Confocal microscopy. The brain and kidney slices were mounted on glass coverslips and incubated in final clearing solution (such as DBE). Then, the cortex regions of the brain slices were imaged with an inverted confocal fluorescence microscope (LSM 710, Zeiss, Germany) equipped with a Fluar 10×/0.5 objective (dry; working distance, 2.0 mm) and Plan-Apochromat 20×/0.8 objective (dry; working distance, 0.55 mm). The z-step interval was 5 μm.

Light sheet fluorescence microscopy. Large samples (such as brain, spinal cord, CNS, kidney, and muscle) were imaged using a light sheet fluorescence microscope (Ultramicroscope, LaVision BioTec, Germany) equipped with an sCMOS camera (Andor Neo), a 2×/0.5 objective lens equipped with a dipping cap, and an Olympus MVX10 zoom microscope body (magnification range of ×0.63 to ×6.3). The cleared tissues were mounted on the sample holder and incubated with the final clearing solution (such as DBE) in the sample reservoir. For entire scanning of whole organs, the z-step interval was 5 or 10 μm, and for image acquisition in the regions of interest, an interval in the range of 2 to 5 μm was used.

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