Importing into Matlab
Contents
Section titled “Contents”1. Before you jump into the rabbit hole
Section titled “1. Before you jump into the rabbit hole”You should read and attempt this only if you have already successfully learned how to track particles in ImageJ using the Mosaic software. If not here is a link to a page that will help you. Molecular Tracking.
Next you must then familiarize yourself with Matlab, and some basics on diffusion coefficients. Ilya has generated a page for this Introduction to Diffusion. The basics of diffusion have been worked out extensively and are outlined here in the first two chapters of “Random Walks in Biology” by Howard S. Berg.
2. Sample codes
Section titled “2. Sample codes”There are a couple main ways to export your data out of Mosaic. The first is to save your entire tracking summery. This gives the added benefit of saving the parameters that you used to link your data. However it also saves summaries of all the trajectories. Te first trajectory saved is the longest, and usually the trajectory of the particle whose path you wish to analyze. To export these data to Matlab and convert your trajectories into a matrix, use the following code written by Ilya. traj_read.m. This code only works if you have a summery file with one trajectorry and needs to be modified to handle text files with more than one trajectory.
The second way to export is to isolate your specific trajectory and save it as an excel spreadsheet. I (Max) have written a code that imports these excel files, graphs the X and Y trajectory, and calculates the diffusion coefficient. xcell_traj_read.m. Using this excell method has the benefit of isolating your specific trajectory, but if you have excessive qunatum dot bliking, it may be nessesary to manually stitch together separate tracking files.