Berlin Meeting 2017 - Digital Embryology Consortium

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Dr Mark Hill's two presentations from the December 2017 Berlin Meeting


  1. Introduction
  2. Blechschmidt Collection


DEC icons thumbnail.jpg

Mark Hill.jpg

Dr Mark Hill


http://tiny.cc/DEC-Berlin_2017

QR-DEC-Berlin 2017.png


Introduction

DEC Beginnings

2013

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

(Described later in the meeting by Dr Thorsten Heupel)

UNSW Foundation donation plaque



Blechschmidt Collection scanning commences.

2016

Slide Scanning
Mark and Embryo.jpg
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
Hill Mirapeix Domenech-Mateu Collection.jpg

Mark Hill and Prof. Rosa Mirapeix

Domenech-Mateu Collection – Universitat Autònoma de Barcelona.

(described later in the Berlin meeting by Prof. Rosa Mirapeix)

Collection HDBR and HuDSeN Collection – Newcastle University.

(described later in the Berlin meeting by Dr Steven Lisgo)

Amsterdam Collection - Amsterdam University, Academic Medical Center.

(described later in the Berlin meeting by Prof. Wouter Lamers)

ANZSCDB Meeting presentation



Image Server
(Described by Dr Jean-Marie Burel later in the meeting)

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).

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.

Hinrichsen Collection

Slide Scanning
Hinrichsen Collection - scanning completed.
Hinrichsen Collection Hill Brand-Saberi.jpg

Mark Hill and Prof. Beate Brand-Saberi

Hinrichsen-Embryo514-Slide-100-Scene01.jpg

Embryo 514, Carnegie stage 21, CRL 23 mm
Sagittal plane, (Stain - Haematoxylin Eosin), Slide 100



(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.

2017 Berlin install 01.JPG MfN DEC Scanner-room.jpg

Summary

2017 completed the second collection scanning and testing of the updated online database software. Delivered teh scanner to Berlin.

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.
DEC-database-stats-2017-12-11.jpg





(Presentation 2 below)

Blechschmidt Collection

Hill Viebahn Blechschmidt Collection.jpg

Mark Hill and Prof Christoph Viebahn

Prof. Erich Blechschmidt

Prof. Erich Blechschmidt (1904 – 1992)[1]
  • 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.[2]
Erich Blechschmidt (1904 – 1992)

Erich Blechschmidt
(1904 – 1992)

Embryo Models

Blechschmidt model collection room.jpg


Model (about 1 M) of Embryo 7.5 mm


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

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.
Ome-logo-400.png


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

References

  1. <pubmed>1476247</pubmed>
  2. <pubmed>13227045</pubmed>

Cite this page: Hill, M.A. (2019, September 22) 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 2019, UNSW Embryology ISBN: 978 0 7334 2609 4 - UNSW CRICOS Provider Code No. 00098G