z_index = 0 for polygons in MERSCOPE

[LucaMarconato]

          This commit seems to solve my issue reported here: https://github.com/scverse/spatialdata-io/issues/208

Is there a reason why only polygons from z_index = 0 are kept? By default the reader select plane z=3.

Originally posted by @MathieuBo in https://github.com/scverse/spatialdata-io/issues/207#issuecomment-2358626502

[LucaMarconato]

@quentinblampey do you have any thought on this? (please see the linked discussion).

[pakiessling]

The Merscope on-board software only performs segmentation on one z-level and saves these polygons for z-indeces 0-6, using the vizgen postprocessing software users have the ability to segment every z-level separately.

I think it would make the most sense to default to the same z-level for polygons and images and give the user the option to choose which z-levels should be loaded.

[quentinblampey]

z_index = 0 was used because the polygons are duplicated for all z-indices. I was not aware of the possibility of segmenting every z-level using VPT, thanks for letting us know @pakiessling! In that case, I agree that it makes sense to let the user decide