Code used in a manuscript by Jing-Jie Peng†, Beate Throm†, Maryam Najafian Jazi, Ting-Yun Yen, Rocco Pizzarelli, Hannah Monyer*‡, Kevin Allen*‡

Setting up

Clone this repository

cd ~
mkdir repo
cd repo
git clone https://github.com/PJJ19/Peng_et.al_2025_noInt.git

Download the data in Dryad

https://doi.org/10.5061/dryad.f7m0cfz80

Concatenate and merge the different sections

Combine files

cat folder.tar.gz.part.* > folder.tar.gz

Extract archive

tar -xzf folder.tar.gz -C /path/to/destination_directory

Setup python Environment

Python environment

Here's a step by step guide to implement the method:

Make sure you have Anaconda or Miniconda installed

First create your conda environment:

conda create -n my_custom_environment python=3.11.5

conda activate my_custom_environment

Install basic packages

conda install -c conda-forge pip ipython jupyter nb_conda ffmpeg

pip install -r requirements.txt

pip install statannotations==0.6.0

pip install seaborn==0.12.2

Note, you might run into a version dependency issue with statannotations and seaborn, ignore it for now, the functions we used did not have this conflict issue.

conda install Cython

Install spikeA

We recommend creating an empty folder to store the custom packages.

cd ~
mkdir repo

cd ~/repo
git clone https://github.com/kevin-allen/spikeA.git
cd ~/repo/spikeA
pip install -e ~/repo/spikeA
cd ~/repo/spikeA/spikeA/
python setup.py build_ext --inplace

Install autopipy

cd ~/repo
git clone https://github.com/kevin-allen/autopipy.git
pip install -e ~/repo/autopipy

Data analysis

The starting point of the analysis are in /Data_analysis

change the PROJECT_DATA_PATH in setup_project.py to the directory you extracted the file from Dryad. The code for each figure is in their corresponding folder.

Note: Some notebooks have if: in empty code blocks, I use this as code breakers for chunks of code to run when I press "Run all". You can skip to the code after the if: block.

Grid cell decoding method

For a step-by-step guide to our decoding method, check out: autopi_grid_cell_decoding_repo