[ome-users] Omero.tables view for images

Fri Oct 28 09:20:15 BST 2016

Hi Will, all,

The key-value annotations work well so far. I have one line per image in
an attached CSV file and I can easily parse this data and annotate it
with an OMERO script as a key-value map. The CSV file is created by
CellProfiler and I just loop the image IDs through it with the LoadData
module.

My image data is actually organized in plates, but I could not make an
OMERO table that would show metadata per image instead of metadata per
well, even if I substitute the well column with an image column in the
HDF file that backs the table.

Cheers,

Frederik

On 27.10.2016 17:11, William Moore (Staff) wrote:
> Hi Frederik,
>
>   The Glencoe webinar is only using HCS data (all the images are in
> Wells & Plates) with the tables data attached to the Plate/Screen.
>
> We don’t yet support the same functionality with images in Datasets. 
>
> Let us know if you have any issues with using Key-Value “Map”
> annotations (and if you need
> OMERO.tables on Datasets) so we can plan for supporting this in the
> future.
>
>  Cheers,
>
>   Will.
>
>
>
>> On 26 Oct 2016, at 09:00, Frederik Grüll <frederik.gruell at unibas.ch
>> <mailto:frederik.gruell at unibas.ch>> wrote:
>>
>> Hi Simon,
>>
>> Thank you for your answer. I think I will go with the key-value store.
>>
>> I saw table information for images in the webinar "OMERO Plus for
>> High Content Screening & Analysis" at 0:46:04. Is this only supported
>> by OMERO Plus?
>> https://glencoesoftware.com/webinars.html
>>
>> Cheers,
>>
>> Frederik
>>
>>
>> On 25.10.2016 14:16, Simon Li wrote:
>>> Hi Frederik
>>>
>>> We don't have a way of directly displaying Table information
>>> alongside images at the moment. However we've done some related work
>>> for the IDR project, where we built a CLI plugin to convert a table
>>> into MapAnnotations on images, e.g. see the Key-Value pairs on
>>> http://idr-demo.openmicroscopy.org/webclient/?show=image-1920093
>>> <http://idr-demo.openmicroscopy.org/webclient/?show=image-1920093>
>>>
>>> The main rationale for this approach was to distinguish between the
>>> raw data held in the table, and the client-visible view of that data.
>>>
>>> It's still considered "developmental", but you can see previousl
>>> conversations on the topic here:
>>> -
>>> http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2016-June/003694.html
>>> <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2016-June/003694.html>
>>> -
>>> http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2016-August/003733.html
>>> <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2016-August/003733.html>
>>>
>>> And some example configuration files here:
>>> -
>>> https://github.com/IDR/idr-metadata/blob/master/idr0018-neff-histopathology/experimentA/idr0018-experimentA-annotation.csv
>>> <https://github.com/IDR/idr-metadata/blob/master/idr0018-neff-histopathology/experimentA/idr0018-experimentA-annotation.csv>
>>> -
>>> https://github.com/IDR/idr-metadata/blob/master/idr0018-neff-histopathology/experimentA/idr0018-experimentA-bulkmap-config.yml
>>> <https://github.com/IDR/idr-metadata/blob/master/idr0018-neff-histopathology/experimentA/idr0018-experimentA-bulkmap-config.yml>
>>>
>>> I'll have to check whether the support for populating Images in
>>> Datasets made it into the last release.
>>>
>>> Hope this helps
>>>
>>> Simon
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 25 October 2016 at 10:54, Frederik Grüll
>>> <frederik.gruell at unibas.ch <mailto:frederik.gruell at unibas.ch>> wrote:
>>>
>>>     Dear all,
>>>
>>>     the OMERO webclient offers a nice overview of table data for
>>>     wells in a
>>>     screen with OMERO.tables. I can import the data with the script
>>>     "Populate Metadata" and see it in the table accordion on the
>>>     right pane.
>>>
>>>     Is there a way to have the same for images instead wells? I made
>>>     some
>>>     experiments, eg. with
>>>     https://github.com/openmicroscopy/openmicroscopy/blob/v5.2.6/examples/OmeroTables/MeasurementTable.java
>>>     <https://github.com/openmicroscopy/openmicroscopy/blob/v5.2.6/examples/OmeroTables/MeasurementTable.java>
>>>     and by adjusting "Populate Metadata", but could not make the table
>>>     appear for images.
>>>
>>>     Cheers,
>>>
>>>     Frederik
>>>
>>>
>>>     --
>>>     Dr. Frederik Grüll | Imaging Expert | G1055, Biozentrum,
>>>     University of
>>>     Basel | Klingelbergstr. 50/70 | CH-4056 Basel Phone: +41 (61)
>>>     207 2250 <tel:%2B41%20%2861%29%20207%202250> |
>>>     frederik.gruell at unibas.ch <mailto:frederik.gruell at unibas.ch> |
>>>     www.biozentrum.unibas.ch <http://www.biozentrum.unibas.ch/>
>>>
>>>
>>>     The University of Dundee is a registered Scottish Charity, No:
>>>     SC015096
>>>
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>>>
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>>>
>>>
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>>
>> -- 
>> Dr. Frederik Grüll | Imaging Expert | G1055, Biozentrum, University
>> of Basel | Klingelbergstr. 50/70 | CH-4056 Basel Phone: +41 (61) 207
>> 2250 | frederik.gruell at unibas.ch | www.biozentrum.unibas.ch
>> _______________________________________________
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>
>
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>
>
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-- 
Dr. Frederik Grüll | Imaging Expert | G1055, Biozentrum, University of
Basel | Klingelbergstr. 50/70 | CH-4056 Basel Phone: +41 (61) 207 2250 |
frederik.gruell at unibas.ch | www.biozentrum.unibas.ch
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