[ome-devel] CellProfiler LoadData module

[Laurent Guerard]

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20180423/e5d6cd4f/attachment.html>