Self-assembly is a key coordination mechanism for large multi-unit systems and a powerful bottom-up technology for micro/nanofabrication. Controlled self-assembly and dynamic reconfiguration of large ensembles of microscopic particles can effectively bridge these domains to build innovative systems. In this perspective, we present SelfSys, a novel platform for the automated control of the fluidic self-assembly of microparticles. SelfSys centers around a water-filled microfluidic chamber whose agitation modes, induced by a coupled ultrasonic actuator, drive the assembly. Microparticle dynamics is imaged, tracked and analyzed in real-time by an integrated software framework, which in turn algorithmically controls the agitation modes of the microchamber. The closed control loop is fully automated and can direct the stochastic assembly of microparticle clusters of preset dimension. Control issues specific to SelfSys implementation are discussed, and its potential applications presented. The SelfSys platform embodies at microscale the automated self-assembly control paradigm we first demonstrated in an earlier platform.