Setup OMERO with different storage locations possible?

Hi all,
can someone tell me whether it is possible to configure an Omero instance in a way that it uses different locations for different groups while keeping the possibility to import via the Omero.importer for all users (i.e. without resorting to in-place imports)? For example, so that the data of users from group A automatically ends up in /opt/omero/omero_datadir/ManagedRepository1 and the data of users from groups B and C ends up in /opt/omero/omero_datadir/ManagedRepository2?
If yes, could you point me to some documentation about this? If no, are there ideas/alternatives how to include different storage locations without disrupting the user experience?
Cheers, Peter


Hi @Peter.Zentis,

We’ll need to discuss a migration strategy, but the configuration property you are looking for is omero.fs.repo.path. More information is also available under FS configuration options — OMERO 5.6.3 documentation and some attractive drawings can be found under Import Workshop - Paris 2014 e.g.


All the best,

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Hi @joshmoore,
Thanks a lot! I think this is indeed what we were looking for! Since you bring up the topic of migration strategy - do you know of a script or so that would allow us to migrate from a config with the default for omero.fs.repo.path to a config with the GroupID in the beginning of the path?
Cheers, Peter

A few high-level comments on the migration:

  • There’s no requirement to move all data into the new layout. OMERO will access the data based on the paths in the database, and those are set at import time. When you restart the server, all new imports will be placed in the new layout.
  • Reversely, if data is moved between groups within OMERO, the layout on disk is not updated.
  • You can use symlinks from the current paths in the database to the new layout that you would like to see and not need to modify your database.
  • There’s a CLI command, omero fs rename, which runs fileset by fileset. Obviously, that’s not great for a large scale migration.


We’re actually having this in operation since a few years by simply using symlinks for those user accounts where the data should reside in a different location. In other words, move the directory from the actual ManagedRepository to its desired location (with the OMERO services being shut down at this very moment) and then put a symbolic link with the original name right there, pointing to the new location.

Admittedly, it requires manual intervention once after the account has been created, but for us it does the job.

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