Abstract
Visualizing the nano-organization of the synapse is fundamental to elucidating the structure-function relationship of the nervous system. The advent of super-resolution microscopy provides a tool to assess and quantify the dynamic organization of numerous proteins at the synapse. Here we present a protocol assessing inhibitory synapse scaffold protein, gephyrin, in rat primary hippocampal cultures using dSTORM microscopy. We delineate the steps for artemisinin treatment, immunocytochemistry, dSTORM image acquisition, single-molecule localization, and the analysis of synaptic scaffold protein dynamics. For complete details on the use and execution of this protocol, please refer to Guzikowski and Kavalali (2022).1.