Code to replicate the figures from Coen, Sit, et al--2023. Code comments and examples may be updated compared to the cited version on Zenodo.
The corresponding data is available here: https://doi.org/10.5522/04/22363180.v1
Once you have downloaded, unzip is such that you have a single directory containing the sub-directories for each mouse (PC011, PC012 etc.) and the two additional folders "XHistology" and "XSupData"
You should then change line 34 in the "helpers/+prc/pathFinder.m" function to match this directory
Requires the "Optimizaton toolbox" in MATLAB
First you need to install the python environment in src/environment.yml
conda env create -f environment.yml
then you need to install src as a package, change your directory to src and do
pip install -e .
The code to generate figures are in src/data/coen2023mouse
Raw data for reproducing analysis is available here: https://doi.org/10.5522/04/22363180.v1
And analyzed data is available here: https://doi.org/10.5522/04/24547576.v1
To generate plots, change paths to the directory where you downloaded and unzipped the data.