File:Hill Mirapeix Domenech-Mateu Collection.jpg|250px]] | |||
Mark Hill and Prof. Rosa Mirapeix | |||
| | |||
[https://human-embryology.org/wiki/Domenech-Mateu_Collection Domenech-Mateu Collection] – Universitat Autònoma de Barcelona. | |||
(described later in the Berlin meeting by Prof. Rosa Mirapeix) | |||
<br><br> | |||
[https://human-embryology.org/index.php?title=HDBR_and_HuDSeN Collection HDBR and HuDSeN Collection] – Newcastle University. | |||
(described later in the Berlin meeting by Dr Steven Lisgo) | |||
<br><br> | |||
[https://human-embryology.org/index.php?title=Amsterdam_Collection Amsterdam Collection] - Amsterdam University, Academic Medical Center. | |||
(described later in the Berlin meeting by Prof. Wouter Lamers) | |||
<br> | |||
<br> | |||
[[Media:ANZSCDB-Poster-MH-Apr2016.pdf|ANZSCDB Meeting presentation]] | |||
|} | |||
<br> | |||
{| | |||
|-bgcolor="FAF5FF" | |||
! colspan=2|Image Server | |||
|- | |||
| (Described by Dr Jean-Marie Burel later in the meeting) | |||
[[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 | |||
|- | |||
| '''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). | |||
|} | |||
==2017 DEC Current== | |||
===DEC Online=== | |||
'''Oct 2017''' - Software was updated to Omero Server (version 5.4). | |||
This topic will be covered in more detail in my presentation on the Blechschmidt collection. | |||
<br><br> | |||
'''The animation below shows the DEC server log-in process.''' | |||
<br><br> | |||
<html5media width="600" height="500">File:OMERO logging in.mp4</html5media> | |||
===Hinrichsen Collection=== | |||
{| | |||
|-bgcolor="FAF5FF" | |||
! colspan=2|Slide Scanning | |||
|- | |||
| [[Hinrichsen Collection]] - scanning completed. | |||
|- | |||
| [[File:Hinrichsen Collection Hill Brand-Saberi.jpg|300px]] | |||
Mark Hill and Prof. Beate Brand-Saberi | |||
| [[File:Hinrichsen-Embryo514-Slide-100-Scene01.jpg|250px]] | |||
'''Embryo 514''', [[Carnegie stage 21]], CRL 23 mm<br>Sagittal plane, {{HE}}, [http://149.171.80.223:8080/webclient/?show=dataset-751 '''Slide 100'''] | |||
|- | |||
|} | |||
<br><br> | |||
(described later in the Berlin meeting by Dr. Nenad Maricic) | |||
* Jun 2017 - about 2500 slides scanned. | |||
* Nov 2017 - scans uploaded to online database. | |||
* Dec 2017 - scanning finished. | |||
<br> | |||
{{Hinrichsen Collection Jun2017scanning_collapsetable}} | |||
<br> | |||
===Embryological Collection MfN=== | |||
December 2017 - scanner delivered and installed. | |||
{| | |||
| [[File:2017 Berlin install 01.JPG|400px]] | |||
| [[File:MfN DEC Scanner-room.jpg|400px]] | |||
|} | |||
===Summary=== | |||
2017 completed the second collection scanning and testing of the updated online database software. Delivered teh scanner to Berlin. | |||
{| class="wikitable mw-collapsible mw-collapsed" | |||
! 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. | |||
|- | |||
| [[File:DEC-database-stats-2017-12-11.jpg|800px]] | |||
|} | |||
<br> | |||
<br> | |||
<br> | |||
<br> | |||
(Presentation 2 below) | |||
=Blechschmidt Collection= | |||
[[File:Hill Viebahn Blechschmidt Collection.jpg|800px|link=https://human-embryology.org/wiki/Blechschmidt_Collection]] | |||
Mark Hill and Prof Christoph Viebahn | |||
==Prof. Erich Blechschmidt== | |||
{| | |||
| Prof. Erich Blechschmidt (1904 – 1992)<ref><pubmed>1476247</pubmed></ref> | |||
* German anatomist and director of Göttingen University’s Anatomical Institute from 1942 until 1973. | |||
* Alternate theories for embryogenesis based upon "morphogenetic fields" | |||
** believed that more than just genes might act to control development. | |||
* Wrote several embryology books and research articles (32 are listed in PubMed between 1955 to 1976) | |||
** all originally published in the German language. | |||
* The collection consists of about 120 human embryos approximately 200,000 serial sections. | |||
** In 1972 some embryos were incorporated into the [[Carnegie Collection]] (assigned Carnegie Nos. 10315-10434), but have since been returned to the University of Goettingen. | |||
* From the serial sections 64 models some more than 1 metre in size.<ref><pubmed>13227045</pubmed></ref> | |||
| [[File:Eric Blechschmidt.jpg|150px|alt= Erich Blechschmidt (1904 – 1992)]] | |||
Erich Blechschmidt<br>(1904 – 1992) | |||
|} | |||
==Embryo Models== | |||
[[File:Blechschmidt model collection room.jpg|600px]] | |||
<gallery mode="packed-hover" caption="10 mm Embryo (stage17)"> | |||
File:Stage17_model_03.jpg|left | |||
File:Stage17_model_05.jpg|ventral | |||
File:Stage17_model_04.jpg|right | |||
File:Stage17_model_06.jpg|dorsal | |||
File:Stage17 model_01.jpg|cranial end | |||
File:Stage17 model_02.jpg|placental cord | |||
</gallery> | |||
Model (about 1 M) of Embryo 7.5 mm | |||
<html5media height="700" width="500">File:Embryo 7.5mm model 02.mp4</html5media> | |||
{| | |||
| valign="bottom"|{{Embryo 1.6mm movie 1}} | |||
| valign="bottom"|{{Embryo 3.1mm movie 1}} | |||
| valign="bottom"|{{Embryo 7.5mm movie 1}} | |||
| valign="bottom"|{{Embryo 10mm movie 1}} | |||
|} | |||
==DEC Online== | |||
{| | |||
| '''Oct 2017''' | |||
* Software has been updated to Omero Server (version 5.4). | |||
* OMERO version 5.4 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 | |||
* RAID 5 - consists of block-level striping with distributed parity. | |||
** Upon failure of a single drive, subsequent reads can be calculated from the distributed parity such that no data is lost. | |||
| width=210px|[[File:Ome-logo-400.png|200px|link=https://www.openmicroscopy.org/community/viewtopic.php?f=11&t=8284]] | |||
|} | |||
<br> | |||
{| class="wikitable mw-collapsible mw-collapsed" | |||
! 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|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}} | |||
====References==== | |||
<references/> | |||
{{Footer}} | {{Footer}} |
Latest revision as of 17:18, 11 December 2017
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Dr Mark Hill's two presentations from the December 2017 Berlin Meeting | |
|
Dr Mark Hill |
Introduction
DEC Beginnings
2013
Research and Presentations | |
---|---|
Museum of Natural History Embryology Seminar | Goettingen Anatomy and 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 |
|
2015
Planned with partners the digitization project.
Presentations | |
---|---|
Kyoto (Nov 2015) | Washington (Dec 2015) |
Purchased slide scanner | |
Zeiss Axioscan.Z1
(Described later in the meeting by Dr Thorsten Heupel) |
UNSW Foundation donation plaque |
<html5media width="480" height="360">https://www.youtube.com/embed/1RbeEqn9Rmo</html5media>
Blechschmidt Collection scanning commences.
2016
Slide Scanning | |
---|---|
Blechschmidt Collection slide scanning completed. (described later in the Berlin meeting by Hannes Sydow ) |
Hinrichsen Collection slide scanning commences. (described later in the Berlin meeting by Dr Nenad Maricic.)
New collections join DEC | |
---|---|
Mark Hill and Prof. Rosa Mirapeix |
Domenech-Mateu Collection – Universitat Autònoma de Barcelona. (described later in the Berlin meeting by Prof. Rosa Mirapeix)
(described later in the Berlin meeting by Dr Steven Lisgo)
(described later in the Berlin meeting by Prof. Wouter Lamers)
|
Image Server | |
---|---|
(Described by Dr Jean-Marie Burel later in the meeting) | |
Testing of online server The Open Microscopy Environment OME Help Using OMERO.web
|
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.
|
Online Database Software
A well supported and freely available software was required for this large image database. |
2017 DEC Current
DEC Online
Oct 2017 - Software was updated to Omero Server (version 5.4).
This topic will be covered in more detail in my presentation on the Blechschmidt collection.
The animation below shows the DEC server log-in process.
<html5media width="600" height="500">File:OMERO logging in.mp4</html5media>
Hinrichsen Collection
Slide Scanning | |
---|---|
Hinrichsen Collection - scanning completed. | |
Mark Hill and Prof. Beate Brand-Saberi |
Embryo 514, Carnegie stage 21, CRL 23 mm |
(described later in the Berlin meeting by Dr. Nenad Maricic)
- Jun 2017 - about 2500 slides scanned.
- Nov 2017 - scans uploaded to online database.
- Dec 2017 - scanning finished.
Hinrichsen Collection Scanning June 2017 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Scan | Box | Serial | Slides | Stage | CRL (mm) | HDD | Cutting/Organ | Comp 85% |
JPEG | Staining | Slides | Test upload slides |
1 | EYO | 226 | 001-114 | 18 | 16 mm | 1 | Sagittal (good) | x | wdp | HE, Tri, Azan | 114 | |
2 | EYO | 226 | 5-100 | 18 | 16 mm | 1 | every 5th slide (good) | x | x | HE, Tri, Azan | 20 | 5 |
3 | EYO | 283 | 002-522 | 20 | 21 mm | 1 | Sagittal (good) | x | x | HE, Tri, Azan | 520 | |
4 | EYO | 294 | 001-174 | ? | 20 mm | 1 | Sagittal (good) | x | x | HE, Tri, Azan | 174 | |
5 | EYO | 335 | 001-270 | 20 | 22 mm | 1 | Frontal horizontal (very good) | x | x | HE, Tri, Azan | 270 | 2, 3, 4 |
6 | EYO | 364 | 001-131 | 14 | 6.5 mm | 1 | Sagittal (average) | x | x | HE, Tri, Azan | 131 | 1, 2, 3 |
7 | EYO | 388 | 009-280 | ? | 19mm | 1 | Sagittal (average) | x | x | HE, Tri, Azan | 271 | 9 |
8 | EYO | 514 | 001-330 | 21 | 23 mm | 1 | Sagittal | x | x | HE, Tri, Azan | 330 | 24, 67, 327 |
9 | EYO | 527 | 001-130 | ? | 20.0 mm | 1 | Transversal | x | HE, Tri, Azan | 130 | ||
10 | ME 32 | 536 | 001-335 | 20 | 22 mm | 1 | Frontal | x | HE, Tri, Azan | 335 | 1, 2 | |
11 | ME 53 | 564 | 006-228 | 18 | 16 mm | 1 | Frontal whole Embryo | x | HE | 52 | 132 | |
12 | ME 54 | 568 | 006-204 | 21 | 22.5 mm | 1 | Frontal whole embryo | x | HE | 46 | ||
13 | ME 65 | ? | 001-037 | 14 | 6.2 mm | 1 | Transverse (moderate)/Heart | x | Toluidinblue | 37 | 1, 6, 12, 20, 30 | |
14 | EYO | 457 | 40 | |||||||||
Total | 2470 |
Embryological Collection MfN
December 2017 - scanner delivered and installed.
Summary
2017 completed the second collection scanning and testing of the updated online database software. Delivered teh scanner to Berlin.
(Presentation 2 below)
Blechschmidt Collection
Mark Hill and Prof Christoph Viebahn
Prof. Erich Blechschmidt
Prof. Erich Blechschmidt (1904 – 1992)[1]
|
Erich Blechschmidt |
Embryo Models
Model (about 1 M) of Embryo 7.5 mm
<html5media height="700" width="500">File:Embryo 7.5mm model 02.mp4</html5media>
|
|
|
|
DEC Online
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. |
|
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.
There are 12 serial sections on this single slide (76 slides in this embryo series). 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 |
References
Cite this page: Hill, M.A. (2024, April 26) Embryology Berlin Meeting 2017 - Digital Embryology Consortium. Retrieved from https://embryology.med.unsw.edu.au/embryology/index.php/Berlin_Meeting_2017_-_Digital_Embryology_Consortium
- © Dr Mark Hill 2024, UNSW Embryology ISBN: 978 0 7334 2609 4 - UNSW CRICOS Provider Code No. 00098G