
PARTICLE DETECTION AND TRACKING GUI PROGRAM
BY OLEG POLYAKOV | PRINCETON UNIVERSITY | 2008 - 2013

This is the particle detection GUI program used to identify the individual particles and then tracking them.

NOTE: This program requires preprocessing in order to work!
You need to have a bandpassed image stack and a thresholded image stack
saved in the folder DATA_IN.

To generate the bandpassed image stack:
First you must take the 4-D stack of particle images and use a bandpass
filter, either one that you wrote yourself, or through ImageJ.
The parameters for the bankpass filter are usually the following
lower_bound = 1 pixel.
upper_bound = 8-10 pixels.
These bounds may be different depending on the type of image that you are
using.
Save this file in DATA_IN in the following format "filename_BP.tiff"
It is important that it has the string 'BP' in the filename!

To generate the thresholded binary image stack:
Take the bandpassed image stack and threshold it to create a binary image
stack. The threshold you use is up to you, but technically it should
include all the beads and exclude all the noise. It is OK for the beads
to be clumped up.

This algorithm works by first selecting breaking the data into clumps of
beads. Then it loops through all of the clumps, identifies how many 3D
intentisy maximums are in the clump, and then fits that number of gaussian
profiles to the clump.

You also need to indicate the parameters of the image stack, such as the number of Z slices, number of T slices, and the resulition of each image.