Feature: Infer OME-Zarr axes_units from BioImage.dimension_properties#58
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BrianWhitneyAI wants to merge 6 commits into
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Feature: Infer OME-Zarr axes_units from BioImage.dimension_properties#58BrianWhitneyAI wants to merge 6 commits into
BrianWhitneyAI wants to merge 6 commits into
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Add OmeZarrConverter._infer_axes_units, which reads real, file-sourced per-axis units from the reader-agnostic BioImage.dimension_properties surface and passes them to the writer, instead of forwarding the user-supplied axes_units passthrough unchanged. An explicit axes_units override still takes precedence. Readers that do not attach units leave them as None, in which case axes_units is omitted entirely rather than fabricated, preserving prior behavior for those formats. Part of #57 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
BrianWhitneyAI
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SeanDuHare,
aswallace,
kmitcham,
pgarrison and
toloudis
Make explicit that the converter already routes the reader's acquisition time interval into the level-0 T coordinate scale: BioImage.time_interval -> scale.T (seconds) -> physical_pixel_size[t] -> writer Axes scale, with the matching "second" unit flowing through _infer_axes_units. Document this in _infer_physical_pixel_sizes so the time path is not an implicit side effect of the spatial scale lookup. Add unit tests (no resource files; stubbed BioImage surface) locking in: - time interval -> T physical size (incl. sub-second, and default 1.0 when the file has no interval) - explicit physical_pixel_size / axes_units overrides win - file units attached from dimension_properties, and graceful omission when a reader attaches no units or exposes no dimension_properties Part of #57 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
BrianWhitneyAI
changed the title
kmitcham
approved these changes
Jul 2, 2026
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Summary
Resolves #57 Populate the OME-Zarr
axes_unitsfrom file-sourced per-axis units exposed through the reader-agnosticBioImage.dimension_propertiessurface.Related
🤖 Generated with Claude Code