CLARITY Resources



Advanced CLARITY for rapid and high-resolution imaging of intact tissues. Tomer R, Ye L, Hsueh B, and K Deisseroth. Nature Protocols 9(7):1682–1697.
High-resolution figures, supplementary videos, and COLM resources.

Three-dimensional printing physiology laboratory technology. Sulkin MS,Widder E, Shao C, Holzem KM, Gloschat C, Gutbrod SR, and IR Efimov. Am J Physiol Heart Circ Physiol 305: H1569–H1573, 2013.
ETC chamber designs

Neuronal calcium-binding proteins 1/2 localize to dorsal root ganglia and excitatory spinal neurons and are regulated by nerve injury. Zhang M-D, Tortoriello G, Hsueh B, Tomer R, Ye L, Mitsios N, Borgius L, Grant G, Kiehn O, Watanabe M, Uhlén M, Mulder J, Deisseroth K, Harkany T, and T G M Hökfelt. PNAS March 2014.
High-resolution Supplementary Video 1     High-resolution Supplementary Video 2

Light microscopy mapping of connections in the intact brain. Kim S-Y, Chung K, and K Deisseroth. Trends in Cognitive Sciences 17(12), 596-599.

CLARITY for mapping the nervous system. Chung K and K Deisseroth. Nature Methods 10(6), 508-513 (June 2013).

Structural and molecular interrogation of intact biological systems. Chung K, Wallace J, Kim SY, Kalyanasundaram S, Andalman AS, Davidson TJ, Mirzabekov JJ, Zalocusky KA, Mattis J, Denisin AJ, Pak S, Bernstein H, Ramakrishnan C, Grosenick L, Gradinaru V, and K Deisseroth. Nature 497, 332–337 (16 May 2013).
PDF     Supplementary Information     Nature Video


CLARITY Protocol and Materials

CLARITY Protocol (4-30-13)

CLARITY Materials Inventory (4-30-13)

ETC Chamber Instructions (4-30-13)

CLARITY Staining Tips (6-15-13)


CLARITY Technical Discussion


CLARITY FAQ (6-16-13)



CLARITY Education

CLARITY training: The Deisseroth laboratory is now offering
short hands-on CLARITY training courses. Details are here:

CLARITY Workshop Information



Supplementary videos from Chung et al. (2013)

Principal Investigator

Karl Deisseroth (Bioengineering/Psychiatry)