Example 4: Analysis of mouse whole-embryo slices across distinct ST technologies.

• Run INSPIRE on the whole-embryo datasets generated by seqFISH and Stereo-seq
  • 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 embryos
  • Spot representations and spatial domain identification
  • Save results
• Analysis of spatial factors
  • Load data
  • Spatial distributions of spatial factors
  • Top ranking genes associated with the spatial factors
• Validate INSPIRE’s gene imputation capability
  • Import packages
  • Manually hold out six marker genes from the seqFISH dataset
  • Run INSPIRE model
  • Analysis of cell representations and spatial factors
  • Perform gene imputation
  • Validate the gene imputation result
• Impute gene expressions for seqFISH data from Stereo-seq data
  • Load results
  • Gene imputation
• Differentially expressed gene analysis based on measured and imputed genes
  • Differentially expressed gene analysis
  • Visualize the results