Technical considerations on confocal based fluorescence micro-optical sectioning tomography for visualizing brain circuits

Imaging brain circuits is the basis for us to understand brain function and dysfunction. However, imaging axon at micrometer resolution while tracing the centimeter-scale axon projection across the whole-brain is still challenging. Here, we developed a fluorescence micro-optical sectioning tomography (fMOST) imaging system based on confocal fluorescence imaging scheme that can obtain whole brain image stack for visualizing brain circuits at neurite level. We use confocal detection to remove fluorescence background to clearly see one single neurite and use acoustical optical deflector (AOD), an inertia-free beam scanner to realize fast and prolonged stable imaging. We had acquired several complete datasets of whole-mouse brain at a one-micron voxel resolution. Based on these datasets, the uninterrupted tracing of brain-wide, long-distance axonal projections was demonstrated for the first time using a systematic reconstruction and annotation pipeline. Our method is believed to open an avenue to exploring both local and long-distance neural circuits that are related to brain functions and brain diseases down to the neurite level.