DEC OMERO Server
About the Collection Server
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| Image Server Update - Nov 2017 |
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| DEC Online Database - for more information about the server database structure and contents see this new page.
Work Experience student - uploaded additional test slides from Blechschmidt and Hinrichsen collections. |
| Image Server Update - Oct 2017 |
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| Dear DEC Users - Software has been updated to Omero Server (version 5.4). You will be able to access the database with your we browser as before.
To upload new images you will need to download and install the latest version of OMERO.Insight (5.4.0). |
| Image Server Update - Apr 2017 |
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| Dear DEC Users - Software is currently being updated to Omero Server (version 5.3, announcement). During this period there will be numerous times that the image server will be unavailable. I apologise for any inconvenience. I will be sending an email to all users when installation and testing has been completed. |
The collection scanned images are currently available as a test site with only a few sample images loaded. There is no unregistered user access available to the server. All users must apply for an account and agree to abide by our access and reuse conditions before being issued a user account. Individual user accounts currently only have access to specific folders. Access to other collection folders can be managed through user rights management.
For server issues, access problems or account requests, please contact Dr Mark Hill.
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Collections have been organised into folders named approximately after the original collection name or location.
OMERO Training Manual
20 July 2017 - Please note error on Page 4 of training manual the server address to enter should be 149.171.80.223 not the full web address shown in the original manual (http://149.171.80.223:8080). My apologies for this error.
Please read the DEC OMERO training manual before uploading images to the test version of the image server.
OMERO Image Server Log In
Only registered users can log in and edit the OMERO website.
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This animation shows the described process.
<html5media width="500" height="400">File:OMERO logging in.mp4</html5media> |
2017 Test Image Link
This only in a trial, final database will vary from this draft structure.
- Folder - Each embryo has own folder (with the original embryo name as it exists in your collection).
- Project Details - CRL in mm and total number of slides available (from catalogue).
- Tag - Plane of embryo section (Sagittal, Frontal, Transverse).
July
Locally uploaded image samples.
- Blechschmidt Collection in Christop Viebahn folder http://149.171.80.223:8080/webclient/?show=dataset-641
- Hinrichsen Collection in Beate Brand-Saberi folder http://149.171.80.223:8080/webclient/?show=dataset-735
- Hubrecht Collection in Peter Giere folder http://149.171.80.223:8080/webclient/?show=dataset-786
June
Selected slides form the Blechschmidt Collection are available for registered user access. Please advise me if you are unable to see the linked files below following log-in.
- 2.57 mm sagittal - 22 slides total 23 (1954-08-10)
- 3.4 mm sagittal - 82 slides total 87 (1954-04-09)
- 4 mm sagittal - 3 slides total 4 (1951-05-05)
- 5.8 mm frontal - 54 slides total 77 (1954-09-20)
- 6.5 mm sagittal - 40 slides total 40 (1953-09-29)
- 11 mm frontal - 29 slides total 76 (1951-09-01)
2016 Test Image Link
Note - You will need to login to access the original image through the links, images appearing on this current page are only screenshots.
Sydney folder -> 2010-08-29-1 -> Stage 22 Human Embryo (Mark Hill-001.svs) dimensions 32538 x 28770
Full Image
Spinal Cord
Spinal cord central canal
Apply for DEC Account
For user account requests, please contact Dr Mark Hill.
Terms of Use
By using the DEC OMERO Server, you agree to the following:
- You agree to the specific conditions set by each collections terms of image reuse, publication and copyright.
- Reuse of images from multiple collections requires approval from each collection.
- You use this service at your own risk, and we provide NO GUARANTEE OR WARRANTY WHATSOEVER regarding uptime, security, data provenance or access, or any other service.
- You should not use the DEC OMERO Server as a repository for any important data, or data that must be held in any secure or specific way.
- The responsibility for any data loaded onto the DEC OMERO Server is entirely your own.
- We reserve the right to remove any images, data, accounts or other data or structure without notice or request.
- We welcome comments or ideas from your use of and experience with the DEC OMERO Server.
About OMERO
OMERO is client-server software for visualization, management and analysis of biological microscope images. © 2000-2016 University of Dundee & Open Microscopy Environment. Creative Commons Attribution 4.0 International License OME source code is available under the GNU General public license or through commercial license from Glencoe Software.
Version - OMERO.web 5.0.8-ice35.
Importing Data
Images are added to the database by the process called "Importing Data" using the software OMERO.insight Version 5
Software Download
Dear DEC Users - Software is currently updated (Oct 2017) to Omero Server (version 5.4, announcement).
MarkHill (talk) 08:30, 25 October 2017 (AEDT)
- 2016 - OMERO 5.3 release - JPGXR announcement
Image Uploader/Insight Software
OMERO Server has recently been updated to version 5.4 (announcement). The associated software suite has also been updated to this new version and should be used to upload your image files. Use the links below to download and install from the original source.
Download Page
OMERO Issues
- Fail - were originally getting lots of "fail to upload" (Version 5.3) for JPGXR files. Recent Oct 2017 update appears to have fixed most problems, still some examples of fails. May need to reconvert files?
- Scrolling - lefthand panel of web interface does not allow scrolling. When an embryo with lots of slides is opened you can only step down by using keyboard down arrow.
- Tags - Tags can only be added to a specific project (not global tags). Therefore currently have to duplicate the tags for each collection. Not sure what this will do to search results, as we would hope to be able to "Search All".
References
<pubmed>20513764</pubmed>
<pubmed>22373911</pubmed>
Links
- The Open Microscopy Environment
- OMERO 5.4 Download
- OME Help
- Using OMERO.web
- Training Course Manual
- Importing Data with OMERO.insight Version 5
- JCB DataViewer
- Fiji (ImageJ)
- Image formats
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