The brain is precisely wired, and this precision directly relies upon the structural organization of the brain. Yet how a brain is structurally organized is still an open question. How are neuronal processes organized in a developing brain to facilitate proper synaptic positioning? To address this, I combine computational modeling of connectomics data with in vivo neurodevelopmental imaging. My work focuses on understanding the C. elegans brain, for which the entire connectome is mapped. I developed novel clustering algorithms to analyze connectomics data and uncovered the structural organization of the brain across neuronal scales (i.e. circuits, bundles, domains). Then I used novel light-sheet microscopy to analyze the in vivo emergence of this organization in the embryo. By linking connectomics, network modeling, and in vivo development I defined the organization of a simple-nervous system and developed novel tools capable of defining this organization in more complex systems.