DEC OMERO Server: Difference between revisions
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===2017 Test Image Link=== | ===2017 Test Image Link=== | ||
Selected slides form the [[Blechschmidt Collection]] are available for registered user access. | |||
* 2.57 mm sagittal - 23 slides total (1954-08-10) | |||
* 3.4 mm sagittal - 187 slides total (1954-04-09) | |||
* 4 mm sagittal - 4 slides total (1951-05-05) | |||
* 5.8 mm frontal - 77 slides total (1954-09-20) | |||
* 6.5 mm sagittal - 40 slides total (1953-09-29) | |||
* 11 mm frontal - 76 slides total (1951-09-01) | |||
Please advise me if you are unable to see the files following log-in. | |||
This only in a trial, final database will vary from this structure. | |||
===2016 Test Image Link=== | ===2016 Test Image Link=== |
Revision as of 17:18, 8 May 2017
About the Collection Server
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- Draft page - notice removed when completed. No unregistered user can edit this site or the linked image database. MediaWiki Help page
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 after their location city, as shown below.
- Amsterdam
- Barcelona
- Berlin
- Bochum
- Göttingen
- Kyoto
- Madrid
- Newcastle
- Sydney
- Washington
OMERO Training Manual
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
Selected slides form the Blechschmidt Collection are available for registered user access.
- 2.57 mm sagittal - 23 slides total (1954-08-10)
- 3.4 mm sagittal - 187 slides total (1954-04-09)
- 4 mm sagittal - 4 slides total (1951-05-05)
- 5.8 mm frontal - 77 slides total (1954-09-20)
- 6.5 mm sagittal - 40 slides total (1953-09-29)
- 11 mm frontal - 76 slides total (1951-09-01)
Please advise me if you are unable to see the files following log-in.
This only in a trial, final database will vary from this structure.
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
Image Formats
The original decision was that scanned slides would be saved in JPGXR format as these are substantially smaller than the uncompressed format. The difficulty is that OMERO server does not support this format so all images will now be stored in an uncompressed format that is compatible with this image server software.
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 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.
OMERO 5.3 release - JPGXR announcement
MarkHill (talk) 14:58, 18 April 2017 (AEST)
Image Uploader/Insight Software
OMERO Server has recently been updated to version 5.3 (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
References
<pubmed>20513764</pubmed>
<pubmed>22373911</pubmed>
Links
- The Open Microscopy Environment
- OME Help
- Using OMERO.web
- Training Course Manual
- Importing Data with OMERO.insight Version 5
- JCB DataViewer
- Fiji (ImageJ)
Main Page | Embryo Collections | Slide Scanning | Image Server | News | Links | Test page | Site Map