In2Research-2024

This repository contains the code written for the In2Research placement of @yousuf-adialwa20 in the Neuroinformatics Unit during the summer of 2024.

Summary

The overall goal of this project was to to use movement for the pre-processing and exploratry analysis of data acquired by the placement co-supervisor Shanice Bailey.

The dataset in question was acquired to investigate the social interaction between pairs of interacting mice and it consists of short videos. The videos had been processed with the pose estimation software DeepLabCut to extract the x, y positions of various body parts at each video frame.

The extracted bodypart positions across time - referred to as predicted pose tracks - were cleaned using movement and then various metrics were calculated to quantify aspects of the social interaction between the mice.

Setup

To run the code in this repository, including the jupyter notebooks, you will need to create a new conda environment with the required dependencies, which are listed in the environment.yml file.

To create the required environment, follow these steps:

1. Clone the repository and navigate to the repository folder:

   git clone https://github.com/neuroinformatics-unit/In2Research-2024
   cd In2Research-2024

2. Create the conda environment from the environment file and activate it:

   conda env create -n In2Research2024 -f environment.yml
   conda activate In2Research2024

Note that we have named the environment In2Research2024, but you can choose any name you like.

Beware that the environment specifically contains movement==0.0.19, because that's the version of the movement package that was used during the placement. If you are using newer versions of the package, some of the code may need adjustments, as the syntax is likely to have changed.