Abstract

Pattern formation is present at many scales in biology, and here I will focus specifically on elucidating how brightly colored cells interact to form skin patterns in zebrafish. Wild-type zebrafish are named for their dark and light stripes, but mutant zebrafish feature variable skin patterns, including spots and labyrinth curves. All of these patterns form as the fish grow due to the interactions of tens of thousands of pigment cells, making agent-based modeling a natural approach for describing pattern formation. However, agent-based models are stochastic and have many parameters, so comparing simulated patterns and fish images is often a qualitative process. Here I will show how to apply methods from topological data analysis to cell-based, time-dynamic systems. In this talk, I will overview our models and present quantitative summaries of messy cell-based patterns forming in time.