Establish connection between Omero-Cellprofiler

Hi,

I’ve been trying to establish a connection between our Omero server at out institution with Cellprofiler(3.1.5) for high-throughput image analysis.

I’ve followed the guide at (https://github.com/CellProfiler/CellProfiler/wiki/OMERO:-Accessing-images-from-CellProfiler) without success, and from my understanding that guide is quite outdated and is not the way to do it. Whatever I try to read into Cellprofiler, it wont understand it as login-credentials to Omero (tried Csv, ice.config, .py and URL)
I’ve also looked into this post (https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=7821) where they clearly get a connection to omero through a simple csv file. When I attempt this, it only loads the file as omero.csv without actually reading it.

Im on a mac running the latest OS, with the latest update of java (8). The Omero server is up and running as I can access it through alternative methods (Matlab & Fiji) so there is no problem on that side.

Can anyone help me/direct me to a solution? :slight_smile:

Thanks in advance,
Oscar

Hi,

Unfortunately my understanding is the OMERO bridge is currently broken in the CP3+ builds; we are working with some of the folks there now to try to rectify this!

In the meantime, I’m afraid CP 2.2 is your only option to do this directly. Sorry about this!

Hi @OscarAndre1

to add some more details on what @bcimini mentioned, with CP 2.2 you are able to establish a connection to an OMERO server that is running any patch-version of the 5.3 series only. Otherwise you have to update the OMERO-related JAR files shipped with CP as explained at the bottom of the wiki page linked by you, but I don’t have any predictions how successful that might be with later OMERO-versions.

Best,
Niko

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I updated the Github page to make it known it’s a bit outdated and point here. Sorry for the inconvenience of outdated documentation!

Hi Oscar

We have built a notebook example on how to use CellProfiler 3.1.3 and IDR (https://idr.openmicroscopy.org/). IDR is using the OMERO 5.4 series. The notebook uses the Python API of CellProfiler.
I have not tested CellProfiler 3.1.5.

Below are links showing how we install CellProfiler 3.1.3 in Docker
(we have other things that you can ignore like r-gateway)

The notebook itself is https://github.com/IDR/idr-notebooks/blob/itr/idr0002.ipynb

If you wish to try it out “live” against IDR data

This might give you an idea on how to interface CellProfiler and OMERO.

Cheers

Jmarie

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I have tested the notebooks with CellProfiler 3.1.8 and it works!

Cheers

Jmarie

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