[ome-devel] CellProfiler LoadData module

[Laurent Guerard]

Hi Sebastien,

Thanks for the answer.

The problem with the CellProfiler forum is that it's really not active. 
I actually posted there 
<http://forum.cellprofiler.org/t/connection-to-omero-reset/5961> and 
waited a couple of days without answer before asking here. It's now 21 
days and still nothing..

As for the wiki, last time I asked about something there, Chris was 
actually the one answering which led me here this time as well... :).

Best,
Laurent Guerard

On 30/04/2018 12:36, Sebastien Besson (Staff) wrote:
> 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) 
> <https://github.com/CellProfiler/CellProfiler/wiki/Source-installation-%28Linux%29>
> [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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