/track-worms

Software for tracking Soybean nematodes (H. Glycines) and other nematodes in a video and calculates a variety of parameters

Primary LanguageMATLABGNU General Public License v3.0GPL-3.0

Software to track nematodes (H. Glycines) and analyze behavior at different drug concentrations

This software is written for our paper in Phytopathology: "Movement and Motion of Soybean Cyst Nematode, Heterodera glycines, Populations and Individuals in Response to Abamectin"

Requirments

Environment Setup

  • Download & Install [Matlab R2016a]
  • Install Image Processing Toolbox
  • Install supported video adaptors for imaging cameras (in our case Q-Imaging)

It was tested on Windows 10 and Mac OS X.

Usage

  • Clone this repo

    git clone https://github.com/ukalwa/track-worms.git
cd track-worms

  • Open Matlab and navigate to this cloned repo

  • To use our video recording software, please run Matlab/Video/Live_Segmentation.m

  • To segment and generate data of the worm from the video, please run Matlab/Video/Segmentation/Live_Segmentation.m

  • To analyze the data, please run Matlab/Analysis/calculate_parameters.m

License

This code is GNU GENERAL PUBLIC LICENSED.

Contributing

If you have any suggestions or identified bugs please feel free to post them!