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.本数据集提供了野生型（wild-type）、shady、nacre及pfeffer斑马鱼斑纹的模型模拟结果，模拟采用了Volkening A与Sandstede B（2018）发表于《Nature Communications》第9卷第3231期的论文"Iridophores as a source of robustness in zebrafish stripes and variability in Danio patterns"中基于智能体的模型（agent-based model）的修改版本。本次模拟中，模型内每一项长度尺度参数均按照正态分布（normal distribution）于每日针对单个细胞随机采样；各参数正态分布的均值均设置为前述论文中给出的默认参数值。我们在不同模拟中调整了噪声的标准差，该信息已存储于文件名中。例如，WT_sigma_1代表标准差设为参数均值1%的随机野生型模拟。shady斑纹的模拟通过关闭虹彩细胞（iridiophores）的细胞增殖生成；nacre斑纹的模拟通过关闭黑素细胞（melanophores）的细胞增殖生成；pfeffer斑纹的模拟则通过关闭黄色素细胞（xanthophores）的细胞增殖生成（详细机制请参见上述参考文献）。所有模拟均在MATLAB环境中运行。每份模拟结果均以.mat格式文件存储。每个.mat文件内包含以下数据：模拟全程所有细胞的位置信息、追踪模拟期间细胞移动距离的数组、记录模拟每日新增、死亡及存活细胞数的向量，以及模拟每日对应的计算域x、y边界。细胞位置信息存储于N×2×T数组中，其中N为模拟总细胞数的上限，T为模拟总天数。例如，cellsM(1:N_M,:,T)代表模拟最后一日的黑素细胞的x、y坐标。同理，cellsIl对应松散虹彩细胞（loose iridophores）的坐标，cellsId对应致密虹彩细胞（dense iridophores）的坐标，cellsXc对应致密黄色素细胞（dense xanthophores）的坐标，cellsXsn对应松散黄色素细胞（loose xanthophores）的坐标。