Neurons for infant social bonding in the mouse zona incerta

Authors

Yuexuan Li^1,2, Zhong-Wu Liu², Gustavo Santana^1,3, Ana Marta Capaz ⁴, Etienne Doumazane ⁴,Xiao-Bing Gao², Nicolas Renier ⁴, Marcelo O.Dietrich^*1,2,3

¹Laboratory of Physiology of Behavior, Department of Comparative Medicine, School of Medicine, Yale University; New Haven, 06520, United States of America
²Department of Comparative Medicine, School of Medicine, Yale University; New Haven, 06520, United States of America
³Department of Neuroscience, School of Medicine, Yale University; New Haven, 06520, United States of America
⁴ Laboratoire de Plasticité Structurale, Sorbonne Université, ICM Paris Brain Institute, INSERM U1127, CNRS UMR7225, AP-HP, 75013 Paris, France

*Corresponding Author

Overview

Analysis is done using Jupyter notebooks. You will need to have Jupyter or Jupyterlab installed on your machine.

Installation

Installation instructions

1. Install Miniconda on your machine https://docs.anaconda.com/free/miniconda/. On Mac you can use these commands in the terminal.

           mkdir -p ~/miniconda3
           curl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh -o ~/miniconda3/miniconda.sh
           bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3
           rm -rf ~/miniconda3/miniconda.sh
   

2. Install jupyterlab in the base environment with nb_conda_kernel

    conda install jupyter
   

3. Once Miniconda is installed create the environment used for nearly all notebooks in this repository by running from the command line.

    conda create -n env python=3.10
    conda activate env
   

4. Install the library needed to run the code by running pip install -e . while in the env environment.

Data

1. Demo data provided in the notebook folder.
2. Download data from Zenodo .

Notebooks

1. For each notebook, first update file path to data.
2. Next, check the versions of packages for reproductivity before running notebooks.