CLARITY Resources


CLARITY News and Techniques

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


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
D-lab Extended Workshop Information


CLARITY Literature

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

More papers using CLARITY



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


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


Labs publishing with CLARITY

Deisseroth lab
Chung lab
Gradinaru lab
Kiehn lab
Hökfelt lab
Efimov lab
Ueda lab
Duyckaerts lab
Mackenzie-Graham lab
Frankland lab
Josselyn lab
Rinaman lab
Karin lab
Shao lab
Pavone lab
Uchida lab
Grof lab

Principal Investigator

Karl Deisseroth (Bioengineering/Psychiatry)