Installation

Downloads (atlas and Neuropixels Trajectory Explorer)

• Mouse: download the Allen CCF mouse atlas from https://osf.io/fv7ed/ *

*(note on where these files came from: they are a re-formatted version of the original atlas, which has been processed with this script)

• Rat: download the Waxholm rat atlas and unzip (https://www.nitrc.org/projects/whs-sd-atlas/)

• Download/clone this repository

The Neuropixels Trajectory Explorer can be run either as a standalone application or through MATLAB:

Option 1: Running as standalone application

• Install the software by running neuropixels_trajectory_explorer_installer.exe (also installs MATLAB runtime environment if not already installed - this does not require a MATLAB license and can be downloaded free by anyone)
• The first time the explorer is run, you will be prompted to select the folder where you installed the CCF atlas. Navigate to the folder with the atlas and hit 'ok'.

Option 2: Running through MATLAB

• Download/clone the NPY-matlab repository: https://github.com/kwikteam/npy-matlab (this is code to load the formatted CCF atlas)

• Add to MATLAB path: the folders with the atlas, the NPY-matlab repository, and this repository (File > Set Path > Add with subfolders... > select the downloaded folder (have to do this for each folder separately), then hit 'Save' and 'Close')

• The MATLAB Statistics toolbox and Image Processing toolbox are required to run the Neuropixels Trajectory Explorer: install these if not already installed

• Run the command in MATLAB:

Mouse:

neuropixels_trajectory_explorer

Rat:

neuropixels_trajectory_explorer_rat