[ome-devel] OMERO.features API development

[Lee Kamentsky]

Hi Vebjorn,
Simon is trying to download the AZ dataset from JBS and found it to be
corrupted. I'd rather not start a 700gb download just to test. Did you
check to see if the files are accessible?

Simon, if you need the data, the most straightforward approach may be for
me to burn a CD and mail it. I think it would be a good dataset to test
what you do at scale.

--Lee


On Mon, Nov 11, 2013 at 12:51 PM, Simon Li <s.p.li at dundee.ac.uk> wrote:

>  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> 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).
>
>
>   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
>> _______________________________________________
>> ome-devel mailing list
>> ome-devel at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>>
>
>  <AZ_use_case.docx>
>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
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