Set rgb argument to auto-detect whether image channels are RGB

[aeisenbarth]

Following issue scverse/napari-spatialdata#150, the logic to decide whether channels should be visualized as RGB has been moved from the viewer napari-spatialdata to the parser in spatial-image, which in the case of RGB sets channel names to ["r", "g", "b"]. The default behavior of to_spatial_image is rgb=False (no change of channel names). That means in order to have the auto-detection as it was in the viewer, we now need to opt-in in the readers, either to auto-detect RGB (rgb=None) or explicitly enforce RGB (rgb=True).

This PR modifies readers to opt in for RGB detection, or explicitly set RGB (where the original data-format is known to always be RGB(A) with 3 or 4 channels).

[aeisenbarth]

Update:
Now spatialdata==0.2.2 (with scverse/spatialdata#587) includes spatialimage>=1.1.0, (with spatial-image/spatial-image#21).
I believe as soon as spatialdata-io is upgraded to spatialdata>=0.2.2, this PR will be ready to merge.

[LucaMarconato]

Thanks for the PR, merging soon!

Btw, I have implemented a more general approach so that users don't have to pass rgb=None: scverse/spatialdata#702, what do you think? Anyway, I'd merge this PR now so that users that install spatialdata-io from GitHub without updating spatialdata would still have the fix.

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 0% with 7 lines in your changes missing coverage. Please review.

Project coverage is 45.82%. Comparing base (54da345) to head (a76de1d).
Report is 175 commits behind head on main.

Files with missing lines	Patch %	Lines
src/spatialdata_io/readers/mcmicro.py	0.00%	3 Missing ⚠️
src/spatialdata_io/readers/_utils/_utils.py	0.00%	2 Missing ⚠️
src/spatialdata_io/readers/merscope.py	0.00%	1 Missing ⚠️
src/spatialdata_io/readers/steinbock.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #78      +/-   ##
==========================================
+ Coverage   35.91%   45.82%   +9.90%     
==========================================
  Files          19       22       +3     
  Lines        1715     2132     +417     
==========================================
+ Hits          616      977     +361     
- Misses       1099     1155      +56     

Files with missing lines	Coverage Δ
src/spatialdata_io/readers/codex.py	43.47% <ø> (ø)
src/spatialdata_io/readers/cosmx.py	18.93% <ø> (-0.15%)	⬇️
src/spatialdata_io/readers/visium.py	19.67% <ø> (-1.17%)	⬇️
src/spatialdata_io/readers/xenium.py	71.79% <ø> (+49.31%)	⬆️
src/spatialdata_io/readers/merscope.py	24.06% <0.00%> (-0.94%)	⬇️
src/spatialdata_io/readers/steinbock.py	42.22% <0.00%> (ø)
src/spatialdata_io/readers/_utils/_utils.py	42.62% <0.00%> (+15.53%)	⬆️
src/spatialdata_io/readers/mcmicro.py	15.92% <0.00%> (ø)

... and 3 files with indirect coverage changes

[LucaMarconato]

In merfish I replaced rgb=True with rgb=None, I think it was a typo. Merging.