Tutorials

• SPACEc: Tissue extractor
  • Downscale CODEX images
  • Segment individual tissue pieces
  • Rename tissue number (optional)
  • Extract individual labeled tissue
• SPACEc: Cell Segmentation
  • Cell segmentation
  • Viusalizing the segmentation result
  • Save the segmentation result
• SPACEc: Signal Preprocessing
  • Filter cells by DAPI intensity and area
  • Normalize data
  • Remove noisy cells
  • Show the spatial distribution for size (Optional)
• SPACEc: ML-enabled cell type annotation (STELLAR)
  • Data Explanation
  • Training
  • Inspect the results
  • Single-cell visualzation
• SPACEc: ML-enabled cell type annotation (SVM)
  • Data Explanation
  • Training
  • Single-cell visualzation
• SPACEc: Clustering
  • Clustering
  • Single-cell visualzation
• SPACEc: Cellular Neighborhood Analysis
  • Cellular Neighborhoods analysis
  • Spatial context maps
  • Barycentric coordinates plot
• SPACEc:Distance permutation analysis
  • Identify potential interactions
  • Visualization
• SPACEc: Patch proximity analysis
  • Compute for proximal cells
  • Visualization
• SPACEc: Using TissUUmaps for interactive visualization
  • Instructions
  • Integrated use

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