Steps from start to finish for the pose estimation and behavioural clustering analysis in Huang-&-Milton-et-al-2022 🐁

Overview

This repository contains the codes and steps used to analyse the pose estimation and behavioural clustering data and create figures for PhenoSys eLife 2022.
The following files are also needed to follow these steps:

• The example import and export files folder.
• The DeepLabCut project folder, which is used to predict the locations of the rodent body parts over time.
• The B-SOiD project folder, which is used to predict the rodent behaviours over time.

Click here to see the full steps for analysis and plotting.
For the complete list of videos that we used, please contact the authors.

Installation

FFMPEG

Follow the steps here to install FFMPEG.
This is used for the video pre-processing.

R

Follow the steps here to install the packages and DLCAnalyzer repository.
I recommend using RGui for the IDE. This is used for generating the zone analysis results.

Python

Follow the steps below to install the packages needed to run these codes.
Most of the analysis and plotting is done in Python.
If you want to use the DeepLabCut and B-SOiD project folders, also install DeepLabCut and B-SOiD.

Install Anaconda Navigator.
Open Anaconda Prompt (on Mac open terminal and install X-Code when prompted).
Download this repository to your home directory by typing in the line below.

git clone https://github.com/Foldi-Lab/PhenoSys-data.git

Change the directory to the place where the downloaded folder is.

cd PhenoSys-data

Create a conda environment and install the dependencies.

conda env create -n PSD -f Python_dependencies.yaml

Close, reopen anaconda prompt and change the directory to the place where the codes are.

cd PhenoSys-data/Codes

Activate the conda environment.

conda activate PSD

Edit and run whichever codes you want to.

python Step_5_Prepare_zone_data_for_analysis.py
python Step_7_Add_row_info.py
python Step_8_Prepare_tracking_data_for_behavioural_clustering.py
python Step_10_Prepare_behavioural_data_for_plotting.py
python Step_11_Create_spider_plots_and_time_bin_heatmaps.py

Acknowledgements

Author:
Harry Dempsey (Andrews lab and Foldi lab)

Credits:
Laura Milton, Stephen Power, Claire Foldi, Zane Andrews, Karsten Krepinsky, Sarah Lockie, Kaixin Huang, Kyna Conn, Amelia Trice, Sheida Shadani

About the labs:
The Foldi lab investigates the biological underpinnings of anorexia nervosa and feeding disorders.
The Andrews lab investigates how the brain senses and responds to hunger.