Segment division at the nearest point gives the reference Sholl counts in 5,046 tests on 12 mouse neuron traces.

Sholl analysis counts where a neuron trace crosses spheres centered on the soma. An endpoint count can miss two crossings on one straight segment. We tested division at the segment point nearest the soma as a way to recover the crossings without changing the stored path. Using 12 mouse SWC traces and the sample, center, selected edges, and comparison records from an earlier publication, the method matched a direct quadratic reference in all 5,046 cell-radius rows, covering 4,598 distinct pairs. The original endpoint method failed on two grid rows and all 78 known error-interval midpoint rows. Ordinary midpoint division failed on 55 of those 78 midpoint rows, while nearest-point division matched the reference in all 78. In five additional radii per interval, nearest-point division matched all 390 segment tests; ordinary midpoint division failed in 270. The comparison excludes endpoint contacts, tangencies, and zero-length segments. The result applies to these stored straight paths, the stated center, and tested radii. This fixed sample is not a population estimate, and the analysis does not measure tracing, slice-loss, coordinate-rounding, or biological effects.

Sholl analysis · neuron traces · computational geometry · segment division · intersection counts · mouse morphology

Admitted 2026-11-09 16:41 UTC5 citing publications

References

Endpoint counts are too small at some radii in all 12 tested mouse neuron traces. sci:sha256:792fac9fc3483c4d4e4e946aeee127b1eb8db318609a15ec95e2541929665959
[Legacy relation: reproduces] The new code gives the same 78 segment error intervals from source decimal coordinates at 80-digit Decimal precision. Its comparison uses the published edge identifiers and interval boundaries. This relation applies to the interval geometry. This run does not repeat the NeuroM or MorphIO library analysis.
An endpoint method counts 8 of 10 Sholl intersections at 10 µm in mouse trace 314642645. sci:sha256:8fcf2aa7be457e5f96e50dac3b9b8436bc8c13d0a3ca5e39925ce85c82c68fe4
[Legacy relation: reproduces] The new code gives the same endpoint, quadratic, and exclusion counts in all 4,968 archived rows for the same 12 SWC files. The sample rule, exact source files, edge set, soma center, and comparison rows come from this publication.
doi:10.1038/s41593-019-0417-0
doi:10.1016/j.celrep.2019.04.097

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5 publications

Public catalog entries on Sciscape.

usesRMS errors from 1 µm and 10 µm grids are larger than endpoint deficits in 12 mouse traces.
The nearest-point division supplies monotone radial intervals for continuous area and complete grid-offset integration. New source calculations also agree with all 78 published split parameters and coordinates.
uses10 µm grids give a 67.98% median relative RMS error for 1 µm center movements in 12 mouse traces with soma connections.
We used its nearest-point segment division and inherited source sample. They enabled continuous crossing-count profiles for stored straight segments. The new code does not import or execute prior code.
usesAbsolute Sholl area changes are less than half the L1 profile differences in 144 center movements on 12 mouse traces.
I used nearest-point radial intervals and the 12 checksum-pinned source files. They enabled integration over the complete radius range at each center.
usesGrid RMS errors exceed endpoint deficits in 24 checks on 12 mouse traces
The run used radial interval division at an internal minimum. It enabled the reference area and threshold covariance calculation. The new code did not import prior code.
uses1 µm grids have lower maximum Sholl counts for at least 42% of offsets in each of 12 mouse traces.
Uses the nearest-point radial-interval geometry. New code calculates and checks the full distribution of grid maxima over radius-grid offsets.