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Updated: Jun 14, 2025
Optical Clearing of the Mouse Central Nervous System Using Passive CLARITY
Published on: June 30, 2016
Rapid and efficient protocol for optical clearing of mouse intestinal tissues for enhanced fluorescence imaging and
Joel Johnson George1, Sierra H Ball1, Elena Wang1
1Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA; Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA; Digestive & Liver Diseases Research Center, Columbia University Irving Medical Center, New York, NY, USA; Columbia Center for Human Development/Center for Stem Cell Therapies, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
Abstract:
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-CreERT2; Rosa26-tdTomato mice. For complete details on the use and execution of this protocol, please refer to Capdevila et al.1.
