Overview

This repository contains all the code required to generate figures for Kinsky, Orlin et al. (2024)

Setup

• This code utilizes several functions from https://github.com/nkinsky/FearReinstatement and https://github.com/diba-lab/NeuroPy. Clone the FearReinstatement and NeuroPy repositories in the same parent directory as the Eraser repo.
• Install a conda/mamba environment using mamba env create -f eraser.yml. You may need to add a few modules manually, e.g. mamba install -c conda-forge notebook to use Jupyter Notebook.
  • Follow instructions in the NeuroPy repository README file to install NeuroPy.
• Download processed neural and behavioral data for each mouse (a permanent repository is being set up).
  • Update SessionDirectories.csv file with the location of individual mouse data on your computer.
  • Update get_comp_name function in eraser_reference.py with locations of data folder and directory to plot things into
  • Download processed neural data for each rat in the Recording_Rats folder.
  • Download group data
• Update location of group data in subjects.py file
  • (You may have to add this path to a few notebooks directly as well)
• Run notebooks in Notebooks folder to generate figure panels.