[ome-devel] OMERO 5.3.3 and CellProfiler "LoadData" module

[Laurent Guerard]

Hi Emil,

I think that, in the long run, the python readers would indeed be the 
most useful way, but right now we'll probably go for the jar method 
since it would probably be the easiest to set up and deploy on all machines.

Do you know where I can find the CellProfiler's OMERO jar ?

Thanks again for your help !

Best,

---------------
Laurent Guerard


On 13/09/2017 20:19, Emil Rozbicki wrote:
> Hi Laurent,
>
> Repackaging the prokaryote.jar with appropriate jars would be probably 
> the most efficient route in your case. Sorry, I wasn't aware you're 
> using the GUI mode - should have asked. We have not attempted yet to 
> package the CellProflier itself with the python readers as we're 
> mainly using it in the headless mode. I happy to document the set up 
> process for python readers if you're interested.
>
> Cheers,
> Emil
>
> On Wed, Sep 13, 2017 at 3:26 PM, Laurent Guerard 
> <laurent.guerard at unibas.ch <mailto:laurent.guerard at unibas.ch>> wrote:
>
>     Hi Emil,
>
>     If I understood everything, all the jars are part of the
>     prokaryote.jar which I would need to extract and rearchive right ?
>
>     Using python readers would be the best solution indeed, and we
>     would be interested in that. However, since we would need to fix
>     this on multiple computers, is it easily deployable ? And would
>     you have some documentation on how to set it up ? :)
>
>     Thanks again !
>
>     Best,
>
>     ---------------
>     Laurent Guerard
>
>
>     On 13/09/2017 10:42, Emil Rozbicki wrote:
>>     Hi Kai,
>>
>>     Have you also updated CellProfiler's OMERO jars? It's possible
>>     that your CellProfiler installation is still using OMERO 5.2 jars
>>     hence the connection issue.
>>
>>     If that's the case the simplest solution is to replace the jars
>>     to match your server version. Alternative solution is to use
>>     python readers instead of java readers - details here:
>>     https://github.com/CellProfiler/CellProfiler/issues/1772
>>     <https://github.com/CellProfiler/CellProfiler/issues/1772>. It
>>     needs some work to set it up put pays back on performance and the
>>     issue free upgrades.
>>
>>     Cheers,
>>     Emil
>>
>>     On Tue, Sep 12, 2017 at 5:19 PM, Kai Schleicher
>>     <kai.schleicher at unibas.ch <mailto:kai.schleicher at unibas.ch>> wrote:
>>
>>         Hi,
>>
>>         We were using CellProfilers "LoadData" module successfully
>>         with OMERO 5.2.4 to fetch images directly from OMERO.
>>
>>         We recently upgraded to the really awesome OMERO 5.3.3 (yay
>>         :)), but coincidentally we seem to now have issues using CPs
>>         LoadData module to fetch the images.
>>
>>         Can you confirm if this connection is still possible with
>>         OMERO 5.3.3 or if there is maybe an issue?
>>
>>         Thanks for your help and cheers,
>>         Kai
>>
>>         -- 
>>
>>                 Please note my NEW PHONE NUMBERS: +41 61 207 57 31
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>>
>>         Kai Schleicher, PhD | Research Associate in Advanced Light
>>         Microscopy | Biozentrum, University of Basel |
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