DEC OMERO Server: Difference between revisions

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[[File:Ome-logo-400.png|300px|link=https://www.openmicroscopy.org]]
[[File:Ome-logo-400.png|300px|link=https://www.openmicroscopy.org]]
==About the Collection Server==
==About the Collection Server==
[[File:OmeroWeb.png|thumb|alt=OmeroWeb|OmeroWeb]]
<br>
{{OMEROlink}}
{{OMEROlink}}
[[File:OmeroWeb.png|thumb|alt=OmeroWeb|OmeroWeb]]
<br>
{{Draft page}}
{|
! Image Server Update -  January 2019
 
|-
| January 2019 - DEC Server upgraded (OMERO  5.4.9), tested and back online.
 
 
[[User:MarkHill|MarkHill]] ([[User talk:MarkHill|talk]]) 14:06, 16 January 2019 (AEDT)
|}


{|
{|
! 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 we browser as before.  
| 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).
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[[User:MarkHill|MarkHill]] ([[User talk:MarkHill|talk]]) 12:07, 11 October 2017 (AEDT)
[[User:MarkHill|MarkHill]] ([[User talk:MarkHill|talk]]) 12:07, 11 October 2017 (AEDT)
|}
|}


{|
{|
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[[File:DEC image server pie 30Jun2017.jpg|thumb|DEC Image database (Jun2017)]]
[[File:DEC image server pie 30Jun2017.jpg|thumb|DEC Image database (Jun2017)]]
Collections have been organised into folders named after their location city, as shown below.


* Amsterdam
Collections have been organised into folders named approximately after the original collection name or location.
* Barcelona
 
* Berlin
==Apply for DEC Account==
* Bochum
For user account requests, please contact [mailto:m.hill@unsw.edu.au?Subject=Apply%20for%20DEC%20account Dr Mark Hill].
* Göttingen
* Kyoto
* Madrid
* Newcastle
* Sydney
* Washington
===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.
===Terms of Use===


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.
By using the DEC OMERO Server, you agree to the following:


[[Media:DEC-OMERO-training-manual-2017.pdf|Manual PDF]]
# 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===
==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.'''
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<html5media width="500" height="400">File:OMERO logging in.mp4</html5media>
<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.
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* 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'''])


===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
<gallery>
File:Test image20160330-1.jpg|Full Image
File:Test image20160330-2.jpg|Spinal Cord
File:Test image20160330-3.jpg|Spinal cord central canal
</gallery>
==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 [https://www.zeiss.com/microscopy/int/products/microscope-software/zen/czi.html  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. Note that the image file extension will still be shown as CZI, but this will be a "compressed" file. 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]). 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.
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 contact their local  IT managers and use anti-virus software to screen before opening, installing or running any such downloaded program.''
===JPEG 2000===
OMERO Bioformats should also be compatible with the [ [https://www.openmicroscopy.org/site/support/bio-formats5.5/supported-formats.html JPEG200 image format], though we have had some initial issues with this on the database. For example the image will upload to the database, but will not be able to generate the thumbnail or process the required pyramid.
* Problem - [http://149.171.80.223:8080/webclient/?show=dataset-790 One Image 3 formats] only the JPG version has generated a thumbnail image, both the TIF and J2K versions show that they are still "generating a pyramid".
* Problem - [http://149.171.80.223:8080/webclient/?show=dataset-655 J2K image] similar problem.
* OK - [http://149.171.80.223:8080/webclient/?show=dataset-786 JPF image] photograph not a scanner image uploaded and displayed without a problem. (see [http://file.org/extension/jpf JPF extension])
JPEG 2000 is both a codec and a file format and the standard is in many parts.
* Part 1 giving (mostly) codec information (how to compress/decompress image data), with a container file format annex (JP2).
* Part 2 gives many extensions, and a more comprehensive container format (JPX).
==Apply for DEC Account==
For user account requests, please contact [mailto:m.hill@unsw.edu.au?Subject=Apply%20for%20DEC%20account 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==
==About OMERO==
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Version - OMERO.web 5.0.8-ice35.
Version - OMERO.web 5.0.8-ice35.
==Importing Data==
Images are added to the database by the process called "Importing Data" using the software [http://help.openmicroscopy.org/importing-data-5.html OMERO.insight Version 5]
* Help - [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight Version 5]


==Software Download==
==Software Download==
Dear DEC Users - Software is currently updated (Oct 2017) to Omero Server (version 5.4, [https://www.openmicroscopy.org/community/viewtopic.php?f=11&t=8254 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.
Dear DEC Users - Software is currently updated (Oct 2017) to Omero Server (version 5.4, [https://www.openmicroscopy.org/2017/10/09/omero-5-4-0.html announcement]).  


[[User:MarkHill|MarkHill]] ([[User talk:MarkHill|talk]]) 08:30, 25 October 2017 (AEDT)
[[User:MarkHill|MarkHill]] ([[User talk:MarkHill|talk]]) 08:30, 25 October 2017 (AEDT)


* [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]
 
* 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===
OMERO Server has recently been updated to version 5.3 ([https://www.openmicroscopy.org/community/viewtopic.php?f=11&t=8254  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.
OMERO Server has recently been updated to version 5.4 ([https://www.openmicroscopy.org/2017/10/09/omero-5-4-0.html 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'''
'''Download Page'''
* [http://downloads.openmicroscopy.org/omero/5.3.0/ OMERO 5.3]
* [https://www.openmicroscopy.org/omero/downloads/OMERO 5.4]
* [http://downloads.openmicroscopy.org/omero/5.3.0/artifacts/?C=N;O=A individuale components]
 


==References==
==References==
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==Links==
==Links==
* [https://www.openmicroscopy.org/site The Open Microscopy Environment]
* [https://www.openmicroscopy.org/site The Open Microscopy Environment]
* [http://downloads.openmicroscopy.org/omero/5.3.3/ OMERO 5.3.3 Download]
* [https://www.openmicroscopy.org/omero/ OMERO 5.4 Download]
* [http://downloads.openmicroscopy.org/omero/5.3.3/artifacts/?C=N;O=A Software Component Downloads]
* [http://help.openmicroscopy.org OME Help]
* [http://help.openmicroscopy.org OME Help]
* [http://help.openmicroscopy.org/web-client.html Using OMERO.web]
* [http://help.openmicroscopy.org/web-client.html Using OMERO.web]

Revision as of 13:07, 16 January 2019

Ome-logo-400.png

About the Collection Server

OmeroWeb
OmeroWeb


Ome-logo-400.png DEC OMERO Server
DEC Users (June 2017) 
Contact Mark Hill DEC Image Server DEC OMERO training manual (PDF)


Image Server Update - January 2019
January 2019 - DEC Server upgraded (OMERO 5.4.9), tested and back online.


MarkHill (talk) 14:06, 16 January 2019 (AEDT)

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).

MarkHill (talk) 12:07, 11 October 2017 (AEDT)

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.

OMERO 5.3 release - JPGXR announcement

MarkHill (talk) 10:24, 21 April 2017 (AEST)


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.


User Help - Image Server Log in  |   DEC Log in


For server issues, access problems or account requests, please contact Dr Mark Hill.

Ome-logo-400.png DEC OMERO Server
DEC Users (June 2017) 
Contact Mark Hill DEC Image Server DEC OMERO training manual (PDF)
DEC Image database (Jun2017)

Collections have been organised into folders named approximately after the original collection name or location.

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:

  1. You agree to the specific conditions set by each collections terms of image reuse, publication and copyright.
  2. Reuse of images from multiple collections requires approval from each collection.
  3. 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.
  4. 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.
  5. The responsibility for any data loaded onto the DEC OMERO Server is entirely your own.
  6. We reserve the right to remove any images, data, accounts or other data or structure without notice or request.
  7. 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.
  1. Click on image server (menu at top of each page).
  2. This opens the DEC Omero Server information page.
  3. Click on the text link "DEC Omero Server"
  4. Log in screen then opens, fill in your "User Name" and "Password" (supplied by email).
  5. Click "Login", will open the database in your user view.
  6. Access projects and images in the folders shown on the left.
  7. Access your user information at the top righthand corner.



 This animation shows the described process.

<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 DEC OMERO training manual before uploading images to the test version of the image server.

Manual PDF


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.

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.


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 - Software is currently updated (Oct 2017) to Omero Server (version 5.4, announcement).

MarkHill (talk) 08:30, 25 October 2017 (AEDT)


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

<pubmed>20513764</pubmed>

<pubmed>22373911</pubmed>

Links


Main Page | Embryo Collections | Slide Scanning | Image Server | News | Links | Test page | Site Map

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