Gottingen Meeting 2017 - Digital Embryology Consortium

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Digital Embryology Consortium

Centre of Anatomy, University Medical Centre Göttingen


2 PM Friday 30 June

http://tiny.cc/DEC-Gottingen_June_2017

Tiny cc DEC-Gottingen June 2017.png
This is a brief introductory 4 part presentation on the Digital Embryology Consortium (DEC).
  1. Human embryology history
  2. DEC beginnings
  3. DEC current
  4. DEC online
World Map-DEC.jpg

1. Human Embryology History

1880

German Embryology
Wilhelm Roux.jpg Wilhelm His.jpg Julius kollmann.jpg
Wilhelm Roux Wilhelm His Julius Kollmann


His Stages
Keibel Mall 034a.jpg Keibel Mall 034b.jpg

1900

USA Embryology
Charles minot.jpg Franz Keibel.jpg Franklin Mall 01.jpg George L. Streeter.jpg George Corner.jpg
Charles Minot Franz Keibel Franklin Mall George Streeter George Corner


1908 Keibel Stages
Keibel1908 plate01.jpg Keibel1908 plate02.jpg
Keibel1908 plate03.jpg Keibel1908 plate04.jpg
Keibel1908 plate05.jpg Keibel1908 plate06.jpg
1910-30 Carnegie Stages
Human Carnegie stage 10-23.jpg
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
Hertig1956 fig02.jpgHertig1956 fig06.jpg

1956 - 2 cell embryo                                              107-cell blastocyst

O'Rahilly R. and Müller F. Developmental Stages in Human Embryos. Contrib. Embryol., Carnegie Inst. Wash. 637 (1987).

O'Rahilly R. and Müller F. The Embryonic Human Brain: An Atlas Of Developmental Stages. (2006) John Wiley & Sons.

1910

Netherlands UK Embryology
Ambrosius Hubrecht.jpg James Hill.jpg
Ambrosius Hubrecht James Hill
Hill Collection
HillH202 Stage 17 500.gif


Faasse P. Faber J. and Narraway J. A brief history of the Hubrecht Laboratory. (1999) Int. J. Dev. Biol. 43(7): 583-90 PMID 10668967

1930

Spain Embryology
Francisco Orts Llorca.jpg

Francisco Orts-Llorca


Juan Aréchaga, Juan Jiménez-Collado, Domingo Ruano-Gil A glance at Spanish embryology and teratology during the XX century through the academic life of Francisco Orts-Llorca (1905-1993). Int. J. Dev. Biol.: 2009, 53(8-10);1165-77 PubMed 19924623


Later his student Javier Puerta developed a second collection held also at the Complutense University of Madrid.


Madrid Collection
Orts Llorca Madrid embryo catalogue.jpg Stage16 bf10.jpg GV 002.jpg
Collection catalogue Embryo CRL 10.5 mm (stage 16) Embryo CRL 15 mm

1950

Blechschmidt Collection
Eric Blechschmidt.jpg
Erich Blechschmidt
Blechschmidt Models
Embryo 1.6mm icon.jpg
 ‎‎Embryo 1.6mm
Page | Play
H090454-1 icon.jpg
 ‎‎Embryo 3.1mm
Page | Play
7.5mm Embryo movie 1 icon.jpg
 ‎‎Embryo 7.5mm
Page | Play
Embryo 10mm surface icon.jpg
 ‎‎Embryo 10mm
Page | Play

Blechschmidt E. The Human Embryo - Documentations on Kinetic Anatomy (Der menschliche Embryo - Dokumentationen zur kinetiscben Anatomie). (1963) Schattauer, Stuttgart. NLA

1960

Japan Embryology
Hideo Nishimura.jpg

Hideo Nishimura

Nishimura H. Semba R. Tanimura T. and Tanaka O. Prenatal development of the human with special reference to craniofacial structures : An atlas. (1977) U.S. Dept. of Health, Education, and Welfare, Public Health Service, National Institutes of Health ; Washington. Bethesda, Md.


Kyoto Embryos
Human Carnegie stage 1-23.jpg



Embryonic Central Nervous System
Stage 13 Stage 14 Stage 16 Stage 21
Human Stage13 sagittal upper half01.jpg

scale bar = 1 mm

Human Stage14 neural01.jpg Human Stage16 neural03.jpg Human Stage21 neural01.jpg
Week 4 Week 5 Week 6 Week 8


Human CNS Images: Carnegie stage 13 | Carnegie stage 13 label | Carnegie stage 14 | Carnegie stage 14 label | Carnegie stage 16 | Carnegie stage 16 label | Carnegie stage 21 lateral | Carnegie stage 21 median | Fetus CRL 240mm | Neural System Development | Cranial Nerves


1969

Hinrichsen Collection
Klaus Volquardt Hinrichsen.jpg
Klaus Hinrichsen


Scanning EM
ME16 001.jpg Humanembryologie 1990.jpg
Embryo ME 16 (stage 17) Humanembryologie (1990)

1970

Domenech-Mateu Collection
Jose Maria Domenech Mateu.jpg
José Doménech Mateu


1996

Australia
Front-page-image.jpg

UNSW Embryology | Google Analytics

2015

UK Embryology
Susan Lindsay.jpg
Susan Lindsay


HDBR and HuDSeN References

Dianne Gerrelli, Steven Lisgo, Andrew J Copp, Susan Lindsay Enabling research with human embryonic and fetal tissue resources. Development: 2015, 142(18);3073-6 PubMed 26395135

Janet Kerwin, Yiya Yang, Paloma Merchan, Subrot Sarma, Jessica Thompson, Xunxian Wang, Juan Sandoval, Luis Puelles, Richard Baldock, Susan Lindsay The HUDSEN Atlas: a three-dimensional (3D) spatial framework for studying gene expression in the developing human brain. J. Anat.: 2010, 217(4);289-99 PubMed 20979583


Summary

While many universities hold small collections of embryos from many species, very few have large well-characterised collections of embryos showing human development. Many of those that are available are historic in nature, consist of whole embryos and histological sections, some with limited additional information. This human material is not generally accessible for research.

Summary - Human Embryology History 
Embryology History


Embryo Collections: Human Embryo Collections | Embryo Collections | Blechschmidt Collection | Carnegie Collection | Domenech-Mateu Collection | Harvard Collection | Hill Collection | Hinrichsen Collection | Hubrecht Collection | Kyoto Collection | Madrid Collection | Embryology Models | DEC Information | DEC


Embryology History: 1600-1699 | 1700-1799 | 1800-1899 | 1900-1909 | 1910-1919 | 1920-1929 | 1930-1939 | 1940-1949 | 1950-1959 | 1960-1969 | 1970-1979 | 1980-1989 | 1990-1999 | Historic Papers | Embryologists


Embryologists: William Hunter | Wilhelm Roux | Wilhelm His | Julius Kollmann | Hans Spemann | Charles Minot | Ambrosius Hubrecht | Charles Bardeen | Franz Keibel | Franklin Mall | Florence Sabin | George Streeter | George Corner | James Hill | Jan Florian | Thomas Bryce | Thomas Morgan | Ernest Frazer | Francisco Orts-Llorca | José Doménech Mateu | Frederic Lewis | Arthur Meyer | Erich Blechschmidt | Klaus Hinrichsen | Hideo Nishimura | Arthur Hertig | John Rock | Mary Lyon | Nicole Le Douarin | Robert Winston | Fabiola Müller | Ronan O'Rahilly | Robert Edwards | John Gurdon | Shinya Yamanaka | Embryology History | Category:People
Related Historic Researchers  
Santiago Ramón y Cajal | Camillo Golgi


Meyer AW. 1932 - Essays on the History of Embryology: Part I | Part II | Part III | Part IV | Part V | Part VI | Part VII | Part VIII | Part IX | Part X | Part XI | Arthur Meyer | Historic Embryology Papers
USA Embryologists The Emergence of Experimental Embryology in the United States by S. Robert Hilfer, Ph.D. 1990.

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 
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 initial slide scanning completed with 1500+ slides scanned (See also collection educational information).



This will be demonstrated under 4. DEC Online.


Ome-logo-400.png DEC OMERO Server


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

Prof. Rosa Mirapeix


Current DEC Embryo Collections



20170607-Lamars-TestImage.jpg



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 By May 1200 slides scanned.
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 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 an example link to the Online Image database - a single section on a slide from the Blechschmidt collection.

Ome-logo-400.png DEC OMERO Server


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.

OMERO.insight (tutorial) - How to install and use the OMERO.insight program.

Blechschmidt Collection

Embryo-1951-09-01-Slide-60.jpg Blechschmidt Collection - more than 1500 slides scanned.
  • 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. This can also be seen on the DEC Embryo Examples

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

Hinrichsen Collection

The Hinrichsen Collection scanning commenced this year and to date 2470 slides have been digitised. See also Hinrichsen online examples.

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
Ome-logo-400.png DEC OMERO Server


Embryo 335 Embryo 514
Carnegie stage 20, CRL 22 mm
Frontal horizontal, Stains (HE, Tri, Azan), Slides 270.
Carnegie stage 21, CRL 23 mm
Sagittal, Stains (HE, Tri, Azan), Slides 330.

Cite this page: Hill, M.A. 2017 Embryology Gottingen Meeting 2017 - Digital Embryology Consortium. Retrieved November 22, 2017, from https://embryology.med.unsw.edu.au/embryology/index.php/Gottingen_Meeting_2017_-_Digital_Embryology_Consortium

What Links Here?
© Dr Mark Hill 2017, UNSW Embryology ISBN: 978 0 7334 2609 4 - UNSW CRICOS Provider Code No. 00098G