[ome-devel] extending OMERO

Tue Apr 29 17:02:41 BST 2014

Hi Douglas,

Thanks, I'll get back to you this!

Kind regards,

Steve

From: Douglas Russell [mailto:douglas.russell at bioch.ox.ac.uk]
Sent: 28 April 2014 09:22
To: Stephen Taylor
Cc: Simon Li; ome-devel at lists.openmicroscopy.org.uk; Roger Noble (roger at coritsu.com)
Subject: Re: [ome-devel] extending OMERO

Hi Steve,

If you want to compile a list of things that you want to do with the API then I can prepare some examples and come up and show you them if you want? Especially with the Python API I have quite a bit of experience now.

Cheers,

Douglas

On 25 April 2014 18:16, Stephen Taylor <stephen.taylor at imm.ox.ac.uk<mailto:stephen.taylor at imm.ox.ac.uk>> wrote:

Hi Simon,

>As Jason pointed out in his email you should definitely be able to obtain all the information you need via the OMERO API, and we can certainly help you once you get started.

>Probably the easiest way to get started is to look at one of the language specific pages. Picking Python as an example, the code samples at >http://www.openmicroscopy.org/site/support/omero5/developers/Python.html#code-samples

>cover the basics of connecting to OMERO, and retrieving/manipulating data. An intro to the full API is at http://www.openmicroscopy.org/site/support/omero5/developers/Modules/Api.html

>

> We are planning to extend OMERO to be able to support our zoomable image and query interface called PivotViewer (for details see http://www.cbrg.ox.ac.uk/data/pivotviewer/intro.shtml) or to view it in action, see the YouTube movie (https://www.youtube.com/watch?v=BvDOPpRo7KM).

>

> We have 3 main goals:

>

> 1) Visualise OMERO projects by :

> i)  Generating indices for PivotViewer by doing an export of metadata (possible from the HDF5 tables) and images from the OMERO database.

>There are methods for listing images in Projects/Datasets/Screens, and for obtaining the raw images data and metadata. Are the HDF5 tables you refer to created using the OMERO.tables >API, or are they created by yourself? If it's the latter there are API methods to retrieve the original HDF5 file (or any other type of file you want to store in OMERO).

OMERO.tables.

> ii) Exporting the images + metadata on the fly.

>Could you expand on what do you mean by "export"? There are examples of rendering images on the fly on the code samples page, for more advanced usage you might want to look at the >source code for OMERO.web.

Ok. Currently we use static PNGs/JPGs and create a tiling pyramid which is read by the viewer, but it would be cool to generate these on the fly, caching the images of interest.

> 2) Use the results of filtering operations to run OMERO.scripts and see the results in PivotViewer.

>As you're probably already aware scripts are run asynchronously in a separate process. If you want something more responsive there may be other options.

No I didn't know that. I'd be interested to hear about the other options...

> 3) Use the results of filtering operations to be able to annotate back to the OMERO database. So for example, I might choose a subset of images that I think are badly stained and tag them as 'stained=bad' or similar.

>This should be straightforward- once you've got a list of images (or any other OMERO objects) you can easily create a tag on them. It's also possible to attach more structured data to ?>an image.

Ok. Sounds good. Is there a link where I can find more info about the different data structures available?

> I am trying to pull together enough technical information to define how much work would be required to do this as part of a grant application. Would anyone on this list be able to >help?

>What kind of interaction do you want to see between OMERO and PivotViewer? Do you see it as a separate standalone application, or part of OMERO.web?

Ultimately it would be good to have as part of OMERO web but I think we have to get a bit more familiar with OMERO's guts before we look at that. Doing it OMERO.web would be useful since we could use the same authentication to secure collections, though I guess if both systems are using LDAP this might not be a problem. What other advantages do you think would be in using OMERO.web?

>

>Do you need real-time updates- that >could be pretty challenging. However we've done (and are planning a lot more) work on integrating analysis tools into OMERO, so if you come across >any issues don't hesitate to mention >them.

I think it would be standalone in the first instance and export the data (images and metadata) from OMERO incrementally and then index it on the file system.

Thanks for your help so far,

Steve

> Also, if any developers are interested in collaborating on this project please let me know!

>

> Kind regards and thanks,

>

> Steve

> =======================================

> Head of Computational Biology Research Group Weatherall Institute of

> Molecular Medicine University of Oxford www.cbrg.ox.ac.uk<http://www.cbrg.ox.ac.uk>

>

>

>

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