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PointillViz · Community Tools

The Tool Store

Spatial-analysis tools for PointillViz: each is one Python file and a manifest, published as a .pvtool bundle, and installing one adds a launcher to the Tools tab.

  1. Find a tool and read its page.
  2. Install it into PointillViz.
  3. Reopen a dataset: the tool is in the Tools tab.

Tools run in your own PointillViz viewer, never on this website.

  • From the viewer

    In the Tools tab, open Community Tools, then Browse Store. Read the tool’s code and press Install. A .pvtool file installs with Install from file.

  • From this website Coming soon

    Connect the store to your viewer, then press Install on a tool’s page.

Either way, the viewer runs the nine gates again before it installs.

Read the safety noteHow tools work · Docs

Tools

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12 tools published

  • Vector Field

    PointillViz reference tools

    Which way a quantity increases across the tissue, as arrows over the section. Gene, cell type or any annotation column — with every arrow that could be noise removed.

    • cells
    • vectors
    • series
    Verified: passed 9 of 9 gates v1.0.0 4 downloads

  • Tissue Permeability

    PointillViz community tools

    Which cells one cell type seals off from the rest of the tissue.

    • cells
    • series
    • table
    Verified: passed 9 of 9 gates v1.0.0 4 downloads

  • Spatial Scale Spectrum

    PointillViz community tools

    How clustered each cell type is, at every length scale.

    • cells
    • series
    • table
    Verified: passed 9 of 9 gates v1.1.0 4 downloads

  • Interface Coherence

    PointillViz community tools

    Whether two cell types meet along one front or in specks.

    • cells
    • matrix
    • series
    • table
    Verified: passed 9 of 9 gates v1.1.0 4 downloads

  • Cell-Type Percolation

    PointillViz reference tools

    Whether a cell type is one connected mass or many islands.

    • cells
    • series
    • table
    Verified: passed 9 of 9 gates v1.0.0 4 downloads

  • Ripley’s Cross-L Function

    PointillViz reference tools

    At what distance cell type B accumulates around cell type A.

    • series
    • table
    Verified: passed 9 of 9 gates v1.1.0 2 downloads

  • Local Cell Density

    PointillViz reference tools

    How crowded the tissue is around every cell.

    • cells
    • series
    Verified: passed 9 of 9 gates v1.1.0 2 downloads

  • Expression Hotspots (Getis-Ord Gi*)

    PointillViz reference tools

    Where one gene forms clusters of high or low expression.

    • cells
    • table
    Verified: passed 9 of 9 gates v1.1.0 2 downloads

  • Conditional Contact Odds

    PointillViz community tools

    How much one extra neighbour of type B changes the odds a cell is type A, holding every other type’s neighbour count fixed.

    • cells
    • matrix
    • table
    Verified: passed 9 of 9 gates v1.0.0 2 downloads

  • Neighborhood Composition & Mixing

    PointillViz reference tools

    How mixed each cell’s neighbourhood is, and who sits next to whom.

    • cells
    • matrix
    • table
    Verified: passed 9 of 9 gates v1.1.0 1 download

  • Categorical Chords

    PointillViz community tools

    Explore spatial contacts or shared membership between categorical annotations with count-weighted ribbons and enrichment colors.

    • chord
    • matrix
    • table
    Verified: passed 9 of 9 gates v1.0.0 1 download

  • Cell-Type Co-occurrence

    PointillViz reference tools

    Which cell types are found near each other more often than expected by chance.

    • matrix
    • table
    Verified: passed 9 of 9 gates v1.2.0 1 download

From the Tools tab to the tissue

Vector Field 1.0.0 · Xenium 5K · mouse colon · 135,232 cells

The Tools tab in PointillViz: the Community Tools group, 12 installed, and its first launchers, starting with Categorical Chords, each with the tool’s artwork, author and version.
Tools tabOnce installed, a tool is a launcher in the Tools tab of each dataset that has what it needs.
Vector Field run on a Xenium 5K mouse colon section: cells coloured by the local mean of Epcam, white arrows along its gradient, and the whole section with the enlarged field boxed.
ResultOnce run, it draws on the section: here the arrows of Vector Field along the gradient of local mean Epcam.

A tool is arbitrary Python

An installed tool runs on your machine with the privileges of whoever started the viewer, like any script you download. The gates report what a tool reaches for; they cannot stop it. “Verified” means the listed version passed every required gate when it was published, not that its code is safe. In PointillViz, Browse Store shows each tool’s code before you install it: read it.

Build & publish a tool

One Python file and a manifest, checked by nine conformance gates before the store lists it.

  1. bundle
  2. manifest
  3. entry
  4. imports, advisory
  5. fixture
  6. result
  7. determinism
  8. edge
  9. no_mutation