CLARITY Resources



Transparent brains reveal effects of cocaine and fear (Nature).
Microscopy: seeing through tissue (Nature Methods).

CLARITY techniques


CLARITY-optimized light-sheet microscopy (COLM).

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


Papers using CLARITY

Simplified CLARITY for visualizing immunofluorescence labeling in the developing rat brain. Zhang H and L Rinaman. Brain Struct Funct Epub ahead of print (2015).

Improved application of the electrophoretic tissue clearing technology, CLARITY, to intact solid organs including brain, pancreas, liver, kidney, lung, and intestine. Lee H, Park J-H, Seo I, Park S-H, and S Kim. BMC Developmental Biology 14(1):48 Epub ahead of print (2015).

Manipulating a “cocaine engram” in mice. Hsiang HL, Epp JR, van den Oever MC, Yan C, Rashid AJ, Insel N, Ye L, Niibori Y, Deisseroth K, Frankland PW, Josselyn SA. J Neurosci 34(42):14115–27 (2014).

Inside Alzheimer brain with CLARITY: senile plaques, neurofibrillary tangles and axons in 3‐D. Ando K, Laborde Q, Lazar A, Godefroy D, Youssef I, Amar M, Pooler A, Potier M-C, Delatour B, and C Duyckaerts. Acta Neuropathol 128:457–459 (2014). Supplemental movies.

Bringing CLARITY to gray matter atrophy. Spence RD, Kurth F, Itoh N, Mongerson CRL, Wailes SH, Peng MS, and AJ MacKenzie-Graham. NeuroImage (2014).

Single-cell phenotyping within transparent intact tissue through whole-body clearing. Yang B, Treweek JB, Kulkarni RP, Deverman BE, Chen C-K, Lubeck E, Shah S, Cai L, and V Gradinaru. Cell (2014).

Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis. Susaki EA, Tainaka K, Perrin D, Kishino F, Tawara T, Watanabe TM, Yokoyama C, Onoe H, Eguchi M, Yamaguchi S, Abe T, Kiyonari H, Shimizu Y, Miyawaki A, Yokota H, and HR Ueda. Cell (2014).

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 (2014). 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 (2013).

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



Supplementary videos from Chung et al. (2013)
CLARITY-optimized light-sheet microscopy (COLM) videos


Labs publishing with CLARITY

Deisseroth lab
Gradinaru lab
Chung lab
Kiehn lab
Hökfelt lab
Efimov lab
Ueda lab
Duyckaerts lab
Mackenzie-Graham lab
Frankland lab
Josselyn lab
Rinaman lab

Principal Investigator

Karl Deisseroth (Bioengineering/Psychiatry)