[ome-users] Omero.tables view for images

Tue Nov 1 10:36:04 GMT 2016

Hi Frederik,

 Yes, it seems that it’s only the clients that need updating to support Images.

Although we currently show Well and Image together in the right panel (image depends on which field the plate is selected for the plate)
this is changing in OMERO 5.3:
The right panel will only show the Well when it’s chosen from the Plate, the containing images will be shown below the main plate,
and clicking these images will load the Image in the right panel.
This means that you can choose whether to annotate the Well or the contained Images.
See https://github.com/openmicroscopy/openmicroscopy/pull/4863 (feedback welcome)!

I’ll make sure we update the display of Tables data, so that when you choose an Image you see any Tables data on Images.

Cheers,

  Will.

On 31 Oct 2016, at 12:45, Frederik Grüll <frederik.gruell at unibas.ch<mailto:frederik.gruell at unibas.ch>> wrote:

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

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/>

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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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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/>
<bulk_annotations.hdf><populateMetadata_example_plate_image.csv>_______________________________________________
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