Zeiss .czi files are not recognized

[kwiechen]

I can upload Zeiss .czi whole slide image files but the image is not shown. Using QuPath these files are imported by Bioformats without problems. I have found a copy of bioformats_package.jar in the girder container. Is it deactivated by default?

Best regards,

Kai

[manthey]

We definitely handle most Zeiss czi files. Internally, we either use the openslide reader or the bioformats reader to handle them, depending on their compression settings. Are you on a recent version of the software? The bioformats package makes perioid releases, and some of them have improved handling certain czi files. I'd have to check their release notes, but please try updating to the latest version of the DSA to see if it resolves the issue.

[kwiechen]

I have used the minimal example: is it possible that java is missing there?

[kwiechen]

java is missing in the minimal example, so import via bioformats does not work. Using devops/dsa .czi import is OK.

There is a copy of bioformats_package.jar within the girder and the worker container. Is it possible to exchange bioformats with a custom version?

[manthey]

Yes, though if you install from the linux wheels from large_Image_wheels you'll get the most recent release of bioformats.jar. Otherwise, it needs to be located as per the python_bioformats package requirements (which I'd have to look up).