Local Cell Density

by PointillViz reference tools

How crowded the tissue is around every cell.

Verifiedv1.1.0

qc
density

cells
series
summary

k-th neighbour density map: a crowded epithelial band over loose stroma, cooling at the section edgeArtwork from the tool’s bundle

Readme

Answers the question: How densely are cells packed around each individual cell?

For each cell $i$ , the tool measures the distance $r_{i}$ to its $k$ -th nearest neighbour within the same section. This distance defines a circle in 2D or a sphere in 3D around the cell that contains its $k$ nearest neighbours. A smaller circle or sphere indicates more closely packed cells and therefore a higher local density. Local density is calculated as:

{density}_{i}

= \frac{k}{π r_{i}^{2}}

in 2D, and:

{density}_{i}

= \frac{k}{(4 / 3) π r_{i}^{3}}

in 3D.

Map. Each cell is colored by its local density: brighter colors indicate higher density, darker colors lower density, and unpainted cells have no result.

Plot. Cells are sorted by local density. The x-axis shows the percentage of cells, and the y-axis shows the corresponding density. A point at (80%, y) means that 80% of cells have a local density of y or lower, while 20% have a higher density. At 50%, the curve therefore shows the median density.

Parameters

Parameter	Type	Default	What it does
Neighbours (k)`k`	int, 3–50	10	Sets how many nearest neighbours are used to estimate local density. Larger values measure density over a broader area and produce a smoother result.
Scale`scale`	select, 2 options	log10 density	Sets whether density is shown directly or on a log10 scale.

Outputs

cellspaints the spatial view
seriesreturns a line chart
summarywrites a summary

Tool check

The nine gates this version passed when it was published.

Verified

Passed 9 of 9 gates

bundle pass
manifest pass
entry pass
imports pass, advisory
fixture pass
result pass
determinism pass
edge pass
no_mutation pass

bundle pass
4 files, 8.0 kB packed and 34.7 kB unpacked, plugin.json at the root.
manifest pass
local-density 1.1.0 by PointillViz reference tools; entry tool.py, outputs cells, series, summary, 120 s and 2048 MB budget.
entry pass
tool.py imported in 0.20 s and defines run(ds, params).
imports advisory pass
1 Python file, importing numpy; no network, subprocess, filesystem-write, dynamic-exec or environment use found.
fixture pass
ran on the 600-cell fixture in 0.28 s of its 120 s budget, returning summary, cells, series.
result pass
returned the declared outputs: summary, cells, series.
determinism pass
two runs with identical parameters produced byte-identical results (17.7 kB of JSON).
edge pass
ran at the minimum corner (k=3) in 0.28 s; ran at the maximum corner (k=50, scale='linear') in 0.29 s.
no_mutation pass
the fixture dataset's 4 files are byte-identical after every run (plugin_cache/, where ds.knn caches, is excluded by design).

Passed every required gate when this version was published. That is a statement about the gates, not about whether the code is safe to run.

Versions

v1.1.013 Oct 2026 latest
v1.0.020 Aug 2026

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