Exploiting external data from Omero server

Hi,

Our team wants to access some images that are external to Omero server. The images are shared using a network share managed by Active Directory.

Has anyone worked in such implementation? How can we view the remote images and manage them through omero?

Thx in advance.

Hi @Ivancn,

if the OMERO server can see the network share, then you can use in-place import to register such files with your OMERO.

There are other threads on the forums if you search for “in-place”, e.g. Managing data with in-place import in remote server - #15 by joshmoore

All the best,
~Josh

Hello @joshmoore,

Thx for your feedback. The remote folder is mounted via samba. Is there an easier way (for users) for example like use a plugin to be able to have the share available via their omero web and import files using the GUI?

Best
Ivan

Hi Ivan,
unfortunately that’s not possible. The only GUI option for importing images is Insight, and it uses the traditional ‘upload and import’ mode. The ‘in-place’ import (images are linked into the OMERO server’s data repository) only works with the command line interface via SSH on the server, because it needs direct file system access.
Kind Regards,
Dominik

Hi @Ivancn ,
@dominikl is of course completely correct but there may be a workaround that you may want to look at: the inplace-importer that @alexra developed. The forum post where it was discussed is here: Inplace importer in Omero Script - #8 by dsudar
In brief: it provides a GUI on the client computer that can see the share so you can use GUI tools to select the files to import into OMERO. It then communicates with the OMERO server (which needs to have an appropriate account set up to allow such access) to initiate the import. The current implementation does an inplace import (as @joshmoore suggested) but you could probably change the code a little bit to make it do a regular import. The current implementation will probably only work as-is on a Linux client but I’m fairly sure it can be made to work on Windows or Mac as well (with some coding expertise).

Cheers,
Damir

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Hi everybody,
the omero inplace importer also works for Mac, I have not tested it on PC, but I do not expect big changes to be required.
I can just add some details on our sharing scenario:
I have 2 file servers (linux) and their shares are permanently mounted to the the omero server via NFS (tested smb before, but was not so happy).
Import into omero is done with the ln_s (In-place import — OMERO 5.6.1 documentation), so the only disk space required on the omero server are the aliases and the caches.
Best wishes
Alex

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Hi @Ivancn,

we use the following script to import via OMERO.web from a mounted share:

Perhaps it would be helpful to go into a little more detail:
the script imports all data from a specified mount path using cli import.
The mount path is composed of MOUNT_PATH, WORKSTATION_NAME and the name of the user who calls this script. This means that the data must be located on the mounted system in a folder with the omero user name. You can also specify file extensions of non-image formats, which are then loaded as attachments.

This script can be uploaded by the administrator via the OMERO.script interface and then be used by everyone.

Perhaps you can use it and adapt it to your needs :slightly_smiling_face:.

Best,
Susanne

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I wonder (a.) if there’d be interest in having such tools be listed somewhere and (b.) where would be (c.) easy enough to maintain and (d.) findable by everyone! ~J

2 Likes

Here’s another example of a user using a script for “getting list of all files in a NAS storage that is mounted on omero server” in order to pick files to be imported with the script.
Only a snippet is provided, not the full script: