[ome-users] Cellomics plate view column index off

William Moore will at lifesci.dundee.ac.uk
Thu May 12 15:32:33 BST 2016

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?


from omero.rtypes import rint
from omero.gateway import BlitzGateway
conn = BlitzGateway(USERNAME, PASSWORD, host="localhost", port=4064)

plate = conn.getObject("Plate", 4468)
gid = plate.getDetails().group.id.val

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)

> On 12 May 2016, at 13:58, Jäälinoja, Harri Tapio <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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