CLARITY Resources


Scientific American Special Report 2016


CLARITY News and Techniques

Comparing Tissue Transparency Methods for Intact Analyses (from Communication in Neural Circuits: Tools, Opportunities, and Challenges. Lerner TN, Ye L, and K Deisseroth. Cell 2016).

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


CLARITY-optimized light-sheet microscopy (COLM).

Hands-on Training: The Deisseroth laboratory offers several hands-on training courses on hydrogel-enabled tissue clearing and imaging, focused specifically on the CLARITY method.
NEW in 2018: Now offering a workshop focused solely on imaging and data analysis of cleared tissue samples as well as a longer, 2-week intensive workshop. Details on all CLARITY-related workshops are here:
CLARITY Workshop Information
D-lab Extended Workshop Information


D-Lab CLARITY Papers

Wiring and Molecular Features of Prefrontal Ensembles Representing Distinct Experiences. Ye L*, Allen WE*,Thompson KR*, Tian Q, Hsueh B, Ramakrishnan C, Wang A-C, Jennings JH, Adhikari A, Halpern CH, Witten IB, Barth AL, Luo L, McNab JA, and K Deisseroth. Cell 165, pp 1–13 2016. *equal contributors
Movie S1: Long-Range Visualization and Tracing of NPAS4+/mPFC-NAc Projecting Cells
Movie 2: Neural connections from the prefrontal cortex across an entire transparent mouse brain.
Supplement: Automated CLARITY Analysis Software Packages

Communication in Neural Circuits: Tools, Opportunities, and Challenges. Lerner TN, Ye L, and K Deisseroth. Cell (Leading Edge Primer) 2016.
Supplementary Table 1: Tools for Neural Circuit Mapping.
Supplementary Table 2: Tissue Transparency Methods for Intact Analyses.
Supplementary Table 3: Activity Readouts for Functional Neural Circuit Analysis.

Multiplexed Intact-Tissue Transcriptional Analysis at Cellular Resolution. Sylwestrak, EL* and Rajasethupathy, P* and Wright, MA* and Jaffe, A and K Deisseroth. Cell 164, pp 792–804 2016. *equal contributors

SPED Light Sheet Microscopy: Fast Mapping of Biological System Structure and Function. Tomer R, Lovett-Barron M, Kauvar I, Andalman A, Burns VM, Sankaran S, Grosenick L, Broxton M, Yang S, and K Deisseroth. Cell 163(7):1796–1806.

Basomedial amygdala mediates top-down control of anxiety and fear. Adhikari A*, Lerner TN*, Finkelstein J*, Pak S, Jennings JH, Davidson TJ, Ferenczi E, Gunaydin LA, Mirzabekov JJ, Ye L, Kim S-Y, Lei A, and K Deisseroth. Nature doi:10.1038/nature15698 (2015).

Intact-brain analyses reveal distinct information carried by SNc dopamine subcircuits. Lerner TN, Shilyansky C, Davidson TJ, Evans KE, Beier KT, Zalocusky KA, Crow AK, Malenka RC, Luo L, Tomer R, and K Deisseroth. Cell 162:635–647 (2015).

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.

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     Data: Tyrosine Hydroxylase (TH) stained mouse brain (z-stack)     Data: Tyrosine Hydroxylase (TH) stained mouse brain (z-stack; dense staining) from Chung et al. (2013)


CLARITY Literature from the Community

Dopamine neurons projecting to the posterior striatum form an anatomically distinct subclass. Menegas M, Bergan JF, Ogawa SK, Isogai Y, Umadevi Venkataraju K, Osten P, Uchida N, and M Watabe-Uchida. eLife 2015;10.7554/eLife.10032 (2015).

PEA-CLARITY: 3D molecular imaging of whole plant organs. Palmer WM, Martin AP, Flynn JR, Reed SL, White RG, Furbank RT, and CP Grof. Nature Scientific Reports 5:13492 (2015).

Hybrid periportal hepatocytes regenerate the injured liver without giving rise to cancer. Font-Burgada J, Shalapour S, RamaswamyS, Hsueh B, Rossell D, Umemura A, Taniguchi K, Nakagawa H, Valasek MA, Ye L, Kopp JL, Sander M, Carter H, Deisseroth K, Verma IM, and M Karin. Cell 162(4) 766–779 (2015).

Fast immuno-labeling by electrophoretically driven infiltration for intact tissue imaging. Li J, Czajkowsky DM, Li X, and Z Shao. Nature Scientific Reports 5(10640):1–7 (2015).

A versatile clearing agent for multi-modal brain imaging. Costantini I, Ghobril J-P, Di Giovanna AP, Mascaro ALA, Silvestri L, Müllenbroich MC, Onofri L, Conti V, Vanzi F, Sacconi L, Guerrini R, Markram H, Iannello G, and FS Pavone. Nature Scientific Reports 5(9808):1–9 (2015)

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).

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


Principal Investigator

Karl Deisseroth (Bioengineering/Psychiatry)