Omero Tips January edition : Fiji Omero plugin (1/3) - Installation


Omero Tips and Tricks gifs from Université Côte d’Azur-EMBRC France are available at : Tips & tricks — Université Nice Sophia Antipolis

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Thanky for posting this, @Sophie_Abelanet!

What are your reasons for recommending against using the update sites?

As far as I can see from the README of imagej-omero:

… there would be many benefits of using the plugin provided by the update sites:

  • blocks of pixels loaded on demand
  • transferring ROIs to/from OMERO as imglib2-roi objects
  • transferring results tables to/from OMERO as scijava-table objects
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If you are using newer versions of the OMERO server (5.5+), using the imagej-omero plugin is not an option. If you enable the update site, it could lead to some jars being in your classpath preventing the OMERO.imagej plugin to work.
In the case of OMERO.imagej plugin ROIs are also transferred (not as imglib2-roi). I have opened a PR to clarify that point.



Thanks for the clarification, @j.burel!

I see there’s an open pull request with some discussion on fixing the compatibility with 5.5+ versions:


I’d be very interested to have this working as well as @stoffelc . But unfortunately with omero insight v5.6, imagej-omero is not working (yet). I think it was on the todo list of @ctrueden , but if it’s not too complicated, I and @stoffelc could also try to help.