Berlin Meeting 2017 - Digital Embryology Consortium: Difference between revisions
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=Blechschmidt Collection= | =Blechschmidt Collection= | ||
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| Erich Blechschmidt (1904 – 1992)<ref><pubmed>1476247</pubmed></ref> was a German anatomist and director of Göttingen University’s Anatomical Institute from 1942 until 1973. He held alternate theories for embryogenesis based upon "morphogenetic fields" and | | Prof. Erich Blechschmidt (1904 – 1992)<ref><pubmed>1476247</pubmed></ref> | ||
* He was a German anatomist and director of Göttingen University’s Anatomical Institute from 1942 until 1973. | |||
* He held alternate theories for embryogenesis based upon "morphogenetic fields" and believed that more than just genes might act to control development. | |||
* He 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 | * 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)]] | | [[File:Eric Blechschmidt.jpg|150px|alt= Erich Blechschmidt (1904 – 1992)]] | ||
Revision as of 01:58, 11 December 2017
Embryology - 14 Jun 2024 Expand to Translate |
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Dr Mark Hill's two presentations from the December 2017 Berlin Meeting | |
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Introduction
DEC Beginnings
2013
Research and Presentations | |
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Goettingen Anatomy and Embryology Seminar | Museum of Natural History Embryology Seminar |
2014
Establish the DEC.
Kyoto Collection Research | |
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<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 |
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2015
Planned with partners the digitization project.
Presentations | |
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Kyoto (Nov 2015) | Washington (Dec 2015) |
Purchased slide scanner | |
Zeiss Axioscan.Z1 | UNSW Foundation donation plaque |
Blechschmidt Collection scanning commences.
2016
Slide Scanning | |
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Blechschmidt Collection slide scanning completed. |
New collections join DEC | |
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Prof. Rosa Mirapeix |
Domenech-Mateu Collection – Universitat Autònoma de Barcelona. (described later in the Berlin meeting by Prof. Rosa Mirapeix)
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Image Server | |
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(Described by Dr Jean-Marie Burel later in the meeting) | |
Testing of online server The Open Microscopy Environment OME Help Using OMERO.web
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Summary
Between 2013 to 2016 following presentations, collection visits, and research the consortium was established.
Summary - DEC Beginnings |
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Slide Scanner
A key to the project was to evaluate the slide scanning options.
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Online Database Software
A well supported and freely available software was required for this large image database. |
DEC Current
2017
DEC Online
Oct 2017 - Software has been now 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 | |
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Hinrichsen Collection - scanning completed. | |
Mark Hill and Prof. Beate Brand-Saberi
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ME 54 Carnegie stage 21, CRL 22.5 mm |
Hinrichsen Collection Scanning June 2017 | ||||||||||||
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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 second collection scanning and testing of the updated online database software.
Summary - DEC Current |
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Scanned Slide Files
This means there are always at least 3 separate copies of the original data in 3 different locations. |
Online Database
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Blechschmidt Collection
Prof. Erich Blechschmidt (1904 – 1992)[1]
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Erich Blechschmidt |
Mark Hill and Prof Christoph Viebahn |
Embryo Models
Embryo Model Movies
Model (about 1 M) of Embryo 7.5 mm
<html5media height="700" width="500">File:Embryo 7.5mm model 02.mp4</html5media>
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DEC Online
This topic will be covered in more detail in my presentation on the Blechschmidt collection.
Online Image Database - Access |
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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. |
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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 |
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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, June 14) 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