/track-worms-using-scanner

Software for tracking centroid locations of Soybean nematodes (H. Glycines) in well plates under a scanner every hour for 24 hours and plot their behavior for different drug concentrations

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]
  • A Flatbed scanner to scan high resolution (atleast 1200 dpi) images of well plates containing worms and taken every hour for 24 hours.

It was tested on Windows 10.

Usage

(This software assumes that the wells have been already scanned and these images are stored in an images folder)

  • Clone this repo

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

  • Open Matlab and navigate to this cloned repo

  • To record worm positions, please run Matlab/Image_Analysis.m and select the images folder in the GUI

  • To calculate and plot the percent movement of the worms, please run Matlab/Motility_Analysis.m

License

This code is GNU GENERAL PUBLIC LICENSED.

Contributing

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