Brain Street View

Load, visualize, and analyze Allen Mouse Brain Connectivity Atlas data (Oh et al., Nature, 2014).

Available in both Python and MATLAB.

Installation

Python:

pip install brain-street-view

Or from source:

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: You need the Allen CCF atlas files accessible locally.

Contents

• Find and fetch connectivity data
• Plot 2D projections
• Plot 3D projections
• Plot injection sites
• Compare regions
• Threshold projections
• Striatum subregion analysis
• Example usage
• Contributing