Fix: Fixed sampling bias in cell_boundaries by excluding endpoint#21
Merged
pcamara merged 1 commit intoCamaraLab:mainfrom Dec 10, 2025
Merged
Fix: Fixed sampling bias in cell_boundaries by excluding endpoint#21pcamara merged 1 commit intoCamaraLab:mainfrom
pcamara merged 1 commit intoCamaraLab:mainfrom
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Summary
This PR fixes a logic error in
src/cajal/sample_seg.pywhere the start and end points of closed cell boundaries were being sampled twice, creating duplicate pointsIssue
skimage.measure.find_contoursreturns closed loops where the first and last points are identical. The previous logic usednp.linspace(..., endpoint=True), which sampled this geometric vertex twiceImpact
The Fix
Updated the
np.linspacecall to useendpoint=Falsetreating the boundary as a periodic cycleVerification
I verified this locally with the dataset that was previously crashing
avg_shape_spt. The fix resolves the crash and prevents the division-by-zero error.Closes #20