SPACEc

This is SPACEc (SPatial Analysis for CodEX data).

Contents

• Overview
  • General outline of SPACEc analysis
  • Installation notes
    • Install
• 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: Clustering
    • Clustering via GUI
    • Single-cell visualzation
  • 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
    • Filter for most significant results
    • Visualization
  • SPACEc: Patch proximity analysis
    • Compute for proximal cells
    • Visualization
  • SPACEc: Using TissUUmaps for interactive visualization
    • Instructions
    • Integrated use
    • Interactive Catplot via the TissUUmaps viewer
• Contributions & Help
  • Issue Reports
  • Documentation Improvements
    • Docstrings
    • Tutorials
    • Read the Docs
  • Code Contributions
    • Submit an issue
    • Quickstart
    • Create an environment
    • Clone the repository
    • Implement your changes
    • Submit your contribution
    • Troubleshooting
  • Maintainer tasks
    • Releases
• License
• Authors
• Changelog
  • Version 0.1 (development)
• Module Reference
  • spacec package
    • Subpackages
    • Module contents

Indices and tables

• Index

• Module Index

• Search Page