Zebrafish patterns simulated with stochastic length scales

We provide model simulations of wild-type, shady, nacre, and pfeffer zebrafish patterns generated using a modified version of the the agent-based model from "Volkening A and Sandstede B (2018) Iridophores as a source of robustness in zebrafish stripes and variability in Danio patterns. Nat. Commun. 9(3231)." These simulations were generated by choosing each length scale parameter in the model randomly per cell and per day from a normal distribution. The mean of the normal distributions was set to the default parameter value (presented in the aforementioned paper) for each parameter. We varied the standard deviation of the noise across the simulations and this information is stored in the file names. For example, WT_sigma_1 corresponds to stochastic wild type simulations with a standard deviation set to 1% the parameter means.

The shady patterns were generated by turning off cell birth for iridiopores; the nacre patterns were generated by turning off cell birth for melanophores; and, the pfeffer patterns were generated by turning off cell birth for xanthophores (see reference above for details). All simulations were run in MATLAB.

Each simulation output contains data in the form of .mat files. Within each .mat file are the cell locations of all cells across the simulation, an array that tracks the distances that the cells moved throughout the simulation, vectors containing the number of cells born/dead/present at each day of the simulation, and the x- and y-boundaries of the domain for each day of the simulations. The cell locations are stored in N X 2 X T arrays, where N is an upper bound on the total number of cells in the simulation, and T is the number of days that the simulation was run for. For example, cellsM(1:N_M,:,T) contains the x- and y-coordinates of the melanophore cells on the last day of the simulation. Similarly, cellsIl contains the cell coordinates of the loose iridophores, cellsId contains the cell coordinates of the dense iridophores, cellsXc contains the cell coordinates of the dense xanthophores, and cellsXsn contains the cell coordinates of the loose xanthophores.