Neural circuits, composed of intercellular connected neurons with distinct properties lay the physical foundation of any brain function. Identifying subtype and connections of individual neurons in a circuit is the key to understand how information is processed and propagated in the brain. In order to obtain a detailed wiring diagram between neurons, we developed a series of multiplex labeling and profiling, sample preparation, and image processing tools to allow neuronal identity and connectivity features being directly measured by super-resolution light microscopy in a densely labeled mouse brain. Designed to be carried out with standard surgical, imaging and computational instrumentation, our comprehensive circuit mapping tool set will allow high-resolution, high-throughput neural circuit mapping in a regular neuroscience laboratory.