[ome-devel] WellSample LSID (Cellomics )

[Josh Moore]

On Thu, Feb 23, 2017 at 5:17 PM, Jäälinoja, Harri Tapio
<harri.jaalinoja at helsinki.fi> wrote:
> Hi,

Hi Harri,


> I'm looking at
> https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/CellomicsReader.java
>
> and wondering where in the OMERO database can I find the info that is store here:
>
> MetadataStore store = makeFilterMetadata();
> ...
>       int fieldIndex = getField(file);
> ...
>         String wellSampleID =
>           MetadataTools.createLSID("WellSample", 0, wellIndex, fieldIndex);
>         store.setWellSampleID(wellSampleID, 0, wellCntr, fieldCntr);

The column `well_index` on `wellsample` contains this information.
This doesn't show up in the Hibernate object, but instead is the
position of the wellSample in the list Well.wellSamples.


> The point is that fieldIndex is read from the filename, and may be different than fieldCntr. For example if the fields are collected in a spiral pattern that does not start in the center, the first fieldIndex may be e.g. 50. OMERO plate viewer shows fieldCntr (or some index starting at 1). If I want to find individual original files that contributed to a field, I need to find this mapping from fieldCntr to the original field index.

You can also attempt to use omero.cmd.UsedFilesRequest:

https://github.com/openmicroscopy/openmicroscopy/blob/develop/components/blitz/resources/omero/cmd/FS.ice#L85

which will give you a list of files that match the particular series.
You can see an example of its usage here:

https://github.com/mtbc/omero-downloader/blob/dev_5_3/src/main/java/org/openmicroscopy/client/downloader/Download.java#L239


> Thanks, best regards,
> Harri

All the best,
~Josh