OMERO update site proposal

Dear Fiji maintainers

We have been running training sessions at a fast pace in the past 20 months demonstrating how to use OMERO and showing integration with 3rd party tools to diverse audiences (biologist, image analysts, etc.). Fiji is (almost) always a tool that we include in our workshop. From the feedback we collected there are needs for both UI interaction and scripting access to OMERO data using the plugin.

Very often the installation of our OMERO.imagej plugin is not as straightforward/easy as one might expect [1], [2] and the lack of an update site was highlighted on several occasions.

A recent problem while using the plugin in Fiji on Windows forced us to review the packaging of the plugin and to work on an update site [3].

The plugin has now been tested on Linux, Windows and Mac using the personal update site.

We would like now to move it from a personal update site to a group update site and propose to create and maintain https://sites.imagej.net/OMERO-5.5 (to match the existing convention) or https://sites.imagej.net/OMERO

If there is no objection, we would like to move forward with that proposal so we can update our installation instructions and have everything ready for another round of workshops coming up in November.

cc @ctrueden @imagejan

Cheers

The OME team

[1] OMERO plugin error in Fiji
[2] Java problem with OMERO Fiji Plugin
[3] https://sites.imagej.net/Jmburel/

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Will you then also maintain https://github.com/imagej/imagej-omero and keep that working on each versioned OMERO update site? I would only be in favor of an officially named “OMERO” update site at https://sites.imagej.net if it also includes the ImageJ-OMERO extension. Any update site shipping only OMERO.insight-ij should be named differently, perhaps https://sites.imagej.net/OMERO-insight.

Hi Curtis

Thanks for the response and the consideration.

We all want to provide a resource that doesn’t confuse any type of users-- experimentalist, analyst, or developer. We definitely are interested in getting resources to maintain the ImageJ/OMERO connectivity. We don’t have that yet but are trying. For the moment, imagej-omero isn’t being actively maintained but we’ll try to include it in the future.

How about we go with an “OMERO-5.5” for the OME plugin update site. We can try to reconcile when/if we (Madison, Dundee or whomever) receives the resources required.

Thanks again. Let us know your thoughts.

On the contrary: I am trying to keep it up to date with the latest build system, OMERO version, etc. I just have a lot on my plate, so I may not be as timely or thorough as you might prefer. But I already updated pom-scijava with the changes needed to make OMERO 5.5 dependencies work correctly from downstream code:

This work was a prerequisite to updating ImageJ-OMERO for 5.5.

I then updated ImageJ-OMERO to use OMERO 5.5:

However, I could not merge it to master yet because the work depends on the not-yet-released pom-scijava 28, which has been near the top of my list since July.

Once pom-scijava 28 is released, I can merge the ImageJ-OMERO update, cut a new release, create the OMERO-5.5 update site, and push the work there.

If you want to also ship OMERO.insight-ij on OMERO-5.5, this makes sense to me, as long as the artifacts we ship do not conflict with one another. Then there remains only one OMERO update site per OMERO version, which is great.

I have now taken the following actions:

  • I pushed an omero-5.5 update branch for imagej-omero-legacy:

    https://github.com/imagej/imagej-omero-legacy/compare/omero-5.5

  • I created the OMERO-5.5 update site.

  • I built imagej-omero and imagej-omero-legacy locally, and uploaded the builds + dependencies to the OMERO-5.5 site. These are still SNAPSHOT versions, until pom-scijava 28 is released.

  • For update sites OMERO-5.0, OMERO-5.1, OMERO-5.2, OMERO-5.4 and OMERO-5.5, I have granted the following users upload rights: Rueden, Awalter2, Jmburel (@OMETeam), Joshmoore (@joshmoore), Sbesson (@s.besson). Let me know if anyone else needs to be added.

I do not have an OMERO 5.5 server to test. So I would greatly appreciate someone from the @ome team testing the OMERO-5.5 update site within Fiji. Do the commands “Import from OMERO” and “Export from OMERO” work? (Type omero into the search bar to access them easily.)

You are welcome to upload other OMERO+ImageJ integration functionality to the OMERO-5.5 update site. But please be careful about dependencies. We need to watch out, because OMERO’s dependencies are so complex. In particular, we should not upload unshaded uber-JARs unless it’s unavoidable.

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Hi Curtis

Apologies for the slow reply, we are deep in Python3 upgrade.

Thanks for setting things up. This is great and very much appreciated.

We had to create an uber jar to fix an issue with the plugin in Fiji on Windows.
We use the following gradle plugin https://github.com/johnrengelman/shadow so hopefully we will not have any clash between imagej-omero and insight-ij.

I have tested the new OMERO-5.5 update site. I installed imagej-omero and OMERO.insight-ij in Fiji and I did not notice any problem. I have only checked on Mac, we will do further testing on Windows later on

I was able to use both successfully i.e. use imagej-omero import/export functionalities against a 5.5 server and also continue to use OMERO.insight-ij

Thanks again for setting things up

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