Rapid and efficient protocol for optical clearing of mouse intestinal tissues for enhanced fluorescence imaging and 3D reconstruction

Histological analysis of intestinal epithelial tissues is enhanced by 3D visualization compared to 2D sections. Here, we present a protocol for 3D visualization of intestinal epithelial cells using an optical clearing approach optimized for endogenous fluorescence and preservation of crypt-villus morphology. We describe steps for clearing and refractive index matching tissue. We provide detailed procedures for imaging and reconstructing tissue to visualize epithelial cells along the crypt-villus axis with high resolution. We illustrate this approach with endogenous tdTomato used for lineage tracing in the small intestine of Fgfbp1-CreER^T2; Rosa26-tdTomato mice. For complete details on the use and execution of this protocol, please refer to Capdevila et al.¹.