Tutorials

• Example 1: Analysis of human dorsolateral prefrontal cortex (DLPFC) dataset.
  • Run INSPIRE on the human DLPFC dataset
  • Calculate benchmarking scores
  • Perform spatial trajectory inference
  • Enrichment or depletion of spatial factors in cortical layers
  • Analysis of spatial factors and their associated gene signatures
  • Run INSPIRE on the human DLPFC dataset (12 sections)
• Example 2: Analysis of mouse brain slices with complementary views.
  • Run INSPIRE on the mouse brain slices with different views
  • Analysis of spatial factors shared among slices and their gene signatures
  • Analysis of spatial factors specific to one slice and their associated gene signatures
• Example 3: Analysis of mouse brain slices across distinct ST technologies.
  • Run INSPIRE on the brain datasets generated by Slide-seq V2 and MERFISH
  • Analysis of the Slide-seq V2 dataset only
  • Screen for cell-cell communication among the identified cortical layers
• 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
  • Analysis of spatial factors
  • Validate INSPIRE’s gene imputation capability
  • Impute gene expressions for seqFISH data from Stereo-seq data
  • Differentially expressed gene analysis based on measured and imputed genes
• Example 5: Analysis of mouse whole-embryo slices across developmental stages.
  • Run INSPIRE on whole-embryo slices across multiple developmental stages
  • Changes in proportions of spots covered by the identified organs and tissues across stages
  • Analysis of the liver region identified by INSPIRE
  • Analysis of INSPIRE’s identified brain region III
  • Analysis of the spatial factor related to choroid plexus and its associated gene signature
  • Analysis of the spatial factor related to smooth muscle cells and its associated gene signature
• Example 6: Spatial registration between two MERFISH hypothalamus sections.
  • Run INSPIRE on adjacent MERFISH slices from mouse hypothalamic preoptic region
  • Analysis of spatial factors
  • Spatially register the two MERFISH sections using rigid transformation with MNNs
• Example 7: Spatial registration between two STARmap PLUS hippocampus sections.
  • Run INSPIRE on STARmap PLUS sections from mouse hippocampus
  • Spatially register the two STARmap PLUS sections using rigid transformation with MNNs
  • Spatially register the two STARmap PLUS sections using rigid transformation with the ICP algorithm
• Example 8: 3D reconstruction of mouse embryo by integrating multiple 2D slices.
  • Run INSPIRE on multiple mouse embryo slices for 3D reconstruction
  • Reconstruct 3D model of the mouse embryo by spatially register adjacent 2D slices
  • 3D reconstructions of liver, heart, and a brain subregion that varies along the left-right axis
  • 3D spatially-resolved gene expression patterns
• Example 9: Analysis of mouse skin data undergoing wound healing
  • Run INSPIRE on the mouse skin sections
  • Analysis of spatial factors
• Example 10: Analysis of human breast cancer Xenium data, revealing microenvironment heterogeneity across tumor subtypes
  • Run INSPIRE on the human breast cancer Xenium sections
  • Spatial region identification in the human breast cancer data analysis
  • Analysis of spatial factors corresponding to myoepithelial subpopulations
  • Analysis of spatial factors corresponding to endothelial subpopulations