TY - JOUR T1 - Optimization of CLARITY for clearing whole brain and other intact organs JF - eneuro JO - eneuro DO - 10.1523/ENEURO.0022-15.2015 SP - ENEURO.0022-15.2015 AU - Jonathan R. Epp AU - Yosuke Niibori AU - Hwa-Lin ( Liz) Hsiang AU - Valentina Mercaldo AU - Karl Deisseroth AU - Sheena A. Josselyn AU - Paul W. Frankland Y1 - 2015/05/08 UR - http://www.eneuro.org/content/early/2015/05/07/ENEURO.0022-15.2015.abstract N2 - The development, refinement and use of techniques that allow high-throughput imaging of whole brains with cellular resolution will help us understand the complex functions of the brain. Such techniques are crucial for the analysis of complete neuronal morphology, anatomical, as well as functional, connectivity and repeated molecular phenotyping. CLARITY is a recently introduced technique that produces structurally intact, yet optically transparent tissue, which may be labeled and imaged without sectioning. However, the utility of this technique depends on several procedural variables during the process in which the light-scattering lipids in a tissue are replaced by a transparent hydrogel matrix. Here, we systematically varied a number of factors (including temperature, hydrogel composition and polymerization conditions) to provide an optimized, highly-replicable CLARITY procedure for clearing mouse brains. We found that for these preparations optimal tissue clearing requires electrophoresis (and cannot be achieved with passive clearing alone) for 5 days with a combination of 37°C and 55°C temperature. Although this protocol is optimized for brains, we also show that it can be used to clear and analyze a variety of organs. Brain or other tissue prepared using this protocol is suitable for high throughput imaging with confocal or single plane illumination microscopy (SPIM). Significance Statement: CLARITY is a novel technique for optical clearance and intact imaging of biological specimens. This method was introduced in 2013 but has been difficult for some researchers to implement. Here, we have optimized the technique to increase the success and consistency of the clearing procedure. Using our protocol, it is possible to clear not only brain, but other tissues as well. In addition, the cleared tissue becomes sufficiently transparent such that no specialized microscopes are necessary to visualize the sample. This optimization of CLARITY will make the technique more widely accessible. ER -