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

[Kai Schleicher]

Dear Ian, dear Mark,

Thank you very much for looking into this.

Since I unfortunately can not influce how the XML files is written by 
the Software and the company does not provide support any more, I think 
my best attempt will be to write a script that generates our own xml 
files that match the data.

I will use the nice example of yours and will try my own version of it.

Thank you again for your help,
Kai


On 07/31/2018 11:26 AM, Mark Carroll wrote:
> 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
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