[ome-devel] OMERO.features API development

[Simon Li]

Thanks Lee.

The features set you calculated for that screen sounds like a good test of our infrastructure. However I'm having trouble downloading the supplementary data from:
http://jbx.sagepub.com/content/early/2013/09/09/1087057113503553/suppl/DC2

Data_S3_reproduce.zip is empty
Data_S2_database.zip seems to be corrupt

Does it look correct from your end?

Thanks

Simon



On 7 Nov 2013, at 20:55, Lee Kamentsky <leek at broadinstitute.org<mailto:leek at broadinstitute.org>> wrote:

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).


[https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png] Ljosa_JBiomolScreen_2013.pdf<https://docs.google.com/a/broadinstitute.org/file/d/0Bzg4PoGEku2FTFFBS0ZsZTFoSXc/edit?usp=drive_web>

[https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png] 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<mailto: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


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<AZ_use_case.docx>


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