[ome-users] Omero.tables view for images

[William Moore (Staff)]

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

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-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
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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The University of Dundee is a registered Scottish Charity, No: SC015096


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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<mailto:frederik.gruell at unibas.ch> | www.biozentrum.unibas.ch<http://www.biozentrum.unibas.ch/>
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