Zebrafish data from alternative models

We provide comparative model simulations of wild-type zebrafish patterns generated using two alternative models based off of 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)."

Aternative model I has the following parameter values: B90(Id) = 115 um, B75(Id) = 25 um, Omega-long(Id) = 230 um, B90(Il) = 130 um, B75(ll) = 10 um, and Omega-long(Il) = 190 um, with all other parameters set to the default values in Volkening and Sandstede (2018). Alternative model II was simulated by removing the weak attraction of Xd cells to Id cells from the agent-based model of Volkening and Sandstede (2018). Patterns generated from alternative model II resemble the idefix mutation. All simulations were run in MATLAB, and we run 1000 model simulations per model.

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(:,:,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.