Mammalian brains are staggeringly complex, with many billions of neurons forming an intricate neural network. A key question in neuroscience is how this neural network produces functional outcomes, such as cognition, emotion and bodily responses. To tackle this question, functional circuit mapping approaches attempt to map the entire anatomical connectivity (‘connectome’) and to identify the function of each neural circuit element (‘functional connectome’). Recent breakthroughs in neuro-technologies, such as optogenetics and CLARITY, are increasingly enabling these challenging investigations. In the first part of my talk, I will illustrate how optogenetics can be used to dissect the anxiety circuitry in the extended amygdala. We identified a surprising new role for the bed nucleus of the stria terminalis (BNST) in the coordinated modulation of diverse anxiety features, and clarified the underlying circuit mechanisms for selection of features for the assembly of the anxious state. In the second part, I will discuss the promises and challenges of the chemical engineering-based CLARITY approach to neuroscience and introduce two novel techniques (termed stochastic electrotransport and SWITCH) that we have been developing to achieve easy, scalable and conservative clearing and rapid, uniform and complete staining of intact tissues, respectively. My goal is to combine cutting-edge systems neuroscience tools to comprehensively understand the circuitry underlying various emotional states, such as anxiety, fear and stress, at all structural, molecular and functional levels.