[ome-devel] OMERO.features API development

[Simon Li]

Hi all

Now that OMERO 5.0 is out of the way, and OMERO.searcher and WND-CHRM are either released or very close to release, I think it's time to restart our OMERO.features discussions.

We got as far as the idea of a 2D table with any number of key-value pairs on each column and row, so for example each row could be as simple as (OmeroType: Image, OmeroId: 123), or in the case of features which are a function of multiple images or channels (OmeroType: Image, OmeroId: 123, Channel1: 0, Channel2: 3), etc. Columns could for example be (FeatureFamily: WndCharm, Feature: Zernike). Each table cell could either be a scalar or array. Retrieving features could be done by providing key-value pairs to be matched.

All of this is still up for discussion, especially since the implementation of this interface could be challenging and there's some redundancy/ambiguity. Just to be clear, the above is a conceptual description of how the API would appear to users, the actual back-end could be completely different.

Lee Kamentsky gave us a use case just before Christmas [1], Chris Coletta and Ivan Cao-berg are planning to summarise how they see WND-CHARM and OMERO.searcher fitting in. I know a few other people are interested in this discussion, so feel free to respond here or in the forums.

A few of us are planning to meet up at the OME Paris meeting- if you're interested drop me an email.

Thanks

Simon

[1] http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2013-November/002573.html


On 7 Nov 2013, at 14:20, 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
>
>
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