[ome-users] OMERO and CellProfilerAnalyst

[Balaji Ramalingam (Staff)]

Hi Kai,

Thank you for the update,
We haven’t tested the integration with CellProfilerAnalyst within the team.

Please give us a day or so, we will test it out locally and give an update on the same.
Hope that works.

Best,
Balaji

From: Kai Schleicher <kai.schleicher at unibas.ch>
Date: Thursday, 27 July 2017 at 16:45
To: OME User Support List <ome-users at lists.openmicroscopy.org.uk>, "Balaji Ramalingam (Staff)" <b.ramalingam at dundee.ac.uk>
Subject: Re: [ome-users] OMERO and CellProfilerAnalyst


Hi Balaji,

thanks for your reply and the link to the guide.

Connecting to our OMERO from Cellprofiler works already like a charm (and was without doubt achieved using your guide :)!

What I wanted to do now is to have CellProfilerAnalyst to also be connected to OMERO.

See the crosspost in the CPA forum<http://forum.cellprofiler.org/t/cellprofileranalyst-and-omero/4962/2> for details.

I was just wondering if anyone had already tried to do the same and had some guidance :)

Thanks and cheers,
Kai

On 07/27/2017 05:27 PM, Balaji Ramalingam (Staff) wrote:

Dear Kai,



To troubleshoot the issue in better detail could you please let us know if you followed all the steps given in the following page,

https://github.com/CellProfiler/CellProfiler/wiki/OMERO:-Accessing-images-from-CellProfiler



specifically,

https://github.com/CellProfiler/CellProfiler/wiki/OMERO:-Accessing-images-from-CellProfiler#omero-server-revisions

This would have helped you match your OMERO server version to the jars present within cell profiler.

(It does look like a server-client mismatch issue)



Thank you,

Best,

Balaji



On 26/07/2017, 16:13, "ome-users on behalf of Kai Schleicher" <ome-users-bounces at lists.openmicroscopy.org.uk on behalf of kai.schleicher at unibas.ch><mailto:ome-users-bounces at lists.openmicroscopy.org.ukonbehalfofkai.schleicher@unibas.ch> wrote:



    sorry for the second email but I forgot to mention what the correct URL

    isntead of the one in the screenshot should have been:



    https://omero.biozentrum.unibas.ch/webclient/img_detail/459060/







    On 07/26/2017 05:09 PM, Kai Schleicher wrote:

    > Dear list,

    >

    > We are using the LoadData module in CellProfiler 2.2 to analyse images

    > fetched directly from our OMERO and this is working really well! I am

    > super happy with that :)

    >

    > What I'd like to find out now is if I could use CellProfilerAnalyst

    > 2.2.1 in the next step, have it connect to our OMERO and get the

    > images within CPA as well via "access CellProfiler Analyst images via

    > URL" from the "ExportToDatabase" module in CellProfiler.

    >

    > Basically this gives me a field into which I can enter the URL to my

    > image on the OMERO server, but I have not figured out the correct way

    > to enter the URL , as you can see from the screenshot.

    >

    > I've attached my LoadData module input csv and the CPA properties file

    > for references.

    >

    > Does anyone have experience setting this up?

    >

    > Thanks and cheers,

    > Kai

    >



    _______________________________________________

    ome-users mailing list

    ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>

    http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users







The University of Dundee is a registered Scottish Charity, No: SC015096

_______________________________________________

ome-users mailing list

ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>

http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users



The University of Dundee is a registered Scottish Charity, No: SC015096
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170727/819421ce/attachment.html>