Reviews: Hydrogel-tissue chemistry (HTC) methods including CLARITY

Annual Review of Biophysics 2018
Cell 2016
Scientific American 2016

HTC Resources

Publications from around the world
Deisseroth Lab Short-Workshop Information
Deisseroth Lab Extended-Workshop Information

Deisseroth Lab HTC Papers

Hydrogel-Tissue Chemistry: Principles and Applications. Gradinaru V, Treweek J, Overton K, and K Deisseroth. Annu Rev Biophysics 47, pp 355–376 2018.

Pathways to clinical CLARITY: volumetric analysis of irregular, soft, and heterogeneous tissues in development and disease. Hsueh B*, Burns VM*, Pauerstein P, Holzem K, Li Y, Engberg X, Wang A-C, Gu X, Chakravarthy H, Arda HE, Charville G, Vogel H, Efimov IR, Kim S, and K Deisseroth. Nature Sci Reports 7:5899, pp 1–16 2017. *equal contributors

Optical and chemical discoveries recognized for impact on biology and psychiatry. K Deisseroth. EMBO Reports 19:5, pp 1–2 2017.

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)