Version Compatibility

Reference examples tested with: matplotlib 3.8+, numpy 1.26+, pandas 2.2+, scanpy 1.10+, scikit-learn 1.4+, scipy 1.12+, squidpy 1.3+

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

• Python: pip show <package> then help(module.function) to check signatures

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 spatial data" → Cluster spots/cells considering both gene expression and physical proximity to define anatomically coherent spatial domains.

• Python: squidpy.gr.spatial_neighbors() → Leiden clustering with spatial graph, or BayesSpace/SpaGCN

Identify spatial domains and tissue regions by combining expression and spatial information.

Required Imports