[ome-users] Import plate data from the FEI MORE as screen in OMERO

[Mark Carroll]

Dear Kai,

> Both the image metadata and the xml file is supposedly compatible with
> the ome data model, but I did not yet find a configuration in which
> these images can be imported into OMERO as a plate/screen.

My previous response demonstrated a way to have the various field TIFFs
import together as a single plate test-plate.companion.ome. I figured I
should also more explicitly address the files you helpfully provided.

They do look like a good try at compliant OME-TIFF. I think the separate
image files are fine standalone. The most obvious issues we see are:

* In the XML files there are multiple channels with the same ID. Channel
IDs are defined by the ome.xsd file as unique keys. (In practice, OMERO
will unify identical ones on import.)

* The second XML file has no WellSample tags tying the field images to
plate wells.

* For a multi-file OME-TIFF, as in the example I provided, UUIDs and
filenames tie the XML file and the field image files together. The
provided XML files do not have a UUID, they do not name the image files,
nor do the image files reference their XML file by filename or UUID.

I suggest these as the first things to fix to make the plates more
compatible with Bio-Formats. You may have already noticed these issues
in comparing my working example with the ones from your acquisition
system. Good luck!

-- Mark

The University of Dundee is a registered Scottish Charity, No: SC015096