1. Requirements

The following are needed for full functionality:

• Images of mouse brain slices (individually cropped or with multiple slices per image; coronal, sagittal, or transverse)
• Know the resolution (in microns per pixel) of these images
• A computer mouse with a scroll wheel
• MATLAB (R2017 on a Windows computer was used for all testing)
• This repository. Add all folders and subfolders to your MATLAB path. All user-oriented scripts are in the 'SHARP-Track' folder.
• The npy-matlab repository
• The Allen Mouse Brain Atlas volume and annotations (download all 4 files from this link)