OMERO Random Interactive Access

Hi,

in the Bioinformatics Würzburg we are hosting a webdatabase for protein research.
http://plateletweb.bioapps.biozentrum.uni-wuerzburg.de/plateletweb.php
We are using key-value pairs for the link out to protein databases and annotation databases.
The keys are suitable for directly linking to imaging data on IDR homepage.
However, I learned OMERO is planing to get interactive features, for direct linking coordinates of an image, e.g. ontology link to surfaces, or rather random interactive access to abritary regions.
Maybe also to create onClick features.
Is this an issue worth to think about?

Kind regards

Johannes Balkenhol

Hi,

We’re not sure what you mean by “interactive features”?
With the iviewer, you can link to a coordinate and zoom like this:
http://idr.openmicroscopy.org/iviewer/?images=4007802&x=1000&y=1300&zm=200
or like this if it’s your default viewer:
http://idr.openmicroscopy.org/webclient/img_detail/4007802/?x=1000&y=1300&zm=200
Iviewer URLs are described at https://github.com/ome/omero-iviewer#supported-urls

But that doesn’t give you linked features.
If you have a ROI saved in OMERO, you can link to it in the main webclient UI with e.g.
http://idr.openmicroscopy.org/webclient/?show=roi-1307816
But that only selects the Image that the ROI is in.
If you open that Image in iviewer, you’ll see the ROIs and can click on them but not edit them (since you don’t have permissions). Unfortunately we don’t yet support linking to ROIs in iviewer as we do for webclient.

Can you give us any more details on what functionality you would like to see?
Thanks,

Will.

Hi Will,

of course you can not be sure about what means “interactive features”, as I formulated it very unsure :). So it’s on me.
I catched up the phrase “random (interactive) access” in an online presentation of @joshmoore in slide 33/33 https://figshare.com/articles/On_Bringing_Bioimaging_Data_into_the_Open_-World_/11352074/1
Therof, I was hoping to hit some familiar term. In anyways, your answer helped me very much already in the way that you can link coordinates in the GET statement.
That is a good start, as I intent to link protein names within a protein database with their location within a tissue or cell within images.
Further, I would be nice to directly link to ROI via ontology, e.g. you annoateted a location ontology (cell membrane, nucleus, Golgi Vesicle) of a protein with a surface in imaris and define the surface as ROI. Than it is possible to directly automatize the linkage from protein server to image server.

I am not sure if you were working on that recently, probably this is to specific.

Anyways, thank you for spending your time

Johannes

Hi Johannes,

With omero-mapr we can link to Images annotated with Ontologies via particular key-value pairs, e.g. http://idr.openmicroscopy.org/mapr/gene/?value=MRFAP1
I guess you’d like to do the same with ROIs?

This would allow you to find ROIs via their annotations in OMERO, instead of having to use OMERO ROI IDs in your ‘protein server’. Although there may be times you want a more direct link to a particular image / ROI?
If so, then the support of linking to an ROI in the iviewer would be useful.

Will.

Hi @will-moore ,

exactly this is a good application. This helps a lot already and we will test that.
Than we will see how good that works and after we think about more direct links.
Thank you for your helpful response.

Best
Johannes