This is an application that can be used to track particles with a series of images. It uses algorithms adopted from the The Matlab Particle Tracking Code Repository.
Right now the program does not support videos yet, so you'll have to take your video and split it into individual frames.
Convert your images to .png format and put them all in the same folder.
Take a look at default_config.m which shows the values of the parameters I used in my analysis. Take a look at this link to get a better understanding of what the parameters are all about. Once you're set, put a copy of this file and name it config.m and put it in the same folder as your images.
Now, run main.m in MATLAB to get started. It will ask you where the images are placed. Navigate to it and select it.
If everything goes well, the program will let you know and ask if you'd like to animate the results. Hopefully, your results look something like this:
If it fails then you'll have to adjust the parameters in your config.m through trial and error. It can be a fairly painful process. Good luck!