merscope reader remove invalid polygons

[ckmah]

Reading invalid polygons causes the Merscope reader to fail. This should be rare, but I have run into this in one of our my datasets.

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 33.33333% with 2 lines in your changes missing coverage. Please review.

Project coverage is 45.50%. Comparing base (54da345) to head (15f8f68).
Report is 206 commits behind head on main.

Files with missing lines	Patch %	Lines
src/spatialdata_io/readers/merscope.py	33.33%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #207      +/-   ##
==========================================
+ Coverage   35.91%   45.50%   +9.59%     
==========================================
  Files          19       22       +3     
  Lines        1715     2149     +434     
==========================================
+ Hits          616      978     +362     
- Misses       1099     1171      +72     

Files with missing lines	Coverage Δ
src/spatialdata_io/readers/merscope.py	24.44% <33.33%> (-0.56%)	⬇️

... and 9 files with indirect coverage changes

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• Flaky Tests Detection - Detect and resolve failed and flaky tests

[MathieuBo]

This commit seems to solve my issue reported here: #208

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

[ckmah]

This commit seems to solve my issue reported here: #208

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

Maybe something like:

if len(z_layer) == 1:
    geo_df = geo_df[geo_df[MerscopeKeys.Z_INDEX] == z_layer[0]
else:
    geo_df = geo_df[geo_df[MerscopeKeys.Z_INDEX] == 0

I assume the provided Merscope cell segmentation is performed only a single z plane, though I'm not familiar with how that's chosen.