Kural Lab

TraCKer

TraCKer is a simple but fast two-dimensional (2D) particle tracking program. It uses a simple threshold determined over a Mexican hat filtered image for detection of fluorescent spots. Detected maxima are then connected in time by linking mutually nearest neighbors. The only required input is the path to the desired movie (2D multipage tiff). You will be prompted with a UI to determine an appropriate threshold for the supplied movie. The output is saved as a .mat file containing the position and intensity of the tracked spots. Additionally, there is a cell array of intensity values which can be input into the slope_finding program.

Slope Finder

The slope finder program determines clathrin coat growth rate distributions from intensity traces. It takes as an argument the cell array of intensity value output by TraCKer, the frame rate of the movie, and a global background value for the movie (i.e. the value of a signal with SNR=1). The output of this function is the slope of the intensity values after they have been normalized to the maximum intensity of that trace. The output is a cell array where each cell is the same length as the corresponding intensity cell. Since it is impossible to apply a consistent slope finding algorithm to the endpoints of the data, they are padded with zeros, so to form a proper slope histogram all zeros should be excluded.

Trace Library

The function named createTraceLibrary is used to group clathrin coat intensity traces into clusters that share similar trace lengths and intensity profiles. The similarity of traces is judged using the trace dist function, which generates a distance metric for each trace with respect to each other trace based on the Euclidian distance between them. Each cluster has an average intensity trace and an associated growth rate histogram. Once generated, this cluster can serve as a library to which future growth rate histograms can be compared using the library lookup function.