SpatialEngine

Pure Python spatial transcriptomics analysis.

Features

• Moran's I spatial autocorrelation
• SVG detection (FDR corrected)
• Spatial domain identification (k-means)
• Neighborhood enrichment (permutation)
• Spatial co-expression network

Usage

pip install squidpy scanpy matplotlib pandas numpy scipy
python spatial_engine.py

Results (Visium H&E mouse brain)

• 2688 spots, 2000 HVGs
• 1332 SVGs (padj<0.05), top: Mbp (Moran I=0.79)
• 7 spatial domains, max neighborhood z=71.3
• 704 co-expression edges