Mean-square-displacement analysis

Performs the mean-square-displacement (MSD) analysis of tracks in Imaris. Mean square displacement (MSD) analysis is a technique commonly used in colloidal studies and biophysics to determine what is the mode of displacement of particles followed over time. In particular, it can help determine whether the particle is: - freely diffusing; - transported; - bound and limited in its movement. On top of this, it can also derive an estimate of the parameters of the movement, such as the diffusion coefficient. This submission allows to do MSD analysis on tracks created with Imaris. It ships several analysis tools (MSD curves, average MSD curve, velocity autocorrelation), and two methods for drift correction adapted to typical use cases. This submission is made of 6 files:

• XTMeanSquareDisplacementFitter.m and XTMeanSquareDisplacementGrapher.m - These two files are the core extensions and are to be moved in the XTensions folder in the Imaris installation directory.
• importTracksFromImarisXT.m - This file is a dependency of the two files above and is to be moved in the same directory.
• msdanalyzer.m - This file is also dependency of the two main files above and is to be moved in the same directory. It actually contains the core of the calculation process, and can be used independently in MATLAB. It is fully documented in the URL attached to this submission.
• DiffusiveParticlesMovie.ims - This example movie contains numerically simulated diffusive particles, to test the accuracy of the MSD analyzer.
• MakeDiffuseParticleMovie.m - This is the MATLAB script that was used to generate the movie above.

For a full introduction to MSD analysis, I advise you to read the tutorial I wrote about MSD analysis, that is linked from this submission. It is solely based on MATLAB and uses only one of the file of this submission. However it is truly relevant if you want to get good insights on how the analysis works.