Fig. S9.

Cell tracking and quantification parameter estimation. (A and B) Parameter search for alignment window length and size. (A) Mean nematic alignment strength for all runs when calculated using the given time window and search radius. (B) Mean number of runs used to calculate the nematic alignment strength for each run. (C) Progression of variable values for cell tracking calculated using bootstrapping. Asterisks show SD of the difference between predicted and measured cell position $\left({\sigma }_{\delta }\right);$ open circles show SD of the difference between predicted and measured cell position $\left({\sigma }_{\mathrm{\Delta }\theta }\right);$ crosses show mean difference between predicted and measured cell position in x and y directions. (D) Transition probabilities estimated using trajectories from manually assigning trajectory segments as forward, reverse, or nonpersistent movement models. Lines of the same color indicate transition probabilities calculated for forward and backward movement models for continuing persistent movement (red), reversing direction (green), transitioning from nonpersistent to persistent (black), and transitioning from persistent to nonpersistent (blue). Cyan line indicates probability of continuing nonpersistent movement. Crosses indicate values used in transition matrix $\pi .$ (E) Error between the transition probabilities estimated using trajectories with manually assigned movement models and that estimated using a Markov chain after a lag of t images. Colors indicate continuing persistent movement (red), reversing direction between the two persistent types (green), transitioning from nonpersistent to persistent (black), transitioning from persistent to nonpersistent (blue), and continuing nonpersistent movement (cyan).