Squidpy · non-lab bundle Comprehensive toolkit for spatial single-cell analysis in Python with MCP DeepWiki integration. Use this skill when users need to: (1) Build and analyze spatial neighbor graphs from spatial coordinates, (2) Compute spatial statistics for cell types and genes (Moran's I, co-occurrence, neighborhood enrichment), (3) Analyze tissue images and extract image features, (4) Identify spatial niches using neighborhood profiles, UTAG, or CellCharter algorithms, (5) Perform ligand-receptor interaction analysis, (6) Read spatial omics data from various platforms (Visium, MERFISH, CosMx, Xenium) using squidpy.read or spatialdata_io, or (7) Visualize spatial data and analysis results.
