domains / families / science / spatial-analysis

spatial-analysis

separate

Analyze spatial cell-cell interactions, neighborhoods, and niches in IMC/MIBI data with squidpy and imcRtools, covering neighborhood-enrichment permutation nulls, the abundance-vs-density confound, inhomogeneous Ripley's K, cellular-neighborhood discovery, graph-construction (contact vs proximity), and edge effects. Use when testing whether cell types co-locate, choosing a spatial null, building a neighbor graph, discovering tissue niches, or deciding whether a spatial pattern is real or a density/segmentation artifact.

When to use

• testing whether cell types co-locate
• choosing a spatial null
• building a neighbor graph
• discovering tissue niches
• deciding whether a spatial pattern is real or a density/segmentation artifact
• analyzing spatial cell interactions in IMC data
• testing cell-type co-location against an explicitly chosen null
• discovering recurrent niches

When not to use

• differential analysis between conditions

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