INSPIRE
v1.0.0
Tutorials
Example 1: Analysis of human dorsolateral prefrontal cortex (DLPFC) dataset.
Example 2: Analysis of mouse brain slices with complementary views.
Example 3: Analysis of mouse brain slices across distinct ST technologies.
Example 4: Analysis of mouse whole-embryo slices across distinct ST technologies.
Example 5: Analysis of mouse whole-embryo slices across developmental stages.
Example 6: Spatial registration between two MERFISH hypothalamus slices.
Example 7: Spatial registration between two STARmap PLUS hippocampus slices.
Run INSPIRE on STARmap PLUS slices from mouse hippocampus
Spatially register the two STARmap PLUS slices with rigid transformation
Evaluate Pearson correlation score and cell type accuracy score
Example 8: 3D reconstruction of mouse embryo by integrating multiple 2D slices.
Installation
INSPIRE
Tutorials
Example 7: Spatial registration between two STARmap PLUS hippocampus slices.
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Example 7: Spatial registration between two STARmap PLUS hippocampus slices.
Run INSPIRE on STARmap PLUS slices from mouse hippocampus
Import packages
Load data
Data preprocessing
Build spatial graph
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
Save results
Spatially register the two STARmap PLUS slices with rigid transformation
Load results
Find anchor cells (MNN cells across slices in the latent space)
Register slice 1 onto slice 2
Register slice 2 onto slice 1
Save result
Evaluate Pearson correlation score and cell type accuracy score
Load results
Calculate the scores