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Differing channel names across images are only a warning (channels pooled by index) #37

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@guijacquemet

Data-flow audit 2026-10-29 (H1/H4), MAJOR. At v0.3.1.

What happens:

  • metadata.py:450-475 reports channel_names_differ as a warning only (contract §8).
  • Histograms are matched by channel index.
  • MorphoFeature (histogram_fit.py:240-246) turns its own channel names into indices and never compares them with the manifest's per-file channel_names.

Failure: image A has OME channel 0 "DAPI", image B has channel 0 "Actin". They are pooled as one channel, and MorphoFeature fits "DAPI" scaling on Actin pixels.

Fix: make differing channel names within one experiment an error. Consumers should check their channel names against the manifest's channel_names when these are present. I'll track the MorphoFeature side with its other findings.

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