Version Compatibility

Reference examples tested with: squidpy 1.4+, scanpy 1.10+, anndata 0.10+, scikit-learn 1.4+; BANKSY (banksy_py / R Banksy), BayesSpace 1.12+ (R), STAGATE/GraphST optional

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• R: packageVersion('<pkg>') then ?function_name to verify parameters

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Spatial Domain Detection

"Identify tissue domains in my section" -> Partition the tissue into spatially contiguous regions of homogeneous expression/composition, using BOTH transcriptional similarity AND spatial proximity, so the output is a region label per spot/cell that is spatially coherent.

• Python: squidpy.gr.spatial_neighbors for the graph, then a neighbor-augmented or graph-based domain method (BANKSY, STAGATE, GraphST)
• R: BayesSpace (spatialCluster), BASS, or Banksy

Governing Principle