A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices
Ezra Kruzich, Rhushikesh A. Phadke, Alison Brack, Dimitri Stroumbakis, Oriannys Infante, Alberto Cruz-Martín
STED, Imaris, MATLAB, prefrontal cortex, imaging, analysis
Advances in super-resolution imaging enable us to delve into its intricate structural and functional complexities with unprecedented detail. Here, we present a pipeline to visualize and analyze the nanoscale organization of cortical layer 1 apical dendritic spines in the mouse prefrontal cortex. We describe steps for brain slice preparation, immunostaining, stimulated emission depletion super-resolution microscopy, and data analysis using the Imaris software package. This protocol allows the study of physiologically relevant brain circuits implicated in neuropsychiatric disorders.