In the nervous system, neurons form complex networks, with thousands of connections within a small volume. Analyzing the structure of these complex network at a single-cell resolution is extremely challenging, as we lack methods to trace individual neurites accurately. We present both experimental and analytical framework to label individual neurons, allowing us to understand how various genetic factors influence neuronal structure. Left gray-scale image is a microscopy image of thousands of neurons, highly connected with each other and it is extremely difficult to trace them. Right hand side image is the result of computationally decoded image (segmented), where each color demonstrates individual neurons.