Example 6: Spatial registration between two MERFISH hypothalamus sections.

• Run INSPIRE on adjacent MERFISH slices from mouse hypothalamic preoptic region
  • Import packages
  • Load data
  • Data preprocessing
  • Build spatial graph
  • Run INSPIRE model
  • Access spot representations, proportions of spatial factors in spots, and gene loading matrix
  • Spatial distributions of spatial factors in tissues
  • Spot representations
  • Porportions of spatial factors visualized on spot representations
  • Save results
• Analysis of spatial factors
  • Load results
  • Visualize proportions of spatial factors in cells on UMAP coordinates
  • Correspondence of spatial factors to cell types
  • Visualize cell typing result
• Spatially register the two MERFISH sections using rigid transformation with MNNs
  • Load results
  • Register section 1 onto section 2
  • Registration result visualization
  • Save result