Release of OMERO 5.5.0

Dear All,

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, https://docs.openmicroscopy.org/bio-formats/6.1.0/about/whats-new.html.

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,(https://blog.openmicroscopy.org/future-plans/community/2019/06/03/omero-5-5/).

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:

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 https://github.com/ome/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 https://downloads.openmicroscopy.org/omero/5.5.0. Clients are no longer available from that location since they will be released more frequently than the server.

OMERO.insight is now available at https://github.com/ome/omero-insight/releases/tag/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 https://github.com/ome/omero-matlab/releases/tag/v5.5.0.

Official Docker images are available on Docker Hub:

Any problems or comments, please use the https://www.openmicroscopy.org/support/.

The OME team

4 Likes

Thanks Jean-Marie and the @ome team - great news! Congrats to the release!

Could you elaborate a bit on this topic, (how?) does this affect CLI imports?

Thanks,
Niko

Hi @ehrenfeu , that was quick!

Answering shortly, the OMERO upload plugin is completely independent of the mechanism for importing images into OMERO at the moment. It is primarily used as a library for uploading files and creating file annotations.

To expand a bit, we have been primarily using it in the case of IDR studies to upload attachments in-place - see e.g. https://idr.openmicroscopy.org/webclient/?show=image-5514374 for an example and https://github.com/IDR/idr0052-walther-condensinmap/blob/master/scripts/upload_and_create_rois.py for the script.

2 Likes

Thanks @s.besson - I realize that my question was slightly misphrased, creating confusion between importing and uploading. In the past I did use the upload plugin for files / annotations. Does this mean in the mid-/long-run this functionality will be removed from the CLI, or replaced by something else?

None of the plugins are going away, but many of them are being moved into separate repositories/python-packages as part of the decoupling work. This means individual plugins can be have bug fixes or new features added and released straight away. Currently the only way to release a plugin is to do a full release of OMERO.

2 Likes

Congratulations @ome team on the release!

I figured I would update ImageJ-OMERO accordingly. But navigating to https://artifacts.openmicroscopy.org/ and searching for omero:blitz, it appears that the newest release is blitz-5.5.0-m2-ice36-b103.jar? Will the 5.5.0 final artifacts appear on the Maven repository soon? Or did the names change?

Hi Curtis

the artifacts for omero-blitz are now under https://artifacts.openmicroscopy.org/artifactory/simple/ome.releases/org/openmicroscopy/omero-blitz/. The current version is now 5.5.2.
The “gateway” code used by client like OMERO.insight to interact with the server has been extracted from omero:blitz and has now its own repository and artifacts, see https://artifacts.openmicroscopy.org/artifactory/simple/ome.releases/org/openmicroscopy/omero-gateway/. The current version is also 5.5.2.

Jmarie

2 Likes

Thanks OME team for releasing 5.5.
When installing on Ubuntu 18.04 I noticed a few errors in the docs on page: https://docs.openmicroscopy.org/omero/5.5.0/sysadmins/unix/server-ubuntu1804-ice36.html

  1. in section: To install Ice 3.6.4: 2nd line, there is a space missing after the -q
  2. in section: To install PostgreSQL 10: 2nd line, it specifies stretch-pgdg instead of bionic-pgdg
  3. in section: Create an omero system user, and a directory for the OMERO repository: there should be a -r in the useradd command if a system user is desired.

Cheers,
Damir

Hi Damir. The first two issues are already fixed in the planned 5.5.1 release. We’ll look into the third point.

FYI these docs are autogenerated from this repo: https://github.com/ome/omero-install/ which is meant to ensure the commands are tested for real. Next time feel free to open a PR directly if it’s easier for you. e.g. this was the PR that fixed (1): https://github.com/ome/omero-install/pull/204