Version Compatibility

Reference examples tested with: matplotlib 3.8+, numpy 1.26+, scanpy 1.10+, 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 Transcriptomics Pipeline

"Analyze my spatial transcriptomics data end-to-end" -> Orchestrate data loading (squidpy/scanpy), QC, normalization, spatial domain detection, deconvolution (cell2location), spatial neighbor analysis, cell-cell communication, and tissue visualization.

Complete workflow for analyzing Visium, Xenium, or other spatial transcriptomics data.

Workflow Overview