Berlin Meeting 2017 - Digital Embryology Consortium: Difference between revisions

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==DEC Online==
==DEC Online==
This topic will be covered in my presentation on the Blechschmidt collection.
This topic will be covered in more detail in my presentation on the Blechschmidt collection.


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Revision as of 20:08, 10 December 2017

Embryology - 28 Mar 2024    Facebook link Pinterest link Twitter link  Expand to Translate  
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This page shows Dr Mark Hill's online presentations from the 2017 Berlin - Digital Embryology Consortium Meeting

http://tiny.cc/DEC-Berlin_2017

QR-DEC-Berlin 2017.png


Introduction

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).

DEC Current

2017

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

Mark Hill and Prof. Beate Brand-Saberi
Nenad Maricic

  • Jun 2017 - about 2500 slides scanned.
  • Dec 2017- scanning finished.
ME54 001.jpg

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


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

Summary

2017 completed second 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.

DEC Online

This topic will be covered in more detail in my presentation on the Blechschmidt collection.

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

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