DEC OMERO Server: Difference between revisions
From Human Embryology
No edit summary |
|||
| (28 intermediate revisions by the same user not shown) | |||
| Line 6: | Line 6: | ||
<br> | <br> | ||
{| | {| | ||
! Image Server Update - | ! Image Server Update - January 2019 | ||
|- | |- | ||
| | | [[User:MarkHill|MarkHill]] ([[User talk:MarkHill|talk]]) 11:11, 29 January 2019 (AEDT) Power failure in University shutdown server. We are checking database before restarting DEC server. | ||
|- | |||
| January 2019 - DEC Server upgraded (OMERO 5.4.9), tested and back online. | |||
[[User:MarkHill|MarkHill]] ([[User talk:MarkHill|talk]]) 14: | [[User:MarkHill|MarkHill]] ([[User talk:MarkHill|talk]]) 14:06, 16 January 2019 (AEDT) | ||
|} | |} | ||
| Line 16: | Line 19: | ||
! Image Server Update - Oct 2017 | ! Image Server Update - Oct 2017 | ||
|- | |- | ||
| Dear DEC Users - Software has been updated to Omero Server (version 5.4). You will be able to access the database with your | | Dear DEC Users - Software has been updated to Omero Server (version 5.4). You will be able to access the database with your web browser as before. | ||
To upload new images you will need to download and install the latest version of [https://www.openmicroscopy.org/omero/downloads/ OMERO.Insight] (5.4.0). | To upload new images you will need to download and install the latest version of [https://www.openmicroscopy.org/omero/downloads/ OMERO.Insight] (5.4.0). | ||
| Line 48: | Line 51: | ||
Collections have been organised into folders named approximately after the original collection name or location. | Collections have been organised into folders named approximately after the original collection name or location. | ||
== | ==Apply for DEC Account== | ||
For DEC user account requests, please contact [mailto:m.hill@unsw.edu.au?Subject=Apply%20for%20DEC%20account Dr Mark Hill]. | |||
Agreement to the following "terms of use" are required either in writing or by email using your official institutional letterhead or email address and signature. Please make special note of conditions 1 and 2 concerning image reuse. Failure to comply with the "terms of use" will result in immediate suspension of user account database access without notice. | |||
===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. | |||
==OMERO Image Server Log In== | |||
{| | {| | ||
| valign=top|'''Only registered users can log in and edit the OMERO website.''' | | valign=top|'''Only registered users can log in and edit the OMERO website.''' | ||
| Line 66: | Line 79: | ||
# Access projects and images in the folders shown on the left. | # Access projects and images in the folders shown on the left. | ||
# Access your user information at the top righthand corner. | # Access your user information at the top righthand corner. | ||
<br> | |||
|- | |||
| '''The animation below shows the above text described process.''' | |||
<br> | |||
<html5media width="500" height="400">File:OMERO logging in.mp4</html5media> | |||
|} | |||
===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 [[Media:DEC-OMERO-training-manual-2017.pdf|'''DEC OMERO training manual''']] before uploading images to the test version of the image server. | |||
[[Media:DEC-OMERO-training-manual-2017.pdf|Manual PDF]] | |||
===2017 Test Image Link=== | ===2017 Test Image Link=== | ||
This only in a trial, final database will vary from this draft structure. | This only in a trial, final database will vary from this draft structure. | ||
| Line 96: | Line 117: | ||
* 6.5 mm sagittal - 40 slides total 40 ([http://149.171.80.223:8080/webclient/?show=project-258 '''1953-09-29''']) | * 6.5 mm sagittal - 40 slides total 40 ([http://149.171.80.223:8080/webclient/?show=project-258 '''1953-09-29''']) | ||
* 11 mm frontal - 29 slides total 76 ([http://149.171.80.223:8080/webclient/?show=project-261 '''1951-09-01''']) | * 11 mm frontal - 29 slides total 76 ([http://149.171.80.223:8080/webclient/?show=project-261 '''1951-09-01''']) | ||
==About OMERO== | ==About OMERO== | ||
| Line 128: | Line 123: | ||
Version - OMERO.web 5.0.8-ice35. | Version - OMERO.web 5.0.8-ice35. | ||
==Software Download== | ==Software Download== | ||
Dear DEC Users - | Dear DEC Users - Log below shows currently updated Omero Server software version. | ||
* Jan 2019 - Software to Omero Server (version 5.4.10) | |||
* Oct 2017 - Software to Omero Server (version 5.4, [https://www.openmicroscopy.org/2017/10/09/omero-5-4-0.html announcement]). | |||
* 2016 - [https://www.openmicroscopy.org/community/viewtopic.php?f=11&t=8254 OMERO 5.3 release] - [http://glencoesoftware.com/2016-08-30-glencoe-software-zeiss-partner-open-source-file-reader-whole-slide.html JPGXR announcement] | |||
===Image Uploader/Insight Software=== | ===Image Uploader/Insight Software=== | ||
| Line 149: | Line 139: | ||
==References== | ==References== | ||
{{#pmid:20513764}} | |||
{{#pmid:22373911}} | |||
==Links== | ==Links== | ||
Revision as of 10:40, 1 February 2019
About the Collection Server
|
DEC OMERO Server | |||||||||||||||
| ||||||||||||||||
| Image Server Update - January 2019 |
|---|
| MarkHill (talk) 11:11, 29 January 2019 (AEDT) Power failure in University shutdown server. We are checking database before restarting DEC server. |
| January 2019 - DEC Server upgraded (OMERO 5.4.9), tested and back online. |
| Image Server Update - Oct 2017 |
|---|
| Dear DEC Users - Software has been updated to Omero Server (version 5.4). You will be able to access the database with your web 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 |
|---|
| 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.
|
|
DEC OMERO Server | |||||||||||||||
| ||||||||||||||||
Collections have been organised into folders named approximately after the original collection name or location.
Apply for DEC Account
For DEC user account requests, please contact Dr Mark Hill.
Agreement to the following "terms of use" are required either in writing or by email using your official institutional letterhead or email address and signature. Please make special note of conditions 1 and 2 concerning image reuse. Failure to comply with the "terms of use" will result in immediate suspension of user account database access without notice.
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.
OMERO Image Server Log In
Only registered users can log in and edit the OMERO website.
|
| The animation below shows the above text described process.
|
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.
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)
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.
Software Download
Dear DEC Users - Log below shows currently updated Omero Server software version.
- Jan 2019 - Software to Omero Server (version 5.4.10)
- Oct 2017 - Software to Omero Server (version 5.4, announcement).
- 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
References
Linkert et al. (2010) Metadata matters: access to image data in the real world. J. Cell Biol. ;189:777-82. PMID: 20513764. DOI.
Allan et al. (2012) OMERO: flexible, model-driven data management for experimental biology. Nat. Methods ;9:245-53. PMID: 22373911. DOI.
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
Main Page | Embryo Collections | Slide Scanning | Image Server | News | Links | Test page | Site Map
