16 Oct 2008
15 May 2009)
Tracking algorithm for cell motion and morphology
% Parameter file for Cmorph03.m
% Filename of avi stack to analyze
% The program will append the avi extension automatically.
% Enter any additional identifiers you want appended to the name of the
% output avi's and centroid matrix files
% Set the image feature desired to track based on. By default, the program
% thresholds the gradient of the image to detect edges. If track gradient
% is false, the program will invert and threshold the image itself.
% Input a point near the center of the cell to be tracked in the first
% frame. Pick this out of ImageJ, top/bottom matrix conventions accounted
% for in program.
% Specify whether the program should perform deconvolution while tracking
% Specify whether to correct for gain errors. Each should be in a *.mat
% file saved as Slope and Intercept. Program will append *.mat.
% Enter the beginning frame in the avi to use for tracking
% Input NaN, and the program will assume 1.
% Enter the ending frame to use for image tracking
% Input NaN, and the program will stop at the end or when the object
% goes off the screen.
% Enter the height of the image data (not including headers) in pixels
% Right now the program assumes there may be a header in the top of the
% vertical direction but no borders around the left and right edges
% If there is header data, indicate whether it is appended to the top of
% the images or bottom. " headertop = true " or " headertop = false "
% Enter whether you wish to reduce the program window when saving the
% output images to save on file size. If so, the tracking algorithm will
% limit the output to +/- 3 bead diameters. " reducewindow = true "
% or " reducewindow = false "
% Enter the approximate diameter of the bead in micrometers.
% Image resolution in pixels/um:
% Enter record speed in fps
% Compression setting to use for output. Pick 'indeo5' or 'none'.
% Indicate whether you would like encode shape data in the
% the generated movie file. If set to true, the program will show
% the major and minor axis with lines and adjust object coloring according
% to deformation. If false, it and coloring is on, it will highlight the
% object with orange so it is easy to follow
% Boolean variable indicating whether to apply a "blurring" filter while
% picking out edges. Sometimes helpful for weak signal situations or with
% ragged edges.
% Blursize is the nXn mask used for blurring. Choose an odd number if
% possible to keep the tracked area in the center of the object. If an
% even number is chosen, however, the tracking will still be good since
% frame-to-frame differences are important.
% In case the center of the bead registers as a bright ring, allow for
% these pixels to be zeroed out. Set the area limits here in pixels.
% When set to "true," this option may slow the program a bit.
% Maximum number of times at each threshold value to look for bead in image.
% If set greater than 1, the program will look at additional data points in
% the vicinity of the first guess.
% Indicate whether separate binary image or overlay is desired.