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Handle autofluorescence channels and pass through unknown image types#368

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MSHelm wants to merge 3 commits intoscverse:mainfrom
MSHelm:fix/macsima_handle_autofluorescence_channels
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Handle autofluorescence channels and pass through unknown image types#368
MSHelm wants to merge 3 commits intoscverse:mainfrom
MSHelm:fix/macsima_handle_autofluorescence_channels

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@MSHelm
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@MSHelm MSHelm commented Feb 5, 2026

Hi everyone,

this fixes #367

I added a dedicated entry for autofluorescence channels to IMAGETYPE_DICT. In addition to future proof this, the parser now passes through unknown image types that are not in the dictionary.

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codecov-commenter commented Feb 5, 2026

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 61.85%. Comparing base (d13a407) to head (7c0b3cd).

Additional details and impacted files
@@           Coverage Diff           @@
##             main     #368   +/-   ##
=======================================
  Coverage   61.85%   61.85%           
=======================================
  Files          26       26           
  Lines        3138     3138           
=======================================
  Hits         1941     1941           
  Misses       1197     1197           
Files with missing lines Coverage Δ
src/spatialdata_io/readers/macsima.py 93.66% <100.00%> (ø)
🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

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MSHelm commented Mar 19, 2026

Small bump for this PR @LucaMarconato if there is anything that you need in addition, let me know.

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macsima reader does not handle autofluorescence channels

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