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

[Emil Rozbicki]

Hi Laurent,

The CellProfiler is using standard OMERO jars which you can download from
OME's website and replace in prokaryote.jar. Probably better way of doing
it is simply building the prokaryote module from source. OmeroReader.class
which CellProfiler is using to access the images is located in blitz.jar so
you should replace the OMERO version in this block:
https://github.com/CellProfiler/prokaryote/blob/1.0.11/pom.xml#L10 with the
one that matches your server version and then build and install the module.

Please mind that as of OMERO 5.3 OmeroReader is deprecated (
https://github.com/openmicroscopy/openmicroscopy/blob/dev_5_3/components/blitz/src/loci/ome/io/OmeroReader.java#L90)
and might be removed in the future versions.

Cheers,
Emil

On Fri, Sep 15, 2017 at 9:16 AM, Laurent Guerard <laurent.guerard at unibas.ch>
wrote:

> 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> 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/CellP
>> rofiler/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
>>>>> <%2B41%2061%20207%2057%2031> (direct) +41 61 207 22 50
>>>>> <%2B41%2061%20207%2022%2050> (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
>>>
>>> _______________________________________________
>>> ome-devel mailing list
>>> ome-devel at lists.openmicroscopy.org.uk
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>>>
>>
>>
>>
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>>
>>
>
>
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