15 May 2009
21 Dec 2009)
Multiparticle Tracking algorithm for cell motion and morphology
% Parameter file for MCShape03.m
% Filename of video stack to analyze, including extension
% If there is header data, indicate whether it is appended to the top of
% the images or bottom. " headertop = true " or " headertop = false "
% Enter the approximate diameter of the bead in micrometers.
% Enter the coefficient of variation in the diameter. Program will search
% for objects +/- 5 standard deviations in diameter. If left as NaN,
% program will default to object size +50 / -80% unless special sizing
% parameters are entered.
% Enter any special sizing guidlines for tracking. If left as NaN, program
% will use +50 / -20%
% Minimum threshold to search for objects in terms of fraction of maximum
% intensity (0-1). Enter 0 to search all the way, but if the image is
% noisy this may result in false object identification.
% Image resolution in pixels/m. If the video is interlaced, enter the
% camera pixel resolution and the program will perform the conversion on
% the deitnerlaced image stack.
% Enter record speed in fps
% Enter whether to deinterlace the video. Boolean true
% or false.
% 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. Alternatively, it
% will invert and threshold the image itself.
% Two options: trackgradient = true
% trackgradient = false
% 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
% Enter the integer height of the image data (not including headers) in
% pixels. The program assumes there may be a header in the top of the
% vertical direction but no borders around the left and right edges
% Enter NaN if the entire image is data.
% Compression setting to use for output. Pick 'indeo5' or 'none'.
% Indicate whether you would like to show the morphological line axes
% on the generated movie file
% Boolean variable indicating whether to apply a spatial mean "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.
% Boolean variable indicating whether to apply a spatial median filter
% The acceleration factor will speed the search by reducing the spacing of
% threshold levels to search the binary image for objects. Set equal to
% an integer. A factor of 1 is the default and provides the most sensitive