Highlights•SeeDB2 is a simple optical clearing method preserving morphology and fluorophores•SeeDB2 is optimized for high-resolution imaging by minimizing spherical aberrations•Volumetric super-resolution imaging enables synaptic-scale connectomic studies•Quantitative synapse mapping is demonstrated for mouse and fly brain samplesSummarySuper-resolution imaging deep inside tissues has been challenging, as it is extremely sensitive to light scattering and spherical aberrations. Here, we report an optimized optical clearing agent for high-resolution fluorescence imaging (SeeDB2). SeeDB2 matches the refractive indices of fixed tissues to that of immersion oil (1.518), thus minimizing both light scattering and spherical aberrations. During the clearing process, fine morphology and fluorescent proteins were highly preserved. SeeDB2 enabled super-resolution microscopy of various tissue samples up to a depth of >100 μm, an order of magnitude deeper than previously possible under standard mounting conditions. Using this approach, we demonstrate accumulation of inhibitory synapses on spine heads in NMDA-receptor-deficient neurons. In the fly medulla, we found unexpected heterogeneity in axon bouton orientations among Mi1 neurons, a part of the motion detection circuitry. Thus, volumetric super-resolution microscopy of cleared tissues is a powerful strategy in connectomic studies at synaptic levels.Graphical abstract

Super-Resolution Mapping of Neuronal Circuitry With an Index-Optimized Clearing Agent