Version Compatibility

Reference examples tested with: scimap 2.0+, scanpy 1.10+, anndata 0.10+, squidpy 1.4+

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/MIBI/IMC multiplexed-imaging data" -> Turn a cell-by-marker protein-intensity matrix into phenotyped cells and spatial neighborhoods, while treating intensity as a continuous, confounded signal.

• Python: per-marker arcsinh/z-score transform -> spillover/batch correction -> scimap.tl.phenotype_cells() (gating) or scimap.tl.cluster() (clustering) -> squidpy.gr.nhood_enrichment()

Governing Principle

Protein intensity is continuous with antibody, batch, and staining confounds -- it is not a molecule count, and treating it like one is a category error that propagates through every downstream result.