Example 5: Analysis of mouse whole-embryo slices across developmental stages.

• Run INSPIRE on whole-embryo slices across multiple developmental stages
  • Import packages
  • Data preprocessing
  • Load preprocessed data
  • Run INSPIRE model
  • Access spot representations, proportions of spatial factors in spots, and gene loading matrix
  • Save results
• Changes in proportions of spots covered by the identified organs and tissues across stages
  • Load results
  • Visualized the proportions of the embryo occupied by different spatial regions
• Analysis of the liver region identified by INSPIRE
  • Load results
  • Find differentially expressed genes in INSPIRE’s detected brain region III
  • Visualize the identified brain region III and the differentially expressed genes
• Analysis of INSPIRE’s identified brain region III
  • Load results
  • Find differentially expressed genes in liver
  • Visualize the identified liver region and the differentially expressed genes
• Analysis of the spatial factor related to choroid plexus and its associated gene signature
  • Load results
  • Spatial distribution of the spatial factor related to choroid plexus in embryos
  • Analyze the gene signature and identify genes associated with the spatial factor
• Analysis of the spatial factor related to smooth muscle cells and its associated gene signature
  • Load results
  • Spatial distribution of the spatial factor related to smooth muscle cells in embryos