linum-m2m : LINUM's Meso to Macro Toolkit

A collection of tools to work with both mesoscale brain data (e.g. the Allen Mouse Brain Connectivity Atlas) and with macroscale brain data (e.g. diffusion MRI acquisitions). These tools were first developed by Mahdi Abou-Hamdan during his 2022 summer internship in both the LINUM lab at UQAM (Canada) and the GIN-IMN at Université Bordeaux (France).

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📖 Full documentation: https://m2m.readthedocs.io/

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Quick Installation

Option 1: Docker (Recommended)

The easiest way to use m2m - no Python installation needed! Pre-built images are available on Docker Hub.

Using docker-compose (with web interface):

# Clone the repository
git clone https://github.com/linum-uqam/m2m.git
cd m2m

# Create data directories
mkdir -p data/input data/output

# Start with Docker Compose
docker-compose up

# Access the web interface at http://localhost:8501

Using the pre-built image directly:

# Run m2m scripts
docker run --rm \
  -v $(pwd)/scripts:/scripts:ro \
  -v $(pwd)/data:/data:rw \
  linumuqam/m2m:latest \
  python /scripts/m2m_download_template.py --help

# Or launch the web interface
docker run -p 8501:8501 \
  -v $(pwd)/data:/data \
  linumuqam/m2m:latest

Option 2: Local Python Installation

For development or if you prefer local installation:

# Clone the repository
git clone https://github.com/linum-uqam/m2m.git
cd m2m

# Create and activate a virtual environment (Python 3.9, 3.10 or 3.11)
python3.11 -m venv .venv
source .venv/bin/activate  # On Windows: .venv\Scripts\activate

# Install the package
pip install --upgrade pip
pip install -e .

Launch the web interface:

streamlit run app/m2m_main_page.py

Use the Python API:

import m2m
# Your code here

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Requirements

• Docker: No Python installation required (Option 1)
• Python 3.9-3.11: Python 3.11 recommended (Option 2)
  • Python 3.12+ is not supported due to AllenSDK dependency constraints

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Getting Help

• Documentation: https://m2m.readthedocs.io/
• Issues: https://github.com/linum-uqam/m2m/issues

Reference

• Abou-Hamdan, M., Cosenza, E., Miraux, S., Petit, L. et Lefebvre, J. (2023). Exploring the Allen mouse connectivity experiments with new neuroinformatic tools for neurophotonics, diffusion MRI and tractography applications. In SPIE Photonics West 2023 (vol. 12365, p. 123650A-123650A‑10). https://doi.org/10.1117/12.2649029