prog_JingjiePeng_2025

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

Python Environment

1. I installed the default Anaconda.

Get an updated link to the installation script from https://www.anaconda.com/products/distribution

You might have to adjust the name of the exact file.

cd ~/Downloads
curl -O https://repo.anaconda.com/archive/Anaconda3-2022.10-Linux-x86_64.sh
chmod u+xrw Anaconda3-2022.10-Linux-x86_64.sh
./Anaconda3-2022.10-Linux-x86_64.sh

2. Get Deeplabcut source code:

git clone https://github.com/DeepLabCut/DeepLabCut.git

3. Modify the DEEPLABCUT.yaml file I remove the [gui] from the DEEPLABCUT.yaml file and added seaborn.

emacs ~/repo/DeepLabCut/conda-environments/DEEPLABCUT.yaml

4. Install the DEEPLABCUT conda environment:

cd DeepLabCut/conda-environments
conda env create -f DEEPLABCUT.yaml

5. conda activate DEEPLABCUT
6. echo "conda activate DEEPLABCUT" >> ~/.bashrc
7. conda install -c anaconda ipykernel
8. python -m ipykernel install --user --name=DEEPLABCUT
9. conda install Cython
10. conda install -c conda-forge jupyterlab
11. Install spikeA (Don't install dependency, use conda to install them if needed)

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

12. Install autopipy

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

13. Install positrack2

The starting point for the analysis is in the README.md located in the behavior_only and electrophys_behavior directories.