Version Compatibility

Reference examples tested with: squidpy 1.4+, scanpy 1.10+, anndata 0.10+, matplotlib 3.8+

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 Visualization

"Plot expression / clusters / a score on my tissue section" -> Render per-feature values at their real spatial coordinates, optionally over the histology image, without inventing structure the assay did not measure.

• Spot/capture fork (Visium, Visium HD, Slide-seq): scanpy.pl.spatial or squidpy.pl.spatial_scatter WITH the dataset's scalefactors and a spot_size/size set to the real capture diameter.
• Imaging/FOV fork (Xenium, MERFISH/MERSCOPE, CosMx): squidpy.pl.spatial_scatter with shape=None for the cell/molecule point cloud, or polygon shapes for segmentation overlays, or a platform viewer (Xenium Explorer, napari, Vitessce, TissUUmaps).

Governing Principle

Plotting differs by the platform-class fork, and rendering choices can manufacture pattern that is not in the data.