Example 6: Spatial registration between two MERFISH hypothalamus slices.

• 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 slices with rigid transformation
  • Load results
  • Find anchor cells (MNN cells across slices in the latent space)
  • Register slice 1 onto slice 2
  • Register slice 2 onto slice 1
  • Save result
• Evaluate Pearson correlation score
  • Load results
  • Calculate the score