BrainReg - Brain Atlas Registration GUI

BrainReg is a high-performance MATLAB-based graphical user interface designed for precision semi-automated registration of Power Doppler and Photoacoustic imaging datasets with the Allen Brain Atlas.

Prerequisites

• MATLAB R2022a or later
• Image Processing Toolbox

Installation

1. Clone this repository to your local machine.
2. Add the directory and subfolders to your MATLAB path:

   addpath(genpath('brainRegistration'));

Quick Start

1. Run BrainReg in the Command Window.
2. Choose your dataset from the "Workspace Variable" dropdown.
3. Use the navigation and registration panels to align the atlas overlay with your imaging data.
4. Once satisfied, click Save JSON for record-keeping and Export Atlas to use the alignment in your scripts.

Acknowledgments

This tool utilizes data and templates from the Allen Mouse Brain Atlas.

Allen Institute for Brain Science (2011). Allen Reference Atlas – Mouse Brain [brain atlas]. Available from atlas.brain-map.org.

For studies utilizing the Common Coordinate Framework (CCFv3), please also cite:

Wang, Q., et al. (2020). "The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas." Cell 181(4): 936-953.