Refining base repo

[heylf]

Describe your changes

Refining the base repo. Filling in also the data_processor stuff.

Checklist before requesting a review

• I have performed a self-review of my code

• Check the correct box. Does this PR contain:

  • Breaking changes
  • New functionality
  • Major changes
  • Minor changes
  • Bug fixes

• Proposed changes are described in the CHANGELOG.md

• CI Tests succeed and look good!

[heylf]

I still try to figure out the cli of openproblems. So I did the PR without proper local testing.

[heylf]

Seems to fail now at the point again where spatialdata object is created for cellpose. So the dataprocessor is kinda done.

[rcannood]

For process_dataset, the logs say:

AssertionError: File 'output_spatial_dataset.zarr' is missing images['image']

Is it expected that the output doesn't have an image, as requested by the api? https://github.com/openproblems-bio/task_spatial_segmentation

[heylf]

Yeah, I did some weird stuff. I made now the proper change and commented out, because so far I dont fully know if the spatialdata needs standard processing. Only the single cell data needs.