Omero FIJI plugin not working on server v5.6

Hi all,

Our ict department has updated our omero server version to version 5.6. Works perfectly on web and via insight.

However i would like the option to open images from the server in FIJI, both the plugin i can download from the omero website, or the 5.5 update site dont allow me to communicate with the server.

How can this issue be solved?

Joost

Hi Joost

The jars used to interact with OMERO in imagej-omero needs to be updated. After update, it will be possible to connect to 5.5 and 5.6 so the 5.5 update site should still be valid.

Cheers
Jmarie

Hello Jean Marie,

I had finally some time to figure this out properly. My plugin makes use of the imageJ 5.5 plugin site and is trying to connect to the server via a gateway.

However the gateway class is in two locations once i have both the 5.5 update site activated as well as the omero_ij-5.5.10-all.jar file in the plugin folder

Both contain the Omero.omero.gateway class. The last jar directly in the omero/omero subfolder of course. For the update site in the omero-gateway-5.5.3.jar file.

I need the update site for the Omerolocation class. which i am using to access the images.
Located in the imagej-omero-0.9.0-SNAPSHOT.jar file.

Of course i can add this manually, but i would like it if users of my plugin would just have to activate a few update sites. This is the easiest way to distribute i have found out, therefore i would like to keep it that way.

If you have any suggestions they would be more than welcome
Joost

Hi Joost

I think removing omero-gateway-5.5.3.jar and probably the blitz.jar coming from the update site will solve the problem.
I have not tested it.

cc @ctrueden
Cheers

Jmarie

It does indeed, however it does not seem like the best solution to have others implement it that way/

Will there in the future be a more permanent solution? If not i’ll just write detailed instructions on how to get it to work properly

Joost

The best solution is to use the latest omero-gateway in imagej-omero
This will require a release of imagej-omero.

Cheers

jmarie

1 Like

Hi @Joost_Willemse1
I was looking at the tag, one option will be to use the tag 29.0.0-beta-1of pom-scijava in the imagej-omero plugin to evaluate. The tag includes the version of the omero dependencies allowing to connect to 5.6 server.

@ctrueden do you a timeline for an official 29.0.0 version (no beta)?

Cheers

Jmarie

Hi Jean-marie,

I tried with this tag, but to no avail. It moves the error forward,
From getting 5.5.3 is not compatible with 5.6.1 i now get 5.5.6 is not compatible with 5.6…1.

Joost

Yes, we have resolved nearly all the conflicts surrounding the 29.0.0 pom-scijava release. Remaining issues can be seen here: https://github.com/scijava/pom-scijava/milestone/3. I expect the final release before next Friday. But of course it depends on if any further problems appear. I am doing another round of integration testing this evening.

Regarding imagej-omero specifically, my hope is to release a new version concurrently with pom-scijava 29.0.0. However, there is currently an issue with the Docker-based imagej-omero integration test no longer working on Travis CI. Once we get this resolved (hopefully with @joshmoore’s help), I can cut the new imagej-omero release. Then we will update the core ImageJ + Fiji update sites, as well as the the OMERO-5.5 update site, with new component versions.

Hi @ctrueden
That’s great. I read this morning the discussion on the PR.
Good luck with the final round of testing.

Cheers

Jmarie