[ome-devel] WellSample LSID (Cellomics )

[Jäälinoja, Harri Tapio]

Hi,

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 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.

Thanks, best regards,
Harri

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Harri Jäälinoja
Light Microscopy Unit
Institute of Biotechnology
University of Helsinki