Inquiry about omexml.py related to schema location

[icaoberg]

imctools/imctools/external/omexml.py

Line 58 in 8983b97

xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2013-06 http://www.openmicroscopy.org/Schemas/OME/2012-03/ome.xsd">

• Why are you referencing to 2 difference schemas in the line above?
• Is it necessary to use an older OME model schema? Could you update this to generate images using a newer schema, e.g. 2016?

[votti]

Thanks for pointing this out!

This part from the imctools v1 release is a verbatim copy from the python-bioformats library at the time (included via copying as python-bioformats comes with a tricky dependency on Java).

I think one needs to ask the python-bioformats maintainers why they referenced two schemas.

Checking it now I saw that they actually did fix this bug in the meanwhile and we just missed to update it in imctools :/

The current supported version of imctools v2 does not depend on this code any more but on the ome.xml generation of xtiff that already use the 2016 version of the schema:
https://github.com/BodenmillerGroup/xtiff/blob/d0a7b5cf2626aaa8cdb3a1f6403d8edd9353c782/xtiff.py#L43

Thus I would suggest to move your workflow to imctools v2.
I will also discuss with my colleagues if we still want to fix this for v1.

[jwindhager]

v1 is not supported anymore