Release of OMERO 5.5.0

Today we are releasing OMERO 5.5.0, a full production-ready release of OMERO.

This release also upgrades the version of Bio-Formats which OMERO uses to 6.1.0.

This version does not require a database upgrade.

For more information about the aim of the 5.5 series and future plan, please read our blog post.

Sysadmin and developers improvements

This release focuses on dropping support for Java 7, Python 2.6 and Ice 3.5, adding support for Java 11 and PostgreSQL 10, and on decoupling the Java components to new, separate repositories, each with a new Gradle build system:

• https://github.com/ome/omero-dsl-plugin
• https://github.com/ome/omero-model
• https://github.com/ome/omero-common
• https://github.com/ome/omero-romio
• https://github.com/ome/omero-renderer
• https://github.com/ome/omero-server
• https://github.com/ome/omero-blitz
• https://github.com/ome/omero-gateway-java
• https://github.com/ome/omero-blitz-plugin
• https://github.com/ome/omero-insight
• https://github.com/ome/omero-matlab
• https://github.com/ome/omero-javapackager-plugin
• https://github.com/ome/omero-api-plugin

This has the goal of enabling more fine-grained releases.

A new restriction is that the names of server configuration properties may include only letters, numbers and the symbols “.”, “_”, “-”.

New plugins like omero-artifact-plugin allow reducing the boilerplate code in the build scripts of the decoupled repositories. Though initially disruptive, we hope this modernization and modularization will ease participation in the development of OMERO.

Beyond the changes for building OMERO, the distribution of OMERO.server and OMERO.web as Docker images is now considered production quality. Examples for using these images in various configurations are available under omero-deployment-examples. Both images will be updated with every OMERO release, and will also be updated with releases of the embedded components and plugins as necessary.

User/client improvements

Additionally, this release improves the Web interface when OMERO is opened to the public and contains some useful CLI improvements.

• build:
  • Remove the generation of Ivy dependencies.html files
• web:
  • Introduce Advanced Search to allow and/or search options
  • Fix description in new Project, Dataset etc.
  • Allow user to create new Map Annotations for multiple selected objects at once
  • Fix date display
  • Remove / from 3rdparty in ome.viewportImage.js
  • Remove usage of deprecated calls
  • Remove apache config
  • Do not break display of Tag dialog when large font size is configured in browser
  • Disable refresh button while existing refresh in progress
  • Improve public user support
  • Add ability to customize incorrect login text
• cli:
  • Disable foreground indexing
  • Improve logging of error when importing data via cli command
  • Clearly indicate empty log files when running a diagnostic
  • Fix bug when running config load passing a directory instead of a file
  • Add option to delete keys from map annotations
  • Add error code discovery
  • Deprecate the CLI upload module and plugin

The software is available at archived downloads. Clients are no longer available from that location since they will be released more frequently than the server.

OMERO.insight is now available at release v5.5.2. The installation process has been improved. Users can now install to their local user folder on Windows and it comes bundled with a Java runtime so those without Administrator’s rights can use the application. It is still possible for those with Java installed to launch the application using a .bat file.

OMERO.matlab is now available at release v5.5.0.

Official Docker images are available on Docker Hub:

• https://hub.docker.com/r/openmicroscopy/omero-web-standalone/
• https://hub.docker.com/r/openmicroscopy/omero-server/

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