Jazi_et.al_2023_noInt

This repository includes Python scripts and notebooks used to analyze data and generate figures for the manuscript from M.N.Jazi and colleagues, 2023, titled 'Hippocampal firing fields anchored to a moving object predict homing direction during path-integration-based behaviour.'

The analysis was performed on a computer running Ubuntu 20.04.

Clone this repository

cd ~
mkdir repo
cd repo
https://github.com/Mrymna/Jazi_et.al_2023_noInt.git

Data set

You will need to download the data set from the Dryad repository. You can use this link to find the dataset: https://doi.org/10.5061/dryad.crjdfn39x The data set is split into two files because of the large size of the data set. You can combine them in a Linux terminal using the following command.

cat Jazi_etal_2023_noInter_part1.tar.gz Jazi_etal_2023_noInter_part2.tar.gz > Jazi_etal_2023_noInter.tar.gz

Create your Python environment

The commands below allow you to set up a Python environment in which you should be able to run the scripts and notebooks provided in this repository. Create your environment.

mkdir ~/python_virtual_environments
python3 -m venv ~/python_virtual_environments/Jazi2023Env

Activate your environment and install the packages listed in the requirements.txt.

source ~/python_virtual_environments/Jazi2023Env/bin/activate
cd ~/repo/Jazi_et.al_2023_noInt
python -m pip install -r requirements.txt

Make venv available for jupyter notebook.

pip install --user ipykernel
python -m ipykernel install --user --name=Jazi2023Env

Run Jupyter Lab or Jupyter Notebook.

jupyter lab
# jupyter notebook

Install the spikeA and autopipy python packages

spikeA: https://github.com/kevin-allen/spikeA autopipy: https://github.com/kevin-allen/autopipy

Make sure your environment is activated and install the two packages.

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

cd ~/repo
git clone https://github.com/kevin-allen/autopipy.git
git checkout 91e6bf671731119f067a65ce7a97f00bbd427ed0
pip install -e ~/repo/autopipy

File description

/fig1/Figure1.ipynb and /fig2/Figure2.ipynb contain the code to generate the first two main figures plus the first 4 Extended data figures. These figures are generated from behavioral data located in the autopi_behavior_2021 dataset. /ExtDataFig5/Olfac_perMouse.ipynb is related to the control odour experiment and only includes behavioural data. The rest of the figures are generated from autopi_ca1. Some extended data figures were generated in the notebook related to its main figure.

1. Please, before running any code, change allDataPath in setup_path.py to the path where you cloned the data directory. Per default it is ~/repo/Jazi_et.al_2023_noInt/data/Jazi_etal_2023_noInter.

2. To generate the summary of the PathTpyes and instantaneous behavioural variables on each trial of all sessions, first run /trials/extract_trials.ipynb

3. You can now run the Jupyter notebooks related to each figure.