Tracking

This repo contains the source codes for tracking particles motion with Matlab.

This repo contains the source codes for tracking particles motion with Matlab. The program can process tracking with fluorescent OR dark filed movies (i.e., the objects should be brighter than the background) AND also phase contrast movies (i.e., the objects shoule be darker than the background).
The function can work with Matlab 2018a and should be OK with previous Matlab version (early to 2014a) too. In early Matlab, function imwrite may cause problems when saving an image into '.tif' stack with Windows OS.
Both '.tif' stack and '.nd2' NIS-Elements files are supported. If your movie (or images) are in another format, such as '.avi' or '.jpg', you can transform the movie into a '.tif' stack with ImageJ.
The movie should be in grayscale (uint16 or unit8). For '.nd2' file, the movie file should be in one series. Now the script use nd2reader to load '.nd2' file into Matlab. It also provied a Linux version at nd2reader-linux. If you are familar with with Bio-Format, you can change this repo to 'ND2withBioFormat' channel to do tracking with Bio-Format.