3D Imaging for Cleared Tissues and Thicker Samples on Confocal and Light-Sheet Microscopes

Advances in fluorescence microscopy, specifically the development of confocal and light-sheet microscopes, have enabled researchers to harness tissue clearing techniques to image-stained intact tissue samples in 3D. Using these techniques, tissue structure and biomarker distributions in 3D structures are preserved, thus allowing researchers to gain a wealth of spatial information about their tissue of interest. However, the execution of imaging these larger tissue samples can be challenging. Broadly speaking, tissue clearing techniques unify the refractive indices inside tissue samples, thus enabling deep tissue imaging on a confocal or light-sheet microscope. Here, we provide an overview to tissue clearing and 3D immunohistochemistry staining in general and discuss some difficulties that researchers may encounter when using these techniques. We then focus on imaging CLARITY-processed samples with both confocal and light-sheet microscopes and optimizing the acquisition parameters, before noting potential issues that may come up in imaging.