fix: apply missing mm-to-µm conversion factor for PhysicalSizeZ#516
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Alpaca233 merged 1 commit intoCephla-Lab:masterfrom Mar 21, 2026
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self._physical_size_z_um was assigned self.deltaZ directly, but deltaZ is stored in mm (set via set_deltaZ(um)/1000). This caused OME-TIFF metadata to record PhysicalSizeZ 1000× too small (e.g. 0.0015 µm instead of 1.5 µm). Add * 1000 to convert mm → µm, consistent with the same pattern used elsewhere in the worker (e.g. z_piezo_um += self.deltaZ * 1000). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
maragall
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Pull request overview
Fixes Z-step metadata unit handling in MultiPointWorker so OME-TIFF (and Zarr) metadata reports PhysicalSizeZ in micrometers rather than millimeters.
Changes:
- Convert
deltaZ(stored in mm) to µm when computingphysical_size_z_umfor acquisition metadata. - Ensure
PhysicalSizeZmetadata uses a positive step size viaabs(deltaZ).
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| self._pixel_size_um = None | ||
| self._time_increment_s = self.dt if self.Nt > 1 and self.dt > 0 else None | ||
| self._physical_size_z_um = self.deltaZ if self.NZ > 1 else None | ||
| self._physical_size_z_um = abs(self.deltaZ) * 1000 if self.NZ > 1 else None |
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If NZ > 1 but deltaZ is 0 (possible since set_deltaZ() accepts 0), this will set physical_size_z_um / z_step_um to 0.0. A 0 Z step is generally invalid for OME metadata and also results in a 0 scale on the Z axis for OME-Zarr coordinate transforms. Consider guarding against this (e.g., set to None when abs(deltaZ) == 0, or validate earlier and prevent NZ > 1 with deltaZ == 0).
Suggested change
| self._physical_size_z_um = abs(self.deltaZ) * 1000 if self.NZ > 1 else None | |
| self._physical_size_z_um = ( | |
| abs(self.deltaZ) * 1000 if self.NZ > 1 and abs(self.deltaZ) > 0 else None | |
| ) |
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Summary
self._physical_size_z_umwas assignedself.deltaZwithout unit conversion.deltaZis stored in mm (viaset_deltaZ(um) / 1000), so OME-TIFF metadata was recordingPhysicalSizeZ1000× too small (e.g.0.0015 µminstead of1.5 µm).* 1000onmulti_point_worker.pyline 144 to convert mm → µm.self.z_piezo_um += self.deltaZ * 1000.Test plan
dz(um)inacquisition_parameters.jsonmatchesPhysicalSizeZin the OME-XML header of the output TIFF (e.g. set dz = 1.5 µm, confirmPhysicalSizeZ="1.5"in the metadata).🤖 Generated with Claude Code