[ome-users] Omero.tables view for images

Thu Oct 27 21:48:34 BST 2016

Hi Frederik,

Have you seen Zegami? This is a useful way to visualise HCS data since it allows querying of the tables after caching OMERO data and also allows linking direct to OMERO. Here is a link to a demo:

http://demo.zegami.com/omero-idr.html

Briefly, facets on the left of the Zegami GUI allow rapid querying of the metadata and this is reflected in the zoomable interface which shows images of the wells. If you click on a well this brings up a metadata panel which shows the data relating to the image. At the top of the panel is an icon of a flask linked to the OMERO Insight Viewer which will give direct access to the raw images stored in OMERO.

More info about Zegami here:

https://www.zegami.com/

Just to be clear, Zegami is spin-out company from Oxford University, and I am one of the founders. There are free for academic versions as well as paid for versions. I’d be interested to know if it’s useful for your needs.

Kind regards and thanks,

Steve
=======================================
Head of Computational Biology Research Group
Weatherall Institute of Molecular Medicine
University of Oxford
+44 1865 222640
www.cbrg.ox.ac.uk<http://www.cbrg.ox.ac.uk/>

From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of William Moore (Staff)
Sent: 27 October 2016 16:12
To: OME User Support List <ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] Omero.tables view for images

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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