Release of OMERO 5.4.0

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Release of OMERO 5.4.0

Helen Flynn (Staff)
Dear All,

We are pleased to announce the release of OMERO 5.4.0, a full production-ready release of OMERO that includes several new updates for users, sysadmins and facility managers. This update of OMERO features a new configurable user role “Restricted Administrators"; further improvements to OMERO.web; additions to OMERO.cli; and many fixes and performance improvements:

  *   added Administrators with restricted privileges to allow sysadmins to delegate management tasks to facility managers without granting them full system admin privileges, or to allow trusted users such as image analysts to carry out tasks on behalf of all other users (see
  *   fixed color conversion to RGBA
  *   added support for exporting images in a plate as OME-TIFF
  *   improved creation of rendering settings for images without any stats e.g. 32bit images
  *   improved performance for moving large Plates
  *   fixed projection of images if the range of timepoints specified is not the full range
  *   added support for transfering ownership of all the data of a given user using CLI
  *   renamed "Reverse Intensity" command to "Invert" in image viewers
  *   added support for ImageColumn with Screen and Plate targets in the populate_metadata script
  *   OMERO.web UI fixes:
     *   improved display of Plates and Wells
     *   fixed label position for Wells
     *   added the ability to display Image and Well metadata in the Tables section for the same Plate
     *   improved copy/paste of rendering settings workflow
     *   improved layout of left-hand panel including the position of the search panel
     *   added support for administrators with restricted privileges to create Project/Dataset for other users
     *   rolled back the display of tables in the viewer
     *   fixed forgotten password functionality

Sysadmin changes include:

  *   added support for the creation of administrators with restricted privileges in OMERO.web admin panel
  *   added method to create administrators with restricted privileges specifying a password
  *   added specific installation instructions for Debian 9
  *   added configuration to limit queries that public users can do in OMERO.web
  *   created minimal NGINX configuration file that can be included in a fixed file to allow custom NGINX options to be defined only once (e.g. SSL options)
  *   installed django-redis by default
  *   CLI improvements and fixes:
     *   fixed admin plugin so “cleanse" can handle larger directories
     *   added to chown plugin ability to target all of given users’ data
     *   adjusted handling of standard input
     *   added infrastructure to load external CLI plugins
     *   dropped support for command "admin ports"

Developer updates include:

  *   added method to JavaGateway to manipulate admin privileges
  *   fixed issue with JSONP decorator
  *   removed SciPy dependency
  *   adjusted OMERO.blitz API to allow some query results to be cached
  *   added support to the rendering engine to update a series of settings in one call
  *   added method to to manipulate advanced rendering settings
  *   allowed the Maven repository to be overridden
  *   removed unused 3rd party libraries in OMERO.web
  *   added support for PyTables version 3.4+
  *   deprecated Path Object in OMERO Model
  *   updated the documentation for server installation on Mac OS to no longer use the homebrew formulae from (these are not working and will not be fixed)

Further changes to the Python BlitzGateway are described in

This release also upgrades the version of Bio-Formats which OMERO uses to 5.7.1, improving support for 12 file formats - see

Upgrade information is on the server upgrade page -
Sysadmins who used the workaround for the 2017-SV4 security advisory rather than upgrading to 5.3.5 will also find instructions for reversing it as
this release includes the security fix and fixes the OMERO.web forgotten password functionality regression.

The software is available at

Any problems or comments, please use the OME Forums or mailing lists -


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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