The brain is modular. Neuronal circuits are embedded in an environment that combines two-dimensional (2D) and three-dimensional (3D) organization, a structure that enhances the combination of localized and global activity, and that increases robustness and flexibility. To understand the principal actors that shape this complex dynamics, in our laboratory we develop tools to engineer neuronal circuits in vitro, which include stamping of adhesive proteins, topographical molds and scaffolds. Spontaneous activity is monitored through fluorescence calcium imaging to render the network collective activity patterns and its effective connectivity traits. Measures such as the dynamical richness, the community statistic or the global efficiency are then used to compare and quantify the differences between different engineered structures. Experimental studies are combined with numerical simulations to better understand the impact of physical constraints on structural connectivity and even to make predictions of the properties of the emerging networks dynamics.