DEC OMERO Server: Difference between revisions
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===JPG XR=== | ===JPG XR=== | ||
The Axioskan slide scanner software can also save or convert images into the JPG XR format. | The Axioskan slide scanner software can also save or convert images into the JPG XR format. This format was selected as it has not licensing requirements, generates smaller good quality images, and the scanner can readily batch generate this format. | ||
The JPG XR file format is a still-image compression standard and format for continuous tone photographic images, based on technology originally developed and patented by Microsoft under the name HD Photo (formerly Windows Media Photo). It supports both lossy and lossless compression, and is the preferred image format for Ecma-388 Open XML Paper Specification documents ([https://en.wikipedia.org/wiki/JPEG_XR Wikipedia]). | The JPG XR file format is a still-image compression standard and format for continuous tone photographic images, based on technology originally developed and patented by Microsoft under the name HD Photo (formerly Windows Media Photo). It supports both lossy and lossless compression, and is the preferred image format for Ecma-388 Open XML Paper Specification documents ([https://en.wikipedia.org/wiki/JPEG_XR Wikipedia]). This file format is also an International Organization for Standardization [https://www.iso.org/standard/45278.html ISO/IEC TR 29199-1:2011]. | ||
This file format is also an International Organization for Standardization [https://www.iso.org/standard/45278.html ISO/IEC TR 29199-1:2011]. | |||
There are several research conversion programs, including [https://fiji.sc Fiji (ImageJ)], that can both read and generate this image format. | There are several research conversion programs, including [https://fiji.sc Fiji (ImageJ)], that can both read and generate this image format. | ||
Additional non-research programs are available for image conversion into this form [https://www.google.com.au/search?en&q=JPGXR+conversion Google search JPGXR conversion]. | Additional non-research programs are available for image conversion into this form ([https://www.google.com.au/search?en&q=JPGXR+conversion Google search JPGXR conversion]). | ||
'''Caution''' - ''Users should be extremely careful when downloading software from the internet and should use anti-virus software to screen before installing or running any such program.'' | :'''Caution''' - ''Users should be extremely careful when downloading software from the internet and should use anti-virus software to screen before installing or running any such program.'' | ||
==Apply for DEC Account== | ==Apply for DEC Account== | ||
Revision as of 13:12, 3 June 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. 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)
This only in a trial, final database will vary from this draft structure.
- Folder - Each embryo has own folder with the original embryo name (date).
- Project Details - CRL in mm and total number of slides available (from catalogue).
- Tag - Plane of embryo section (Sagittal, Frontal, Transverse).
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. Note that OMERO server will accept embryology images in a variety of formats, including uncompressed images, the problem will be the overall size of the database would be unmanageable.
Following collection scanning, each collection manager should also hold an uncompressed archive of their own images. Should you require images of this quality/resolution, please contact the original collection managers.
CZI
The Axioskan slide scanner generates images in the CZI file format that was developed by ZEISS to specifically meet the requirements of imaging in microscopy. This is an excellent uncompressed research image format, but generates images that would be far too large for easy access on the DEC image database.
JPG XR
The Axioskan slide scanner software can also save or convert images into the JPG XR format. This format was selected as it has not licensing requirements, generates smaller good quality images, and the scanner can readily batch generate this format.
The JPG XR file format is a still-image compression standard and format for continuous tone photographic images, based on technology originally developed and patented by Microsoft under the name HD Photo (formerly Windows Media Photo). It supports both lossy and lossless compression, and is the preferred image format for Ecma-388 Open XML Paper Specification documents (Wikipedia). This file format is also an International Organization for Standardization ISO/IEC TR 29199-1:2011.
There are several research conversion programs, including Fiji (ImageJ), that can both read and generate this image format.
Additional non-research programs are available for image conversion into this form (Google search JPGXR conversion).
- Caution - Users should be extremely careful when downloading software from the internet and should use anti-virus software to screen before installing or running any such program.
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
