Restore full scikit-image regionprops output for cell statistics (2D and 3D)#157
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Restore full scikit-image regionprops output for cell statistics (2D and 3D)#157
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Co-authored-by: Pablo1990 <[email protected]>
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[WIP] Restore cell statistics with all scikit features
Restore full scikit-image regionprops output for cell statistics (2D and 3D)
Mar 10, 2026
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The 3D branch of
_calculate_cell_statisticsonly computedareaandlabel, yielding ≤ 4 columns in the exported CSV. The 2D branch was also missingintensity_std.Changes
src/epitools/analysis/cell_statistics.py["area", "label"]to the full set ofregionprops_tableproperties valid for 3D images — shape descriptors (axis_major/minor_length,feret_diameter_max,solidity,extent, …), all centroid variants, inertia tensor, moments, intensity stats includingintensity_std. 2D-only properties (eccentricity,orientation,perimeter,perimeter_crofton) are explicitly excluded.intensity_std; removed staleTODOand dead commented-out entries.tests/test_cell_statistics.pytest_calculate_cell_statistics_2d_properties: asserts key 2D properties and neighbour columns are present.test_calculate_cell_statistics_3d_properties: asserts full 3D property set is present and 2D-only properties (eccentricity,perimeter,orientation) are absent.Original prompt
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