Meandros

Overview

Meandros is a specialized tool for analyzing and processing biological images, with a focus on axolotl limb development and regeneration studies. The software provides a comprehensive suite of tools for ROI detection, axis approximation, and statistical analysis.

System Requirements

• Python 3.8 or higher
• Git (for cloning the repository)
• Operating Systems supported:
  • Windows (with Git Bash or WSL)
  • Linux
  • macOS

Installation

Quick Start

1. Get the code (choose one option):

   a. Clone from GitHub:

   git clone https://github.com/RodCor/Meandros
   cd Meandros

   b. Download from Zenodo:

   • Download and extract the ZIP file
   • Navigate to the extracted folder

2. Run the installation script:

   # On Windows (using Git Bash)
   bash install_meandros.sh
   
   # On Linux/macOS
   ./install_meandros.sh

The installation script will:

• Check for Python installation
• Create a virtual environment
• Install all required dependencies
• Set up the necessary configuration

Manual Installation (Alternative)

If you prefer to install manually, you can:

1. Create a virtual environment:

   python -m venv .venv

2. Activate the virtual environment:

   # On Windows
   .venv\Scripts\activate
   
   # On Linux/macOS
   source .venv/bin/activate

3. Install dependencies:

   python -m pip install --upgrade pip
   python -m pip install uv
   python -m uv pip install .

Running Meandros

After installation, you can run Meandros using:

# On Windows (using Git Bash)
bash run_meandros.sh

# On Linux/macOS
./run_meandros.sh

Features

• ROI (Region of Interest) Detection
• Axis Approximation
• Statistical Analysis
• Data Export Capabilities
• Interactive Visualization

Troubleshooting

If you encounter any issues during installation:

1. Ensure Python 3.8+ is installed:

   python --version

2. Check if the virtual environment was created properly:

   # The .venv directory should exist
   ls .venv

3. Try removing the virtual environment and running the installation script again:

   rm -rf .venv
   bash install_meandros.sh

Citation

Publication

Arce, H., Ceccarelli, A.S., Córdoba, R.C. et al. Modeling proximalisation in axolotl limb regeneration. Sci Rep 15, 26839 (2025). https://doi.org/10.1038/s41598-025-10527-8

License

MIT License Copyright © 2025

Contact

For questions and support, please contact the Authors of the project.