System Requirements: MATLAB. The software was tested on MATLAB R2023b.

Installation: Download the repository from GitHub: https://github.com/Projectomics/MATLAB

Install time: Less than 10 minutes.

Instructions for use: Run main_menu_selector from the main folder.

Demo: All necessary files to run the software have been provided in the /data folder. Examples output files are found in the /output folder. The MOp6 data were randomized 1,000 times. The presubiculum data were randomzied 100,000 times.

The Janelia MouseLight data in /data/Mouse_Neurons/MouseLight-neurons/*.json, in /data/Mouse_Neurons/MouseLight_PRE_SWC_files/*.swc, and in /data/brainAreas.json are a static download of the NeuronBrowser data, which were frozen at the time of publication  [Wheeler DW, Banduri S, Sankararaman S, Vinay S, Ascoli GA. Unsupervised classification of brain-wide axons reveals the presubiculum neuronal projection blueprint. Nature Communications 2024 Feb 20;15(1):1555]. Mappings between neuron labels and DOI's are in /data/MouseLight_DOI_mappings.xlsx.

Licensing: The Janelia MouseLight data, which were downloaded from the database and NeuronBrowser, are made available for use under the CC-BY NC license (https://creativecommons.org/licenses/by-nc/4.0/legalcode). The accompanying Copyright License document applies to all other materials.