Our understanding of the nervous system is fundamentally influenced by fluorescence imaging methods. With an unsurpassed precision level, the development of several super-resolution microscopy techniques and customized fluorescent probes allows for direct observation of the neuronal structure and protein groupings in cellular sub-compartments. Superresolving visualization techniques in neurons reveal a fresh understanding of the sub-synaptic structure and function, cytoskeletal composition, distribution, motility, and signalling of membrane proteins, as well as the relationship between neurons and glia. When studying disease pathophysiology using cutting-edge imaging techniques, well-defined molecular targets in autoimmune and neurodegenerative disease models serve as great beginning points.