CLARITY

CLARITY is a method of making tissue transparent using acrylamide-based hydrogels built from within, and linked to, the tissue, and as defined in the initial paper, represents "transformation of intact biological tissue into a hybrid form in which specific components are replaced with exogenous elements that provide new accessibility or functionality". When accompanied with antibody or gene-based labeling, CLARITY enables highly detailed pictures of the protein and nucleic acid structure of organs, especially the brain. It was developed by Kwanghun Chung and Karl Deisseroth at the Stanford University School of Medicine. Several published papers have applied the CLARITY method to a wide range of tissues and disease states such as immuno-oncology for human breast cancer, Alzheimer's disease human brains, mouse spinal cords, multiple sclerosis animal models, and plants. CLARITY has also been combined with other technologies to develop new microscopy methods including confocal expansion microscopy, SPIM light sheet microscopy, and CLARITY-optimized light sheet microscopy (COLM). Procedure The process of applying CLARITY imaging begins with a postmortem tissue sample. Depending on the tissue type pre-processing steps such as demineralization or decolorization may be necessary after sample fixation. Next a series of chemical treatments must be applied to achieve transparency, in which the lipid content of the sample is removed, while almost all of the original proteins and nucleic acids are left in place. The purpose of this is to make the tissue transparent and thus amenable to detailed microscopic investigation of its constituent functional parts (which are predominantly proteins and nucleic acids). To accomplish this, the preexisting protein structure has to be placed in a transparent scaffolding which preserves it, while the lipid components are removed. This 'scaffolding' is made up of hydrogel monomers such as acrylamide. The addition of molecules like formaldehyde, paraformaldehyde, or glutaraldehyde can facilitate attachment of the scaffolding to the proteins and nucleic acids that are to be preserved, and the addition of heat is necessary to establish the actual linkages between the cellular components and the acrylamide.