[ome-users] Cellomics plate view column index off

William Moore will at lifesci.dundee.ac.uk
Thu May 12 21:37:30 BST 2016 

Hi Harri,

 See the script service example at 
https://github.com/openmicroscopy/openmicroscopy/blob/develop/examples/Training/python/Scripting_Service_Example.py <https://github.com/openmicroscopy/openmicroscopy/blob/develop/examples/Training/python/Scripting_Service_Example.py>

You just need to replace “Image” and imageId with “Plate” & plateId etc everywhere.
Then put the plate processing code in the place indicated.

(NB: this only handles a single object (plate/image) at at time. Add an extra for loop if you want to handle multiple plates).

You can probably remove all the conn.SERVICE_OPTS (group context) lines
if you’re using the script service, since it should set the context correctly anyway.

Then you can upload it as described
http://www.openmicroscopy.org/site/support/omero5.2/developers/scripts/user-guide.html#upload-script <http://www.openmicroscopy.org/site/support/omero5.2/developers/scripts/user-guide.html#upload-script>

 Hope that helps,

  Will.



> On 12 May 2016, at 17:42, Jäälinoja, Harri Tapio <harri.jaalinoja at helsinki.fi> wrote:
> 
> Hi Will,
> 
> cool, thanks! I ran it from command line on the server as omero user, as that's where I have the omero modules. Would it be possible to install the same on the server so that you can run it from the script menu? Maybe that should be left as an exercise for me :)  
> 
> I'm waiting for a new server where to set this up, with the specific aim of helping our CellInsight users. Of course some of them may still want to image the whole plate, so this fix wouldn't be enough, but some might agree to leave an empty column just to get the benefit of browsing the data easier.
> 
> Best,
> Harri
> From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk <mailto:ome-users-bounces at lists.openmicroscopy.org.uk>> on behalf of William Moore <will at lifesci.dundee.ac.uk <mailto:will at lifesci.dundee.ac.uk>>
> Sent: 12 May 2016 17:32:33
> To: OME User Support List
> Subject: Re: [ome-users] Cellomics plate view column index off
>  
> Hi Harri,
> 
>  I played a bit with a Python script to fix the Well offset,
> but unfortunately the 12th column is still missing (not imported at-all).
> But maybe useful if the 12th column is not used for a Plate?
> 
>   Will.
> 
> 
> from omero.rtypes import rint
> from omero.gateway import BlitzGateway
> conn = BlitzGateway(USERNAME, PASSWORD, host="localhost", port=4064)
> conn.connect()
> 
> conn.SERVICE_OPTS.setOmeroGroup("-1")
> plate = conn.getObject("Plate", 4468)
> gid = plate.getDetails().group.id.val
> conn.SERVICE_OPTS.setOmeroGroup(gid)
> 
> wellGrid = plate.getWellGrid()
> 
> for row in wellGrid:
>     toSave = []
>     for w in row:
>         if w is not None:
>             well = w._obj
>             col = well.column.val
>             print col
>             well.column = rint(col - 1)
>             toSave.append(well)
>     conn.getUpdateService().saveArray(toSave)
> 
> 
> 
> 
>> On 12 May 2016, at 13:58, Jäälinoja, Harri Tapio <harri.jaalinoja at helsinki.fi <mailto:harri.jaalinoja at helsinki.fi>> wrote:
>> 
>> Hi Will,
>> 
>> it's the same in Insight client:
>> https://wiki.helsinki.fi/display/LMU/OMERO+troubleshooting?preview=/196947403/196949286/omeroi_cellomics.png <https://wiki.helsinki.fi/display/LMU/OMERO+troubleshooting?preview=/196947403/196949286/omeroi_cellomics.png>
>> 
>> I uploaded a full plate, one field per well, about 20MB.
>> 
>> Thanks!
>> Harri
>> 
>>   
>> From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk <mailto:ome-users-bounces at lists.openmicroscopy.org.uk>> on behalf of William Moore <will at lifesci.dundee.ac.uk <mailto:will at lifesci.dundee.ac.uk>>
>> Sent: 12 May 2016 12:57:37
>> To: OME User Support List
>> Subject: Re: [ome-users] Cellomics plate view column index off
>>  
>> Hi Harri,
>> 
>> I wonder if you could check whether you get the same UI issue in the Insight client?
>> If so, then this is likely an issue with initial reading of the Plate on import.
>> The easiest way for us to look at this would be if you could send us an example file.
>> Do you have an example that is quite small?
>> If you could upload it at https://www.openmicroscopy.org/qa2/qa/upload/ <https://www.openmicroscopy.org/qa2/qa/upload/>
>> that would be great - thanks,
>> 
>>   Will.
>> 
>> 
>>> On 11 May 2016, at 11:07, Jäälinoja, Harri Tapio <harri.jaalinoja at helsinki.fi <mailto:harri.jaalinoja at helsinki.fi>> wrote:
>>> 
>>> Hi,
>>> 
>>> I uploaded some Thermo CellInsight plate data to OMERO 5.2.3, and noticed that there is a problem with the well column index. The wells are numbered A01 -> H12, but OMERO webclient viewer seems to think the index starts from A00, and shifts the wells to the right. Here are some screenshots to show what I mean:
>>> https://wiki.helsinki.fi/display/LMU/OMERO+troubleshooting <https://wiki.helsinki.fi/display/LMU/OMERO+troubleshooting>
>>> 
>>> In case of a full plate, the right-most column is not shown at all.
>>> 
>>> hajaalin at dhcp-asv-66:~/tmp$ ls LMU-CELLINSIGHT_151117170001/|head -2
>>> LMU-CELLINSIGHT_151117170001_A01f00d0.C01
>>> LMU-CELLINSIGHT_151117170001_A01f01d0.C01
>>> hajaalin at dhcp-asv-66:~/tmp$ ls LMU-CELLINSIGHT_151117170001/|tail -7
>>> LMU-CELLINSIGHT_151117170001_H12f14d0.C01
>>> LMU-CELLINSIGHT_151117170001_H12f15d0.C01
>>> 
>>> 
>>> As you see in omero_cellomics.png, part of the code has the index right. There "General" tab on the right shows E04 when viewer says E5. Same goes for field index.
>>> 
>>> I have also a feature request related to the viewer: would it be difficult to show a montage of the fields of a given well? It wouldn't even have to be a real stiched image. 
>>> 
>>> Best regards,
>>> Harri
>>> 
>>> ---
>>> Harri Jäälinoja
>>> Light Microscopy Unit
>>> Institute of Biotechnology
>>> University of Helsinki
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