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 Preprocessing

"Preprocess my spatial transcriptomics data" → Calculate spatial QC metrics (genes/spot, mitochondrial fraction), filter spots by expression and tissue coverage, normalize, and select variable genes.

• Python: scanpy.pp.calculate_qc_metrics() → filter_cells() → normalize_total() on spatial AnnData

QC, filtering, normalization, and feature selection for spatial data.

Required Imports