Development reliably produces complex organisms despite external perturbations and intrinsic stochasticity. It remains a central challenge not only to understand specific examples of development in vivo, but also to infer underlying principles that extend beyond any particular model system. In this talk, we will first introduce the formation of dorsal branches in the Drosophila larval trachea as a model for structural developmental defects. In each branch, progenitor cells robustly organize themselves into distinct cell fates, driven by an external morphogen concentration. By perturbing the external signal, partially penetrant stochastic phenotypes emerge in which a variable number of "terminal" cells are specified. Using live imaging to capture both morphology and expression of key genes, we observe dynamically how successful fate patterning occurs and how it fails. Partially penetrant phenotypes are modeled by geneticists using "threshold-liability", a phenomenological model with unspecified molecular details. Here, we are able to connect the abstract model to the molecular implementation by directly measuring receptor activation. Next, we consider self-organization theoretically by introducing a minimal model of cell patterning via local cell-cell communication. Recent advances have clarified how isolated cells can respond to an exogenous signal, but cells often interact and act collectively. In our framework we prove that a trade-off between speed and accuracy of collective pattern formation exists. Moreover, for the first time we are able to quantify how information flows between interacting cells during patterning. Our analysis reveals counterintuitive features of collective patterning: globally optimized solutions do not necessarily maximize intercellular information transfer and individual cells may appear suboptimal in isolation.