Many natural and social phenomena involve individual agents coming together to create group dynamics, whether they are cells in a skin pattern, voters in an election, or pedestrians in a crowded room. Here I will focus on the example of pattern formation in zebrafish, which are named for the dark and light stripes that appear on their bodies and fins. Mutant zebrafish, on the other hand, feature different patterns, including spots and labyrinth curves. All these patterns form as the fish grow due to the interactions of tens of thousands of pigment cells. The longterm motivation for my work is to better link genotype, cell behavior, and phenotype — I seek to identify the specific alterations to cell interactions that lead to mutant patterns. Toward this goal, I develop agent-based models to simulate pattern formation and make experimentally testable predictions. In this talk, I will overview my models and highlight several future directions. Because agent-based models are not analytically tractable using traditional techniques, I will also discuss the topological methods that we have developed to quantitatively describe cell-based patterns, as well as the associated nonlocal continuum limits of my models.