<div dir="ltr">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).<div>
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<a href="https://docs.google.com/a/broadinstitute.org/file/d/0Bzg4PoGEku2FTFFBS0ZsZTFoSXc/edit?usp=drive_web" target="_blank" style="display:inline-block;overflow:hidden;text-overflow:ellipsis;white-space:nowrap;text-decoration:none;padding:1px 0px;border:none;width:100%"><img style="vertical-align: bottom; border: none;" src="https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png"> <span dir="ltr" style="color:#15c;text-decoration:none;vertical-align:bottom">Ljosa_JBiomolScreen_2013.pdf</span></a></div>
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<a href="https://docs.google.com/a/broadinstitute.org/file/d/0Bzg4PoGEku2FLVZkTEZqUDJ5X1k/edit?usp=drive_web" target="_blank" style="display:inline-block;overflow:hidden;text-overflow:ellipsis;white-space:nowrap;text-decoration:none;padding:1px 0px;border:none;width:100%"><img style="vertical-align: bottom; border: none;" src="https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png"> <span dir="ltr" style="color:#15c;text-decoration:none;vertical-align:bottom">Ljosa_JBiomolScreen_2013_supplement.pdf</span></a></div>
<br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Nov 7, 2013 at 9:20 AM, Simon Li <span dir="ltr"><<a href="mailto:s.p.li@dundee.ac.uk" target="_blank">s.p.li@dundee.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Some notes from our meeting yesterday:<br>
<a href="http://www.openmicroscopy.org/site/community/minutes/minigroup/omero-features-meetings/2013-11-06-omero-features-google-hangout" target="_blank">http://www.openmicroscopy.org/site/community/minutes/minigroup/omero-features-meetings/2013-11-06-omero-features-google-hangout</a><br>
<br>
Summary:<br>
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.<br>
<br>
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.<br>
<br>
Outside of OMERO we still need a format for transporting features, so we're thinking some form of HDF5.<br>
<br>
Simon<br>
<br>
<br>
The University of Dundee is a registered Scottish Charity, No: SC015096<br>
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</blockquote></div><br></div>