[ome-users] Omero.tables view for images

Mon Oct 31 12:45:10 GMT 2016

Hi Will, all,

Thank you for the clarification. I did a few tests with the Populate
Metadata script and it picked up the column with the image ID as
expected and wrote it into the HDF file (bulk_annotations) with the
right column type (::omero::grid::ImageColumn). It even added the image
name as an extra column. So I think only the presentation in the clients
would need to be updated. I have attached the CSV file I used for
testing and the resulting HDF for reference.

The feature would be nice to have. In the meantime I'm good because I
think I can work with the Key-Value Pairs as a replacement.

Cheers and thanks again,

Frederik

On 31.10.2016 13:24, William Moore (Staff) wrote:
> Hi Frederik,
>
>  Ah, OK - sorry I misunderstood you there.
> Yes, I’m afraid that we only support the display of OMERO.tables data
> associated with Wells, not Images within the Well.
>
> But, again, if this feature is important for you, let us know so we
> can consider adding it.
> I’ve added this to the card
> at https://trello.com/c/iFe4XS0z/51-refactor-rewrite-populate-metadata-py.
>
>  Cheers,
>
>    Will.
>
>
>
>> On 28 Oct 2016, at 09:20, Frederik Grüll <frederik.gruell at unibas.ch
>> <mailto:frederik.gruell at unibas.ch>> wrote:
>>
>> 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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>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>
>>>
>>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>>
>>>
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>>> ome-users mailing list
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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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