Single Omics Spatial Domain Identification

• Spatial Clustering Demonstration of Breast cancer (10xVisium)
  • Loading package
  • Loading data
  • The ground truth of breast cancer
  • Construct a neighbor graph and train PointNet++Encoder
  • We use mclust for clustering
  • The clustering result of breast cancer
  • Calculate supervision metrics ARI and NMI
• Spatial Clustering Demonstration of 12 Slices from the DLPFC Dataset(10xVisium)
  • Loading package
  • Loading and Pre-processing 151674 slice data
  • Ground truth of 151674 slice
  • Constructing neighbor graph and training Pointnet++Encoder
  • Clustering with mclust ,Clustering results can be found in adata.obs['3d-OT']
  • 151674 clustering results
  • Quantitative evaluation of clustering performance
  • 151673 slice
  • 151675 slice
  • 151676 slice
  • 151507 slice
  • 151508 slice
  • 151509 slice
  • 151510 slice
  • 151669 slice
  • 151670 slice
  • 151671 slice
  • 151672 slice
• Spatial Clustering Demonstration of mouse visual cortex(Starmap)
  • Loading package
  • Loading and Pre-processing mouse visual cortex
  • The ground truth of mouse visual cortex
  • Constructing neighbor graph and training Pointnet++Encoder
  • Clustering with mclust ,Clustering results can be found in adata.obs['3d-OT']
  • The clustering result of mouse visual cortex
  • Quantitative evaluation of clustering performance