From structural principles to single‐molecule localization. A) Schematic drawing of an isolated synaptosome retaining an intact synapse with its major components: neurotransmitter‐laden synaptic vesicles (sv), the presynaptic active zone (az), and postsynaptic density (psd). B) Representative electron micrograph of an isolated synaptosome showing preserved synaptic architecture with ubiquitous structural compartments labelled. (P, presynaptic terminal). Solid arrowheads point to synaptic vesicles. White and black dashed lines encircle the pre‐ and postsynaptic compartments, respectively. Figure panel was adapted with permission.29 Copyright 2017, Springer Nature. Representative images showing differences in resolving the localization of pre‐ and postsynaptic structures with synaptic markers serving as “landmarks” (in red: Bassoon, a presynaptic active zone marker; in green: Homer1, a postsynaptic density marker) by C) confocal microscopy and D) dSTORM. Images correspond to resolution limits described by Miklosi et al. and others.26, 29, 35 E) Localization of DAT (blue) clusters at super‐resolution within the presynaptic active zone (Bassoon, red) shows single molecules and their clusters intracellularly and on the membrane surface. Boundaries of the pre‐ and postsynaptic compartments were delineated in (D,E) (dashed lines). Scale bars = 500 nm (B,C), 200 nm (D,E).