[ome-devel] extending OMERO

[Douglas Russell]

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> 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
>
> >
>
> >
>
> >
>
> > _______________________________________________
>
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>
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>
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>
>
>
>
>
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