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Masks have no plane identity (T/Z) #36

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@guijacquemet

Data-flow audit 2026-10-29 (H1), BLOCKER. At v0.3.1.

What happens:

  • masks.py:387-390 requires every mask to be 2D and checks only its Y and X size.
  • The manifest's masks entry (:114-123) records the image, type, path and source, but no t or z.

Failure, two ways:

  • One 2D mask paired with a 50-frame time-lapse or a Z-stack is accepted with no plane identity. A consumer would apply it to every plane, which guesses object identity across T and Z.
  • Per-plane masks (TYX/ZYX) are refused as mask_not_2d, although MorphoFeature's FovFiles supports masks with T and Z axes.

Fix: refuse a 2D mask for an image with more than one Z or T plane, unless the mask carries those axes. Record each mask's planes in the manifest, and accept masks with T and Z axes.

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