[ome-users] Omero.tables view for images
Frederik Grüll
frederik.gruell at unibas.ch
Mon Oct 31 13:12:48 GMT 2016
Hi Steve,
Thank you for the link. At the moment we are going for automated image
analysis for one or two plates only and not high-content screens. I will
keep it in mind, the visualization looks definitely impressive.
Kind regards,
Frederik
On 27.10.2016 22:48, Stephen Taylor wrote:
>
> 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-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,
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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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--
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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