Aberrant neural circuit assembly is implicated in neurodevelopmental defects. Therefore, it is essential to understand the molecular mechanisms of functional neural circuit development. Dendrites play an important role in integrating incoming signals in single neurons. Reflecting their individual roles in the brain, dendrites display a wide range of morphologies. To ensure the proper structure of dendrites into functional neural circuit, their morphogenesis is regulated in a spatially restricted manner. To identify key molecular players which underlie the spatial control of dendritic morphogenesis, we utilize the aCC (anterior corner cell) motoneuron in the Drosophila embryonic central nervous system (CNS), because of its highly reproducible placement of dendrite formation. With this model in hand, we have previously demonstrated that (1) the coordinate of aCC dendritic outgrowth is determined by an inter-neuronal interaction with its partner neuron, the MP1; and (2) the aCC-MP1 contact provides a scaffold for the adhesive interaction of Dscam1 receptors (Down syndrome cell adhesion molecule) expressed on the aCC and the MP1. The first part of this dissertation identifies Slit, an axon guidance molecule, as a facilitator of the Dscam1 complex assembly at the aCC-MP1 contact site, explores how this molecular complex might be assembled during development, and discusses the implication of the role of Slit/Dscam1 signaling in a broader context of neural circuit assembly. The second part of this thesis reports our efforts to build a color palette of split fluorescent proteins. Using rational design and directed evolution, we generate a variety of split FP variants across the entire visible spectrum and demonstrate their use in multiplexed imaging of cellular proteins. In the long term, this work will provide insights into the molecular mechanisms underlying neural circuit assembly and propose a general method to study the dynamic network of proteins in living animals.