Omero dundee

5.6.14 (November 2024)

This release includes the following upgrade of the OMERO.server Java components:

• omero-gateway-java 5.10.0
• omero-blitz 5.8.0
• omero-server 5.7.0
• omero-renderer 5.6.0
• omero-romio 5.7.0
• omero-common 5.7.0
• omero-model 5.7.0

The Java components listed above have been built via Java 11 with the compatibility flag on for Java 8. Due to limited testing on Java 8, we recommend to upgrade to Java 11 or higher.

Improvements include:

• Add new lookup tables. See #6398.
• Ugrade of Bio-Formats to version 8.0.1.
• Bump slf4j dependencies. See #6409.

This version of the OMERO.server has been tested with:

• OMERO.py 5.19.5
• OMERO.web 5.28.0

5.6.13 (August 2024)

This release reverts a change to the build process introduced in 5.6.12 that resulted in unused copies of old jars being included in the release.

5.6.12 (July 2024)

This release includes the following upgrade of the OMERO.server Java components:

• omero-gateway-java 5.9.2
• omero-blitz 5.7.3
• omero-server 5.6.12
• omero-renderer 5.5.17
• omero-romio 5.7.7
• omero-common 5.6
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  Bio-Formats is a software tool for reading and writing image data using standardized, open formats. Bio-Formats is a community driven project with a standardized application interface that supports open source analysis programs like ImageJ, CellProfiler and Icy, informatics solutions like OMERO, and commercial programs like MATLAB.

  Bio-Formats documentation includes a complete version history, guides for using Bio-Formats as a plugin for ImageJ/Fiji, extensive information on which formats are supported and the level of that support, and also information for developers wanting to extend Bio-Formats or use it in their own software.

  Read the Docs

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  Development and Licensing

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  Bio-Formats is developed by the Open Microscopy Environment consortium, including development teams at University of Dundee and Glencoe Software. Licensing and citing information is on the OME licensing page.

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  File Formats

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  Bio-Formats 5 improves support for High Content Screening, time lapse imaging, digital pathology and other complex multidimensional image formats, reading over 160 file formats

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  Openmicroscopy.org down?

  The [pom-scijava-base](https://github.com/scijava/pom-scijava-base) ancestor POM… includes [configuration hardcoding several links](https://github.com/scijava/pom-scijava-base/blob/master/pom.xml#L412-L455) for the javadoc tool. This configuration makes classes for SciJava-based projects clickable, pointing uniformly to [javadoc.scijava.org](https://javadoc.scijava.org/) endpoints aggregating multiple components. For example, the URL https://javadoc.scijava.org/SciJava/ includes javadoc for many components in the [scijava GitHub org](https://github.com/scijava) with groupId `org.scijava`. The general pattern is "Maven groupId = GitHub org = javadoc.scijava.org endpoint". ## Problems 1. __Reproducibility.__ The javadoc.scijava.org endpoints are not reproducible. They are like SNAPSHOTs, always serving the latest javadoc. Properly, we should be linking to stable API javadoc corresponding to the versions depended upon by each built project. Otherwise, rebuilding the javadoc later will produce a different result, and potentially javadoc build errors if e.