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).
Please refer to https://m2m.readthedocs.io/ for up-to-date installation & usage instructions and the API documentation.
- To install the tool, we recommend to use Anaconda. Once the source code is cloned / downloaded, open a terminal in the source code location and install it with
conda env create -f environment.yml
conda activate m2m
pip install -e .- To use the software, you then need to activate the Anaconda
m2menvironment. For example, to use the m2m web application:
conda activate m2m
streamlit run app/m2m_main_page.py- Mahdi Abou-Hamdan, Elise Cosenza, Sylvain Miraux, Laurent Petit, Joël Lefebvre, "Exploring the Allen mouse connectivity experiments with new neuroinformatic tools for neurophotonics, diffusion MRI and tractography applications," Proc. SPIE 12365, Neural Imaging and Sensing 2023, 123650A (14 March 2023); https://doi.org/10.1117/12.2649029