Spatial Transcriptomics with OmicVerse

This skill covers spatial analysis workflows organized into three stages: Preprocessing, Deconvolution, and Downstream Analysis. Each stage includes the critical function calls, parameter guidance, and common pitfalls.

Defensive Validation: Always Check Spatial Coordinates First

Before ANY spatial operation, verify that spatial coordinates exist and are numeric:

# Required check before spatial analysis
assert 'spatial' in adata.obsm, \
    "Missing adata.obsm['spatial']. Load with ov.io.spatial.read_visium() or set manually."
# Cast to float64 to prevent coordinate precision issues during rotation/cropping
adata.obsm['spatial'] = adata.obsm['spatial'].astype('float64')

Stage 1: Preprocessing

Crop, Rotate, and Align Coordinates