Original Article
Kwanghun Chung, Jenelle Wallace, Sung-Yon Kim, Sandhiya Kalyanasundaram, Aaron Andalman, Tom J. Davidson, Kelly A. Zalocusky, Joanna Mattis, Sally Pak, Viviana Gradinaru, Hannah Bernstein, Julie Mirzabekov, Charu Ramakrishnan, and Karl Deisseroth, “Structural and molecular interrogation of intact biological systems”, Nature, 2013, 497, 332-337 (This paper was featured in the New York Times and the Guardian)

Related Article
Sung-Yon Kim, Jae Hun Cho, Evan Murray, Naveed Bakh, Heejin Choi, Kimberly Ohn, Sara Vassallo, Luzdary Ruelas, Austin Hubbert, Meg McCue, Philipp Keller and Kwanghun Chung. Stochastic electrotransport selectively enhances the transport of highly electromobile molecules, PNAS, 2015 Nov 17: 112(46): E6274-83. doi: 10.1073/pnas.1510133112. Epub 2015 Nov 2. PubMed PMID: 26578787; PubMed Central PMCID: PMC4655572.

Sung-Yon Kim, Kwanghun Chung*, Karl Deisseroth* “Light microscopy mapping of connections in the intact brain”, Trends in Cognitive Science, 2013, 17, 12, 596-599 (co-correspondence).

Kwanghun Chung*, Karl Deisseroth*, “CLARITY for mapping the nervous system”, Nature methods, 2013, 10, 508-513 (co-correspondence)



CLARITY is the technique that renders a thick biological tissue optically transparent and macromolecule-permeable.

Innovation in clarity can be broken down into 3 steps:

  1. Perfuse a mouse with hydrogel monomer solution to allow it to permeate throughout the tissue of interest, then incubate it further to ensure maximal and even diffusion.
  2. Polymerize that solution inside the tissue by raising temperature under a nitrogen blanket. This ultimately forms what we call a “tissue-hydrogel hybrid.”
  3. Use a buffer solution containing anionic detergents to solubilize and remove lipids from the sample. Electrophoresis is used to speed up this process.


The full protocol can be downloaded here.