Skeleton Analysis

Overview

The Skeleton Analysis package provides tools to process spatial graphs exported from Amira. It allows for the correction of collapsed vessels, extraction of topological metrics, and visualization of the processed networks.

Features

The package enables:

• Correction of collapsed vessels in spatial graphs
• Extraction of vascular and network metrics, including:
  • Topological Generation
  • Strahler Order
  • K-means Cluster Order
  • Tortuosity
  • Mean Radius
  • Murray’s Law
  • Branching Angle (between child vessels and parent-child connections)
  • Intervessel Length-Diameter Ratio
  • Branching Ratio
• Visualization of computed metrics in Amira
• Graph merging for combined analysis of multiple spatial graphs
• Detection and correction of bad edges
• Outlier correction for accurate metric computation

Installation

# Clone the repository from GitLab
git clone https://github.com/JosephBrunet/skeleton-analysis.git
cd skeleton-analysis

# Install skeleton-analysis
pip install .

⚠️ Warning: To avoid dependency conflicts, it's recommended to use a virtual environment

Usage

Step 1: Prepare Input Files

• Export your Amira spatial graph as an ASCII file.
• Identify the root node IDs using Amira.
• Save the spatial graph in .am format.

Step 2: Run the Ordering Script

from skeleton_analysis import run_ordering

input_file = "path/to/spatial_graph.am"
output_file = "path/to/output_graph.am"
run_ordering(input_file, output_file)

This process corrects the spatial graph and computes the Strahler Order and Topological Generation.

....

Contributing

Contributions are welcome! To contribute:

1. Clone the repository from GitHub.

   git clone https://github.com/JosephBrunet/skeleton-analysis.git

2. Create a feature branch:

   git checkout -b feature-branch

3. Commit your changes:

   git commit -m "Add new feature"

4. Push to GitHub:

   git push origin feature-branch

5. Create a Pull Request (PR)! 🎉

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Issues & Support

If you encounter any issues or have feature requests, please open an issue on GitLab.

License

This project is licensed under the MIT License.

Contact

For questions or support, feel free to reach out to:

• Claire Walsh – c.walsh.11@ucl.ac.uk
• Joseph Brunet – j.brunet@ucl.ac.uk

Thank you for using skeleton-analysis! --🚌