[ome-devel] CellProfiler LoadData module

[Sebastien Besson (Staff)]

Hi Laurent

A quick search suggests the CellProfiler wiki [1] is probably the placeholder for the building
instructions although I cannot see any details on the dependency management.

For any more specific answers, the CellProfiler forum [2] is probably the reference place
to post your question. I suspect you are not the only person interesting in doing this
and the answer would be of general interest for the CellProfile community.


Best,
Sebastien

[1] https://github.com/CellProfiler/CellProfiler/wiki/Source-installation-(Linux)
[2] http://forum.cellprofiler.org/

On 23 Apr 2018, at 08:22, Laurent Guerard <laurent.guerard at unibas.ch<mailto:laurent.guerard at unibas.ch>> wrote:

Hello Chris,

Once again thanks for your help.

may have to build CellProfiler, and some of its dependencies, from source as a result

Is there any documentation about how to do that and what to modify for each version ? We're in the process of upgrading OMERO to 5.4.x and the link with CellProfiler was one of the things we wanted to test before completely upgrading.

The way CellProfiler interacts with OMERO is actually via Bio-Formats and the OmeroReader so the number of potential locations to investigate such a problem is actually quite high.

Hmm I see, not that simple then. I guess closing CellProfiler and reopening it again once the connection is closed is the best solution so far.

Thanks again.

Best,
Laurent Guerard

On 20/04/2018 16:14, Chris Allan wrote:
Hello, Laurent:

Comments inline.

On 4/19/2018 12:56, Laurent Guerard wrote:
Hi all,

It is possible to connect between CellProfiler and OMERO using the LoadData module and a CSV generated from OMERO.

That's correct.  However, CellProfiler 3.0.0, released back in October 2017, currently has broken OMERO support.  It also targets OMERO 5.3.x. If you want to use CellProfiler with OMERO you will have to be quite specific about which versions you would like to work with and may have to build CellProfiler, and some of its dependencies, from source as a result.


However, it seems that after a while the connection between OMERO and CellProfiler is closed and it doesn't prompt again for it. Is there a command using Python that I could use to improve that module and check if the connection is still open ?

Not that I am aware of.  The way CellProfiler interacts with OMERO is actually via Bio-Formats and the OmeroReader so the number of potential locations to investigate such a problem is actually quite high.


Thanks.

--
Best,
Laurent Guerard

Hope that helps.

-Chris

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