Second-level high-speed 3D isotropic imaging of whole mouse brain using deep-learning spinning-disk light-sheet microscopy

Abstract Axially-swept light-sheet microscopy (ASLM) has emerged as a distinguished tool for 3D imaging owing to its excellent spatial resolution. However, the acquisition time is significantly elongated due to the extra time consumed in axial scanning. Meanwhile, the spatial information provided in a single scan is fundamentally limited by the compromise between field-of-view and resolution. The overall inadequate optical throughput of current ASLM techniques impedes their widespread application in acquiring large samples. Here we demonstrate a spinning-disk-based ASLM (SDLM) approach that enables wide field-of-view (15 × confocal range of the gaussian beam), isotropic 3D imaging of large organisms at 100 Hz full camera frame rate. In addition to the new optical design, we combine a recurrent neural network image restoration model to further improve the resolution of raw images. We demonstrate seconds scale stitching-free 3D imaging of the entire mouse brain (~ 9*8*5 mm size) at isotropic single-cell resolution (1.5 µm voxel). With the high-quality data readily obtained by our approach, we also demonstrate the visualization of long projecting neurons and two genotypes of whole mouse brain cell profiling across the 3D space. Further transformation into in vivo research would broaden the application of SDLM.