SPACEc

This is SPACEc (SPatial Analysis for CodEX data).

Contents

General

• Overview
  • General outline of SPACEc analysis
  • In-depth introduction to SPACEc
  • Installation notes
    • Install
• API
  • spacec package
    • Subpackages
    • Module contents
• 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: Cell Segmentation - The effect of channel selection on segmentation
    • Cell segmentation
    • Perform segmentation
    • Viusalizing the segmentation result
  • SPACEc: Preprocessing - Signal Preprocessing
    • Filter cells by DAPI intensity and area
    • Normalize data
    • Remove noisy cells
    • Show the spatial distribution for size (Optional)
  • SPACEc: Preprocessing - Fluorescence spillover compensation
    • Load data
    • Run compensation
    • Visualize compensation results
    • Save the dataframes for further processing.
  • SPACEc: Clustering
    • Clustering
    • Single-cell visualzation
  • SPACEc: Clustering - GUI assisted
    • 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: 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: TissUUmaps for interactive visualization
    • Instructions
    • Integrated use
    • Interactive Catplot via the TissUUmaps viewer
• Examples
  • CODEX human healthy colon
    • Inspecting the dataset
    • Reproducing the cell type annotation
    • Getting insights into cell type distribution
    • Identifying spatial neighborhoods
    • Perform Cell-Cell distance analysis
  • CODEX human healthy intestine
    • Cell type composition
    • Vessel tracing
    • Patch proximity analysis
  • IMC Breast Cancer
    • Scatter plot
    • Cell type composition
    • Neighborhood analysis
    • Spatial context map
    • Barycentric coordinate plots
    • Patch proximity analysis
  • MERFISH Brain analysis
    • Scatter plot
    • Cell type composition
    • Neighborhood analysis
    • Spatial context map
    • Barycentric coordinate plots
  • MIBI-TOF human colorectal carcinoma
    • Scatter plot
    • Cell type composition
    • Neighborhood analysis
    • Spatial context map
    • Barycentric coordinate plots
    • Patch proximity analysis
  • Visium mouse brain
    • Clustering
    • Scatter plot
    • Cell type composition
    • Neighborhood analysis
    • Spatial context map
    • Barycentric coordinate plots

Other

• 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)

Indices and tables

• Index

• Module Index

• Search Page