Pattern features of zebrafish upon varying long-range interaction scale in melanophore cell birth

We provide summary pattern features of model simulations of wild-type, shady, and pfeffer zebrafish patterns generated using 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)."

The simulations were run by varying the inner radius parameter corresponding to the long-range interaction scale in melanophore cell birth from 10 to 400 um in increments of 25 um (default parameter value from the model is 210 um). We ran 100 simulations under each parameter regime for wild-type, pfeffer, and shady (the nacre mutation lacks melanophore cells so we don't include it in this dataset).

The shady patterns were generated by turning off cell birth for iridiopores, and, the pfeffer patterns were generated by turning off cell birth for xanthophores. All simulations were run in MATLAB.

For wild type, the summary pattern features provide statistics about the simulation outputs in terms of topological betti numbers of the stripe patterns, stripe width, straightness of stripes, local cell-cell distances and local cell-cell densities, day in which stripes the second and third interstripes X1V and X1D form, and the melanophore coefficient of variation. For the shady and pfeffer mutations, the summary pattern features provide statistics about the simulation outputs in terms of topological betti numbers of the spot patterns, size of each cluster/spot, alignment of the spots, roundness of the spots (pca ev ratio), local cell-cell distances and local cell-cell densities, and the melanophore coefficient of variation. All of these pattern features were computed automatically using the methods from "McGuirl M, Volkening A, and Sandstede B (2019) Topological data analysis of zebrafish patterns. arXiv. 1910.08433."

All data are in the form of .mat files and the pattern features are contained in the pattern_info variable. We also provide .csv files which the data from each parameter regime in a single file.