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

[Emil Rozbicki]

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>
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. 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>
> 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 (direct) +41 61 207
>>>> 22 50 (central)<<
>>>>
>>> Kai Schleicher, PhD | Research Associate in Advanced Light Microscopy |
>> Biozentrum, University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel |
>> Phone: +41 61 207 57 31 (direct) +41 61 207 22 50 (central) |
>> kai.schleicher at unibas.ch | www.biozentrum.unibas.ch |
>> www.microscopynetwork.unibas.ch
>>
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>
>
>
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