Worm_Tracker

This is a worm tracker used in Dr. Gourgou's research project. For more details, please visit:
Spatial learning, navigation and decision-making in C. elegans

Requirement

--Python 3
--Numpy
--Scipy
--Matplotlib
--Opencv

How to run

If tracking a worm inside a T-maze

/bin/bash python3 worm_tracker.py --input_dir[your video directory] --H[video height] --W[video width]

If tracking a worm on an opensurface, i.e. the clockwise / counter clockwise detection

/bin/bash python3 worm_tracker.py --input_dir[your video directory] --H[video height] --W[video width] --is_clock

If using IDE

You can change the command line in run_my_code.sh and run it in your IDE.

Results

Tracking a worm inside a T-maze

The tracker will generate a tracking video and a summary plot for each input video, some sample frames of the tracking video and a sample summary plot are shown below:

The worm is on the left side of the T-maze, and it's moving along the floor.

The worm is in the middle of the T-maze, and it's moving along the floor.

The worm is on the right side of the T-maze, and it's moving along the wall.

Summary plot

Tracking a worm on an opensurface

Summary plot 1

Summary plot 2

Feel free to change parameters and give feedbacks!