README.md

Multi-ROI Animal Tracking and Attention Analysis

Usage

Clone the repository

git clone https://github.com/shankarchawla1776/multi-ROI-attention-tracking.git

To set up a virtual enviornment, run:

python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt

Configure the toml file:

[video]
filepath = # str: path to your video
frames = # str: number of frames in your video

[h5]
filepath = # str: path to your sleap h5 file

[rois]
count = # int: number of rois you want to define

[rois.names]
# for each roi:
roi_numbers = roi_name # int = str

[markers]
bout_marker = # marker to find bouts for 

[parmas]
bout_threshold = # theshold for a bout to be valid (s)

To run analysis, first run the ROI labeling GUI:

python3 src/main.py

This will output basic ROI analysis consisting of marker-ROI overlap in the project's main directory as a .csv file.