Example 8: 3D reconstruction of mouse embryo by integrating multiple 2D slices.

• Run INSPIRE on multiple mouse embryo slices for 3D reconstruction
  • 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
• Reconstruct 3D model of the mouse embryo by spatially register adjacent 2D slices
  • Load results
  • Build the 3D model by spatially register adjacent slices
  • Save result
• 3D reconstructions of liver, heart, and a brain subregion that varies along the left-right axis
  • Load results
  • Liver
  • Heart
  • The brain subregion which varies along the left-right axis
• 3D spatially-resolved gene expression patterns
  • Load results
  • 3D expression of gene Afp in liver
  • 3D expression of gene Myl7 in heart
  • 3D expression of gene Neurod6 in brain