Scene numbering in OMERO from multi-scene CZI files

Hi OME team,

We regularly image TMA (tissue micro-array) slides with a Zeiss Axioscan. The resulting CZI files store the individual TMA cores as Scenes. OMERO/Bio-Formats happily reads those Scenes but assign a numbering scheme that makes the ordering of the Scenes problematic. Two issues:

  • in Zeiss/ZEN the scene numbering starts with 1, while in OMERO the scene numbering starts with 0
  • the scene numbers being assigned there is no zero padding so the core order when displayed in OMERO is 0, 10, 11, 12, 13,…, 1, 20, 21, etc. instead of 0, 1, 2, 3, 4, etc. Would it be possible to zero-pad the assigned Scene numbers?

Thanks,
Damir

Hi @dsudar, if I have understood correctly this is the value set by Bio-Formats as the image name and displays as Scene #0, Scene #1 etc. I have opened a PR (https://github.com/ome/bioformats/pull/3610) to update these values based on your feedback.

Thanks @dgault. I’ll find a smallish example file with > 10 scenes and upload it for testing.
Cheers,
Damir

2 Likes

Hi @dgault, I’ve just uploaded a czi file (TMA101_HE.czi) that has 37 Scenes. No confirmation from the QA uploader yet. Hopefully this will serve to test your PR and if it works well, I look forward seeing it in an upcoming Bio-Formats and OMERO release.
Thanks,
Damir

Thanks Damir thats a great help, looks like we got the file successfully. That fix should be available in the next Bio-Formats 6.6.0 release.