Particle tracking software
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II. Staff Sign-off Sheet (BMC)
III. Simulating Brownian Motion
IV. Microscope HowTo
VI. Particle tracking software
VII. Current Software
The particle tracking software
The particle tracker is implemented in Matlab (download). The first step in tracking is to filter the images in a movie to reduce noise. Then the particle tracker converts each image to bilevel (bright and dark) by comparing every pixel to a cutoff threshold. After this process, the particles in the image should be represented by groups of connected bright pixels. (It expects bright particles on a dark background. The software will invert your movie automatically, if necessary.) The tracker then removes any particles that are too small or touching an edge of the frame and estimates the center location of all remaining bright objects. An algorithm then stitches the particle centers into trajectories.
Using the particle tracking software
To get stared, run Matlab and change the current directory to your "BIO Lab Work" folder. Type: "ParticleTracking" and press return. Once the user interface window comes up, set the "Scale", "Timestep", and "Object Diameter" parameters according to the experimental conditions. The value of "Noise Diameter" characterizes the typical size of noise artifacts; 1 is usually a good value for CCD cameras. "Minimum Threshold" specifies the number of standard deviations above the average value of the image to set the cutoff value. Good values for this parameter are in the range of 2-10. Higher values seem to work better for the onion movies where there tend to be more background structures in the image. If you select the "Subtract Average" box, the average value of each pixel over the entire movie will be subtracted from every frame. This is useful in onion movies to subtract off the stationary background elements in the movie.
Click the "Load Movie" button and select the directory of the movie you want to process. Check all of your parameters and click "Process Movie" to run the tracker. Computed values are displayed in a text window. Additional computed values are available on the Matlab desktop in a variable called "particle". Type "particle{1}.averageVelocityX" for example to see the computed average velocity of particle 1 in the x direction.
