CLARITY stands for Clear, Lipid-exchanged, Anatomically Rigid, Imaging compatible, Tissue hYdrogel and is a technique developed by the Deisseroth lab in Stanford, California, and published in May 2013 in Nature.

With this state-of-the-art method in neuroscience it is possible to turn a brain transparent using the detergent SDS, which strips away lipids that normally block the passage of light. Here, the brain is first infused with acryl­amide, which binds proteins, nucleic acids and other biomolecules. When the acrylamide is heated, it polymerizes and forms a tissue-wide mesh that secures the molecules. By using this technique it is possible to visualize and trace, quantify and map the axonal projections of the histaminergic neurons in an intact system in whole fluorochrome-expressing brains.

Mouse brain cleared using the CLARITY technique. Expression of Histone2B-GFP nuclear reporter in hypothalamic BSX neurons. The whole intact tissue imaging technique allows an accurate representation of the 3D morphology of BSX neurons in the mouse hypothalamus.