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Optical clearing of the mouse brain and light attenuation quantitation

Optical clearing allows the reduction of light scattering in biological tissue, enabling 3D morphological information to be obtained deep within tissue using techniques such as optical projection tomography and light sheet microscopy. However, the extent of the clearing is dependent on the technique that is used. There is therefore a need for methods to quantify the quality of the clearing process and thereby to compare clearing techniques. In this study, we developed such a method using a custom spectroscopy system and applied it to compare three techniques that were applied to mouse brain: BABB (Murray’s clear), pBABB (a modification of BABB which includes the use of hydrogen peroxide), and passive CLARITY.