Documentation

MSD

MSD calculations are carried out using vectorized numpy arrays. Calculations are carried out according to the formula <MSD> = (x-x0)^2 + (y-y0)^2. Video-wide geometric averages are also reported.

Hyak

MSD calculations can be parallelized using a computer cluster. An example implementation is provided here for use on the Shared Scalable Computer Cluster for Research (Hyak) at the University of Washington.

Visualization

Current visualization tools include a histogram plot of MSD/Diffusion distributions.