Version Compatibility

Reference examples tested with: cell2location 0.1.4+, scvi-tools 1.0+, scanpy 1.10+, anndata 0.10+, numpy 1.26+

RCTD/SPOTlight/STdeconvolve are R packages (spacexr, SPOTlight, STdeconvolve via Bioconductor); call them from R or via rpy2.

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

• Python: pip show <package> then help(module.function) to check signatures
• R: packageVersion('<pkg>') then ?function_name to verify parameters

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Spatial Deconvolution

"What cell types are in each spot?" -> Decompose a multi-cell capture spot into the fractions (or absolute numbers) of each cell type, using an annotated scRNA-seq reference as the basis.

• Python: cell2location (RegressionModel -> Cell2location), stereoscope/DestVI (scvi-tools), Tangram (tg.map_cells_to_space), STdeconvolve (reference-free, R)
• R: RCTD (spacexr::create.RCTD/run.RCTD), SPOTlight, SpatialDWLS (Giotto), CARD