Version Compatibility

Reference examples tested with: anndata 0.10+, numpy 1.26+, pandas 2.2+, scanpy 1.10+, spatialdata 0.1+, 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 Data I/O

"Load my Visium spatial data" → Read spatial transcriptomics outputs (Visium, Xenium, MERFISH, Slide-seq) into AnnData objects with spatial coordinates and tissue images.

• Python: squidpy.read.visium('spaceranger_out/'), spatialdata.read_zarr()

Load and work with spatial transcriptomics data from various platforms.

Required Imports