Minutes-timescale 3D isotropic imaging of entire organs at subcellular resolution by content-aware compressed-sensing light-sheet microscopy

Abstract

We here report on a compressed sensing-enabled Bessel light-sheet microscopy system able to achieve fast scalable mapping of entire organs at an isotropic subcellular resolution. A dualside confocally-scanned Bessel light-sheet with a millimeter-to-centimeter tunable range was developed to illuminate regions-of-interest from a few cells to entire organs, providing uniform optical sectioning of deep tissues with 1-5 μm ultra-thin axial confinement. We also present a new computation pipeline termed content-aware compressed sensing (CACS), which can further improve the contrast and resolution of a 3D image based on a single input of its own, allowing satisfying spatial resolution with data acquisition shorten by two-orders of magnitude.Using this method, we can image any region-of-interest of a selected mouse brain at submicron isotropic resolution in seconds, after screening multiple whole brains in minutes, and then in toto reconstruct the digital whole brain (~400 mm 3 ) at a teravoxel scale with a short acquisition time of ~15 minutes. We also demonstrate subcellular-resolution minute-timescale dual-color imaging of neuromuscular junctions in thick mouse muscles. Various system-level cellular analyses, such as mapping cell populations at different brain sub-regions, tracing long-distance projection neurons over the entire brain, and calculating neuromuscular junction occupancy across whole tissue, were enabled by our high-throughput high-resolution imaging method. `