Difference between revisions of "Berlin Meeting 2017 - Digital Embryology Consortium"

From Embryology
Line 207: Line 207:
 
* Server is currently being tested for remote uploading of files from international locations.
 
* 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.
 
 
{|
 
| width=210px|[[File:Ome-logo-400.png|200px|link=https://www.openmicroscopy.org/community/viewtopic.php?f=11&t=8284]]
 
|
 
'''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.
 
|}
 
<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>
 
 
<br><br><br><br>
 
  
 
=Blechschmidt Collection=
 
=Blechschmidt Collection=

Revision as of 02:44, 11 December 2017

Embryology - 2 Mar 2021    Facebook link Pinterest link Twitter link  Expand to Translate  
Google Translate - select your language from the list shown below (this will open a new external page)

العربية | català | 中文 | 中國傳統的 | français | Deutsche | עִברִית | हिंदी | bahasa Indonesia | italiano | 日本語 | 한국어 | မြန်မာ | Pilipino | Polskie | português | ਪੰਜਾਬੀ ਦੇ | Română | русский | Español | Swahili | Svensk | ไทย | Türkçe | اردو | ייִדיש | Tiếng Việt    These external translations are automated and may not be accurate. (More? About Translations)

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


  1. Introduction
  2. Blechschmidt Collection


DEC icons thumbnail.jpg

Dr Mark Hill

QR-DEC-Berlin 2017.png http://tiny.cc/DEC-Berlin_2017


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 
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. (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).

DEC Current

2017

Hinrichsen Collection

Slide Scanning
Hinrichsen Collection - scanning completed.
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


Embryological Collection MfN

December 2017 - scanner delivered and installed.

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

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.

Blechschmidt Collection

Erich Blechschmidt (1904 – 1992)[1] was a German anatomist and director of Göttingen University’s Anatomical Institute from 1942 until 1973.


The collection consists of 64 models[2] and from about 120 human embryos approximately 200,000 serial sections. Some of these embryo serial section sets were incorporated in 1972 into the Carnegie Collection (assigned Carnegie Nos. 10315-10434), but have since been returned to the University of Goettingen.

Erich Blechschmidt (1904 – 1992)

Erich Blechschmidt
(1904 – 1992)

Hill Viebahn Blechschmidt Collection.jpg

Mark Hill and Prof Christoph Viebahn

Embryo Models

Embryo Model Movies

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


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. (2021, March 2) 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 2021, UNSW Embryology ISBN: 978 0 7334 2609 4 - UNSW CRICOS Provider Code No. 00098G