Brain Street View¶
Load, visualize, and analyze Allen Mouse Brain Connectivity Atlas data (Oh et al., Nature, 2014).
Available in both Python and MATLAB.
📦 Source code: github.com/Julie-Fabre/brain_street_view
Installation¶
Python: (3.9–3.12). We recommend a fresh conda environment:
conda create -n bsv python=3.11
conda activate bsv
pip install brain-street-view
A venv works equally well, and plain pip install brain-street-view is fine if you
don’t want a dedicated environment.
Or from source:
conda create -n bsv python=3.11
conda activate bsv
git clone https://github.com/Julie-Fabre/brain_street_view.git
cd brain_street_view
pip install -e .
MATLAB: Clone the repository and add it to MATLAB’s path. Requires MATLAB >= 2019a. Also needs npy-matlab, brewermap, and prettify-matlab.
Both: The Allen CCF atlas files (~2.4 GB) are downloaded automatically the first time a plotting function is called and saved to your allen_atlas_path. You can also download them manually from figshare.