Release of OMERO 5.3.0

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Release of OMERO 5.3.0

Helen Flynn (Staff)
Dear All,

Today we are releasing OMERO 5.3.0, a full production-ready release of OMERO 5.3.0; featuring a major reworking of OMERO.web and web apps; dropping support for Windows for the server and for deploying OMERO.web using Apache; and introducing new user features and many fixes and performance improvements:

• improved support for many file formats via Bio-Formats 5.4.0
• introduced ROI Folders
• new UI for displaying Screen Plate Well data in OMERO.web and OMERO.insight
• support for lookup tables and reverse intensity rendering
• color mapping for multiple channels without set colors has been improved to use RGBRGB rather than RGBBB (i.e. to loop through red, green, blue rather than setting all later channels to blue)
• support for histograms in the clients and server
• ability to filter by ratings in OMERO.web
• added 'Open With...' functionality to OMERO.web
• color of shapes is now handled according to the data model, using RGBA rather than ARGB format (an sql script is available to upgrade existing shapes; this will not happen automatically as part of the OMERO upgrade)
• improved performance for moving and deleting data
• Wells can now be annotated and searched by annotations
• enabled downloading/exporting of plate data
• improved reading of tables data
• script improvements including ability to create tiled images from big ROIs, fixes for creating standard images from ROIs, and to stop the Combine_Images script from ignoring pixel sizes set on the target images
• names for plates and images set in the metadata read by Bio-Formats are now imported into OMERO and the filename (which was previously used) is only used where an alternative has not been set
• many bug fixes

Sysadmin changes include:
• added support for Ice 3.6.3
• official OMERO.web apps are now all installable from PyPI
• OMERO.web has been decoupled from the server and can now be deployed separately
• dropped support for Windows for OMERO.server
• OMERO.web deployment via Apache is no longer supported
• OMERO.web also now requires Python 2.7
• CLI improvements including updates to the import output to make it more usable by scripts etc.
• options added for customizing the tree in OMERO.web
• introduced hide-password option in CLI
• new options added to `omero config`
• removed deprecated client menu properties

Also note that the database upgrade script drops keywords and namespaces from ROIs - see for further details.

Developer updates include:
• performed major code cleanup
• major Web API rework
• adjustment to support the upcoming Java 1.9
• made python testing package public so it can be used by external clients
• improved build system integration with local Maven
• made Scripts repository and official OMERO.web apps pep8 and flake8 compatible
• removed restriction on name length
• added support for enumeration changes
• utils script classes deprecated
• deprecated shares
• deprecated search bridges
• disabled jquery cache

Work on the Web API is ongoing and will include moving away from the use of JSONP and introducing Django CORS.

Further details are available on the What's New pages for users (, sysadmins ( and developers (

The software is available at:

Upgrade information is at


The OME Team

Dr Helen Flynn
OME Technical Writer
Centre for Gene Regulation & Expression
Open Microscopy Environment
University of Dundee<>

The University of Dundee is a registered Scottish Charity, No: SC015096

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