FlatST_Tutorial

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Contents:

• Setup of the FlatST environment
  • Build the pytorch framework and PyG
  • Download FlatST from github repository
  • Configure FlatST
• Tutorial 1: 10x Visium (DLPFC dataset)
  • Import the necessary modules
  • Set the necessary parameters
  • Run FlatST
  • Find the best-performing model
  • Draw the result
  • Match colors
  • Run_umap
• Tutorial 2: MERFISH dataset
  • Import the necessary modules
  • Run FlatST
  • Find the best-performing model
  • Draw the result
  • Match colors
• Tutorial 3: Denoising of FlatST
  • Import the necessary modules
  • Data preprocessing
  • Denoising
  • Screen specific genes
  • Compare with STAGATE
  • Draw the gene expression map
• Tutorial 4: 2D dataset
  • Import necessary modules
  • Read the clustered dataset
  • Calculate the overall IoU
  • Calculate the IoU of a single region
• Tutorial 5: 3D dataset
  • Data generation
  • calculate_iou_3d
  • plot_region_boundaries_3d
  • Run_FlatST