Faster spatial statistics

gustaveroussy / sopa

Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)

https://gustaveroussy.github.io/sopa/

BSD 3-Clause "New" or "Revised" License

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Faster spatial statistics #3

Closed quentinblampey closed 11 months ago

quentinblampey commented 12 months ago

Use shapely Polygons to describe connected components

quentinblampey commented 11 months ago

Done

Run Delaunay graph
Remove simplices in between niches
Create connected components (boundary simplex = less than 2 neighbors)
Join edges to make cycles
Creates shapely polygons
Clean low quality or small components
Run geopandas operations