[ome-devel] OMERO.features API development

[Lee Kamentsky]

I promised to roughly describe the CellProfiler use case - we recently
published a paper whose data should be available on-line, so I based it on
that. Enclosed is what I wrote up as well as the paper and the supplement.
The supplement is actually more important because it has more details about
the analysis (and the features).


 Ljosa_JBiomolScreen_2013.pdf<https://docs.google.com/a/broadinstitute.org/file/d/0Bzg4PoGEku2FTFFBS0ZsZTFoSXc/edit?usp=drive_web>

 Ljosa_JBiomolScreen_2013_supplement.pdf<https://docs.google.com/a/broadinstitute.org/file/d/0Bzg4PoGEku2FLVZkTEZqUDJ5X1k/edit?usp=drive_web>



On Thu, Nov 7, 2013 at 9:20 AM, Simon Li <s.p.li at dundee.ac.uk> wrote:

> Some notes from our meeting yesterday:
>
> http://www.openmicroscopy.org/site/community/minutes/minigroup/omero-features-meetings/2013-11-06-omero-features-google-hangout
>
> Summary:
> We're thinking of representing features as a 2D array, with metadata
> stored as key-value maps attached to the array, or individual columns or
> rows. These keys could describe things such as the feature name (column),
> sample metadata (row), algorithm parameters, calculation pipelines, etc.
>
> This should work as an OMERO API- in order to retrieve features you'd pass
> in a set of key-value pairs, for instance to specify which features you
> want and which images/ROIs etc, and OMERO would handle the logic and return
> the feature table(s) matching those parameters. Since everyone has
> different requirements the keys could be anything, however we're trying to
> define a small set of standard keys- any suggestions are very welcome.
>
> Outside of OMERO we still need a format for transporting features, so
> we're thinking some form of HDF5.
>
> Simon
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
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