Example 3: Analysis of mouse brain slices across distinct ST technologies.

• Run INSPIRE on the brain datasets generated by Slide-seq V2 and MERFISH
  • Import packages
  • Load data
  • Data preprocessing
  • Build spatial graph and prepare node features for LGCN
  • 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 and spatial domain identification
  • Save results
• Analysis of the Slide-seq V2 dataset only
  • Load data
  • Follow Scanpy pipeline to perform spatial region identification
• Screen for cell-cell communication among the identified cortical layers
  • Load results
  • Visualize INSPIRE’s identified cortical layers
  • Screen for cell-cell communication