PYME plugin for OMERO interoperability

Hi All,

We have found OMERO exceptionally useful in lab for organizing and discussing data. In order to include our localization data more easily in this we’ve added the ability to upload images/localizations from PYME to OMERO as well as open them in the PYME viewers. Current list of plugin functionality is on the github.

Many thanks to the OME team for all of their (documentation) efforts making this possible and fun!



Hi Andrew

Thanks for your message-- glad OMERO is working for you. Thanks for the plugin list-- that’s quite cool.

If you need anything you know where to find us.



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Hi Andrew,

Not directly related to the OMERO aspect, I notice that the plugin seems to implement the plugin registration now as an automatic component of an install. Can this serve as the blueprint for other plugin repos? Would be pretty cool.

Is there maybe even a way to make this part of some PYME mdule to pull this in for each plugin repo without having to explicitly copy? (no worries if not)


Registration has always been mostly automatic if the plugin is distributed as a conda package. Recommended approach is to maintain an etc/PYME shadow directory in the plugin repository and have the / bld.bat script for your conda package copy this into %PREFIX%/etc.

We could look at including a script / function within PYME to do this, but IMO that would only really be useful for source installs (using it within a plugins build process would make python-microscopy a build dependency rather than just a runtime dependency and significantly slow down builds, which is why the above is the preferred route).

Thanks @jrswedlow! Will certainly reach out if we run into anything.

@csiscf and @DavidBaddeley I’ll suggest any continued discussion on plugin install take place in a separate thread to keep things organized and e.g. stop ping’ing @jrswedlow. Short answer though is running the script automatically as a follow-on to setuptools develop/install is straightforward and I’d be happy to add the outline to the plugin template. Installation of PYME plugins through a GUI within PYME itself is certainly possible for plugins which you can build a conda package for, and we have some discussion on that in this pull request and associated issue, both of which could stand to be revisited.

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Thanks @barentine, for info and apologies to @jrswedlow for hijacking the thread. Will try to avoid in future; and trying the OMERO plugin + server is now on our ToDo list.