Version Compatibility

Reference examples tested with: anndata 0.10+, 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 Proteomics Analysis

"Analyze my CODEX/IMC spatial proteomics data" → Process multiplexed imaging data including cell segmentation, protein phenotyping, spatial neighborhood analysis, and protein colocalization scoring.

• Python: scimap.tl.phenotype_cells(), squidpy.gr.nhood_enrichment()

Data Loading

Goal: Process multiplexed spatial proteomics data (CODEX/IMC/MIBI) through cell phenotyping, spatial neighborhood analysis, and protein colocalization scoring.