Revision as of 00:50, 22 February 2017

CLARITY Technique

• Structural and molecular interrogation of intact biological systems K Chung, J Wallace, S-Y Kim, S Kalyanasundaram, AS Andalman, TJ Davidson, JJ Mirzabekov, KA Zalocusky, J Mattis, AK Denisin, S Pak, H Bernstein, C Ramakrishnan, L Grosenick, V Gradinaru, and K Deisseroth. Nature 2013, 497: 332-337.
  • Supplementary Information

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

• Advanced CLARITY for rapid and high-resolution imaging of intact tissues R Tomer, L Ye, B Hsueh, and K Deisseroth. Nature Protocols 2014, 9(7): 1682-1697.

• Simplified method to perform CLARITY imaging E Poguzhelskaya, D Artamonov, A Bolshakova, O Vlasova, and I Bezprozvanny. Molecular Neurodegeneration 2014, 9: 19.

• Optimization of CLARITY for clearing whole-brain and other intact organs JR Epp, Y Niibori, H-L Hsiang, V Mercaldo, K Deisseroth, SA Josselyn, and PW Frankland. eNeuro 2015, 2(3): e0022-15.2015.

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

• Quantification of light attenuation in optically cleared mouse brains A d'Esposito, D Nikitichev, A Desjardins, S Walker-Samuel, and MF Lythgoe. Journal of Biomedical Optics 2015, 20(8): 80503.

• CLARITY-compatible lipophilic dyes for electrode marking and neuronal tracing KHR Jensen and RW Berg. Scientific Reports 2016, 6: 32674.

• Optical clearing of the mouse central nervous system using passive CLARITY DG Roberts, HB Johnsonbaugh, RD Spence, A MacKenzie-Graham. Journal of Visualized Experiments 2016, 112: e54025.

• Clarifying CLARITY: Quantification optimization of the diffusion based delipidation protocol for genetically labeled tissue C Magliaro, AL Callara, G Mattei, M Morcinelli, C Viaggi, F Vaglini, and A Ahluwalia. Frontiers in Neuroscience 2016, 10: 179.

• A look inside the brain K Deisseroth. Scientific American October 2016

ETC Technology

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

• Improved application of the electrophoretic tissue clearing technology, CLARITY, to intact solid organs including brain, pancreas, liver, kidney, lung, and intestine H Lee, J-H Park, I Seo, S-H Park, and S Kim. BMC Developmental Biology 2014, 14: 48.

• Stochastic electrotransport selectively enhances the transport of highly electromobile molecules S-Y Kim, JH Cho, E Murray, N Bakh, H Choi, K Ohn, L Ruelas, A Hubbert, M McCue, SL Vassallo, PJ Keller, and K Chung. PNAS 2015, 112: E6274-E6283.

• ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging E Lee, J Choi, Y Jo, JY Kim, YJ Jang, HM Lee, SY Kim, H-J Lee, K Cho, N Jung, EM Hur, SJ Jeong, C Moon, Y Choe, IJ Rhyu, H Kim, and W Sun. Scientific Reports 2016, 6: 18631.

RNA detection with CLARITY

• Multiplexed intact-tissue transcriptional analysis at cellular resolution EL Sylwestrak, P Rajasethupathy, MA Wright, A Jaffe, and K Deisseroth. Cell 2016, 164: 792-804.

• Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing S Shah, E Lubeck, M Schwarzkopf, T-F He, A Greenbaum, CH Sohn, A Lignell, HMT Choi, V Gradinaru, NA Pierce, and L Cai. Development 2016, 143: 2862-2867.

Analysis Using CLARITY

• Bringing CLARITY to gray matter atrophy RD Spence, F Kurth, N Itoh, CRL Mongerson, SH Wailes, MS Peng, and AJ MacKenzie-Graham. NeuroImage 2014, 101: 625-632.

• Manipulating a "cocaine engram" in mice H-L Hsiang, JR Epp, MC van den Oever, C Yan, AJ Rashid, N Insel, L Ye, Y Niibori, K Deisseroth, PW Frankland, and SA Josselyn. The Journal of Neuroscience 2014, 34(42): 14115-14127.

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

• Basomedial amygdala mediates top-down control of anxiety and fear A Adhikari, TN Lerner, J Finkelstein, S Pak, JH Jennings, TJ Davidson, E Ferenczi, LA Gunaydin, JJ Mirzabekov, L Ye, S-Y Kim, A Lei, and K Deisseroth. Nature 2015, 527(7577): 179-185.

• Dopamine neurons projecting to the posterior striatum form an anatomically distinct subclass W Menegas, JF Bergan, SK Ogawa, Y Isogai, KU Venkataraju, P Osten, N Uchida, and M Watabe-Uchida. eLife 2015, 4:e10032.

• Synaptic targets of medial septal projections in the hippocampus and extrahippocampal cortices of the mouse G Unal, A Joshi, TJ Viney, V Kis, and P Somogyi. Journal of Neuroscience 2015, 35(48): 15812-15826.

• Expanding the power of recombinase-based labeling to uncover cellular diversity NW Plummer, IY Evsyukova, SD Robertson, J de Marchena, CJ Tucker, and P Jensen. Development 2015, 142: 4385-4393.

• CLARITY and PACT-based imaging of adult zebrafish and mouse for whole-animal analysis of infections MR Cronan, AF Rosenberg, SH Oehlers, JW Saelens, DM Sisk, KL Jurcic Smith, S Lee, and DM Tobin. Disease Models & Mechanisms 2015, 8: 1643-1650.

• Wiring and molecular features of prefrontal ensembles representing distinct experiences L Ye, WE Allen, KR Thompson, Q Tian, B Hsueh, C Ramakrishnan, A-C Wang, JH Jennings, A Adhikari, CH Halpern, IB Witten, AL Barth, L Luo, JA McNab, and K Deisseroth. Cell 2016, 165: 1776-1788.

• Astroglia in thick tissue with super resolution and cellular reconstruction SJ Miller and JD Rothstein. PLoS One 2016, 11(8): e0160391.

• Prefontal cortex corticotropin-releasing factor receptor 1 conveys acute stress-induced executive dysfunction A Uribe-Marino, NC Gassen, MF Wiesbeck, G Balsevich, S Santarelli, B Solfrank, C Dournes, GR Fries, M Masana, C Labermeier, X-D Wang, K Hafner, B Schmid, T Rein, A Chen, JM Deussing, and MV Schmidt. Biological Psychiatry 2016, 80: 743-753.

CLARITY of rat tissue

• Simplified CLARITY for visualizing immunofluorescence labeling in the developing rat brain H Zheng and L Rinaman. Brain Structure and Function 2016, 221: 2375-2383.

• Light-sheet microscopy imaging of a whole cleared rat brain with Thy1-GFP transgene M Stefaniuk, EJ Gualda, M Pawlowska, D Legutko, P Matryba, P Koza, W Konopka, D Owczarek, M Wawrzyniak, P Loza-Alvarez, and L Kaczmarek. Scientific Reports 2016, 6: 28209.

CLARITY of spinal cord

• Neuronal calcium-binding proteins 1/2 localize to dorsal root ganglia and excitatory spinal neurons and are regulated by nerve injury M-D Zhang, G Tortoriello, B Hsueh, R Tomer, L Ye, N Mitsios, L Borgius, G Grant, O Kiehn, M Watanabe, M Uhlen, J Mulder, K Deisseroth, T Harkany, and TGM Hokfelt. PNAS 2014, 111(12): 1149-1158.

• Imaging serotonergic fibers in the mouse spinal cord using the CLARITY/CUBIC technique H Liang, E Schofield, and G Paxinos. Journal of Visualized Experiments 2016, 108: e53673.

CLARITY of lung tissue

• Regulatory T cells in tumor-associated tertiary lymphoid structures suppress anti-tumor T cell responses NS Joshi, EH Akama-Garren, Y Lu, D-Y Lee, GP Chang, A Li, M DuPage, T Tammela, NR Kerper, AF Farago, R Robbins, DM Crowley, RT Bronson, and T Jacks. Immunity 2015, 43: 579-590.

• Nestin-expressing vascular wall cells drive development of pulmonary hypertension F Saboor, AN Reckmann, CUM Tomczyk, DM Peters, N Weissmann, A Kaschtanow, RT Schermuly, TV Michurina, G Enikolopov, D Muller, A Mietens, and R Middendorff. European Respiratory Journal 2016, 47: 876-888.

CLARITY of heart tissue

• Comparison of different tissue clearing methods and 3D imaging techniques for visualization of GFP-expressing mouse embryos and embryonic hearts H Kolesova, M Capek, B Radochova, J Janacek, and D Sedmera. Histochemistry and Cell Biology 2016, 146: 141-152.

CLARITY of liver tissue

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

CLARITY of intestines

• Large-scale tissue clearing (PACT): Technical evaluation and new perspectives in immunofluorescence, histology, and ultrastructure PH Neckel, U Mattheus, B Hirt, L Just, and AF Mack. Scientific Reports 2016, 6: 34331.

CLARITY of mammary glands

• Imaging the mammary gland and mammary tumours in 3D: Optical tissue clearing and immunofluorescence methods B Lloyd-Lewis, FM Davis, OB Harris, JR Hitchcock, FC Lourenco, M Pasche, and CJ Watson. Breast Cancer Research 2016, 18: 127.

CLARITY of skeletal muscle

• Clearing skeletal muscle with CLARITY for light microscopy imaging A Milgroom and E Ralston. Cell Biology International 2016, 40(4): 478-483.

CLARITY of human brain tissue

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

• Bringing CLARITY to the human brain: visualization of Lewy pathology in three dimensions AKL Liu, MED Hurry, OTW Ng, J DeFelice, HM Lai, RKB Pearce, GT-C Wong, RC-C Chang, and SM Gentleman. Neuropathology and Applied Neurobiology 2016, 42: 573-587.

CLARITY of plants

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

CLARITY of organoids

• CYP3A5 mediates effects of cocaine on human neocorticogenesis: studies using an in vitro 3D self-organized hPSC model with a single cortex-like unit C-T Lee, J Chen, AA Kindberg, RM Bendriem, CE Spivak, MP Williams, CT Richie, A Handreck, BS Mallon, CR Lupica, D-T Lin, BK Harvey, DC Mash, and WJ Freed. Neuropsychopharmacology 2017, 42: 774-784.

Nanoparticle detection with CLARITY

• Three-dimensional optical mapping of nanoparticle distribution in intact tissues S Sindhwani, AM Syed, S Wilhelm, DR Glancy, YY Chen, M Dobosz, and WCW Chan. ACS Nano 2016, 10(5): 5468-5478.

CLARITY extensions, variations, and new directions

• Single-cell phenotyping within transparent intact tissue through whole-body clearing B Yang, JB Treweek, RP Kulkarni, BE Deverman, C-K Chen, E Lubeck, S Shah, L Cai, and V Gradinaru. Cell 2014, 158: 945-958.

• Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis EA Susaki, K Tainaka, D Perrin, F Kishino, T Tawara, TM Watanabe, C Yokoyama, H Onoe, M Eguchi, S Yamaguchi, T Abe, H Kiyonari, Y Shimizu, A Miyawaki, H Yokota, and HR Ueda. Cell 2014, 157: 726-739.

• iDISCO: A simple, rapid method to immunolabel large tissue samples for volume imaging N Renier, Z Wu, DJ Simon, J Yang, P Ariel, M Tessier-Lavigne. Cell 2014, 159: 896-910.

• Expansion microscopy F Chen, PW Tillberg, ES Boyden. Science 2015, 347: 543-548.

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

• Simple, scalable proteomic imaging for high-dimensional profiling of intact systems E Murray, JH Cho, D Goodwin, T Ku, J Swaney, S-Y Kim, H Choi, Y-G Park, J-Y Park, A Hubbert, M McCue, S Vassallo, N Bakh, MP Frosch, VJ Wedeen, HS Seung, and K Chung. Cell 2015, 163: 1500-1514.

• Scalable and Dil-compatible optical clearance of the mammalian brain B Hou, D Zhang, S Zhao, M Wei, Z Yang, S Wang, J Wang, X Zhang, B Liu, L Fan, Y Li, Z Qiu, C Zhang, and T Jiang. Frontiers in Neuroanatomy 2015, 9: 19.

• Clarifying intact 3D tissues on a microfluidic chip for high-throughput structural analysis YY Chen, PN Silva, AM Syed, S Sindhwani, JV Rocheleau, and WCW Chan. PNAS 2016, 113: 14915-14920.

• Simplified three-dimensional tissue clearing and incorporation of colorimetric phenotyping K Sung, Y Ding, J Ma, H Chen, V Huang, M Cheng, CF Yang, JT Kim, D Eguchi, D Di Carlo, TK Hsiai, A Nakano, and RP Kulkarni. Scientific Reports 2016, 6: 30736.

• Rationalisation and validation of an acrylamide-free procedure in three-dimensional histological imaging HM Lai, AKL Liu, W-L Ng, J DeFelice, WS Lee, H Li, W Li, HM Ng, RC-C Chang, B Lin, W Wu, and SM Gentleman. PLoS One 2016, 11(6): e0158628.

• Optimization of the optical transparency of rodent tissues by modified PACT-based passive clearing J Woo, M Lee, JM Seo, HS Park, and YE Cho. Experimental & Molecular Medicine 2016, 48(12): e274.

• Elevated-temperature-induced acceleration of PACT clearing process of mouse brain tissue T Yu, Y Qi, J Zhu, J Xu, H Gong, Q Luo, and D Zhu. Scientific Reports 2017, 7: 38848.

Combined CLARITY and diffusion tensor imaging

• The role of myelination in measures of white matter integrity: Combination of diffusion tensor imaging and two-photon microscopy of CLARITY intact brains EH Chang, M Argyelan, M Aggarwal, T-SS Chandon, KH Karlsgodt, S Mori, and AK Malhotra. NeuroImage 2017, 147: 253-261.

Microscopy

• Light microscopy mapping of connections in the intact brain S-Y Kim, K Chung, and K Deisseroth. Trends in Cognitive Sciences 2013, 17(12): 596-599.

• SPED Light Sheet Microscopy: Fast Mapping of Biological System Structure and Function R Tomer, M Lovett-Barron, I Kauvar, A Andalman, VM Burns, S Sankaran, L Grosenick, M Broxton, S Yang, and K Deisseroth. Cell 2015, 163: 1796-1806.

• Rapid, simple and inexpensive production of custom 3D printed equipment for large-volume fluorescence microscopy AL Tyson, ST Hilton, LC Andreae. International Journal of Pharmaceutics 2015, 494: 651-656.

• Enhancing image quality in cleared tissue with adaptive optics MR Reinig, SW Novak, X Tao, LA Bentolila, DG Roberts, A MacKenzie-Graham, SE Godshalk, MA Raven, DW Knowles, and J Kubby. Journal of Biomedical Optics 2016, 21(12): 121508.

Tissue clearing review articles

• Clarifying tissue clearing DS Richardson and JW Lichtman. Cell 2015, 162(2): 246-257.

• Clearing and labeling techniques for large-scale biological tissues J Seo, M Choe, and S-Y Kim. Molecules and Cells 2016, 39(6): 439-446.