The brain is an incredibly complex organ. Much of the brain’s complexity may be attributed to the circuitry that resides within. Synaptic connections are the key units of information transduction and therefore and therefore an increasing amount of research focus has centered on understanding how they normally function and how they are disrupted in diseased states. In neurodevelopmental disorders such as autism spectrum disorders (ASD), synaptic connections are thought to be altered, thus affecting brain circuitry. However, to grasp the mechanisms that underlie this process, researchers must often rely on complex genetic tools as well as the availability of robust antibody-mediated detection methods. Here, we describe the generation of two multifunctional mouse lines that allow for the visualization of synaptic proteins (and consequently their role in synapse formation) as well as identifying their cell of origin. Using this data, we will perform three-dimensional mapping of these cells to gain deeper insight into the brain circuits that they impact. When completed, this project will not only benefit the synaptic biology and ASD research communities in providing critical information about the normal function of these two proteins and how their disruption leads to disease, but will also set the stage for interrogating virtually any difficult-to-grasp brain protein in space and time.