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

• Optical and chemical discoveries recognized for impact on biology and psychiatry K Deisseroth. EMBO Reports 2017, 18(6): 859-860.

• Improved clearing of lipid droplet-rich tissues for three-dimensional structural elucidation M Lai, X Li, J Li, Y Hu, DM Czajkowsky, and Z Shao. Acta Biochimica et Biophysica Sinica 2017, 49(5): 465-467.

• Pathways to clincial CLARITY: volumetric analysis of irregular, soft, and heterogeneous tissues in development and disease B Hsueh, VM Burns, P Pauerstein, K Holzem, L Ye, K Engberg, A-C Wang, X Gu, H Chakravarthy, HE Arda, G Charville, H Vogel, IR Efimov, S Kim, and K Deisseroth. Scientific Reports 2017, 7: 5899.

• Quantitative validation of immunofluorescence and lectin staining using reduced CLARITY acrylamide formulations DM Krolewski, V Kumar, B Martin, R Tomer, K Deisseroth, RM Myers, AF Schatzberg, FS Lee, JD Barchas, WE Bunney, H Akil, and SJ Watson Jr. Brain Structure and Function 2017, doi: 10.1007/s00429-017-1583-z

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.

• Optimized CLARITY technique detects reduced parvalbumin density in a genetic model of schizophrenia J Bastrup and PH Larsen. Journal of Neuroscience Methods 2017, 283: 23-32.

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.

• Exposing the three-dimensional biogeography and metabolic states of pathogens in cystic fibrosis sputum via hydrogel embedding, clearing, and rRNA labeling WH DePas, R Starwalt-Lee, L Van Sambeek, SR Kumar, V Gradinaru, and DK Newman. mBio 2016, 7(5): e00796-16.

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.

• Exploring passive clearing for 3D optical imaging of nanoparticles in intact tissues S Sindhwani, AM Syed, S Wilhelm, and WCW Chan. Bioconjugate Chemistry 2017, 28(1): 253-259.

• Three-dimensional imaging of transparent tissues via metal nanoparticle labeling AM Syed, S Sindhwani, S Wilhelm, BR Kingston, DSW Lee, JL Gommerman, and WCW Chan. Journal of the American Chemical Society 2017, 139: 9961-9971.

Neural 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.

• Progressive nigrostriatal terminal dysfunction and degeneration in the engrailed 1 heterozygous mouse model of Parkinson's disease U Nordstrom, G Beauvais, A Ghosh, BCP Sasidharan, M Lundblad, J Fuchs, RL Joshi, JW Lipton, A Roholt, S Medicetty, TN Feinstein, JA Steiner, ML Escobar Galvis, A Prochiantz, and P Brundin. Neurobiology of Disease 2015, 73: 70-82.

• Transcription factor p63 controls the reserve status but not the stemness of horizontal basal cells in the olfactory epithelium N Schnittke, DB Herrick, B Lin, J Peterson, JH Coleman, AI Packard, W Jang, and JE Schwob. PNAS 2015, 112(36): e5068-e5077.

• The peptidergic control circuit for sighing P Li, WA Janczewski, K Yackle, K Kam, S Pagliardini, MA Krasnow, and JL Feldman. Nature 2016, 530: 293-297.

• 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.

• Selective enhancement of dopamine release in the ventral pallidum of methamphetamine-sensitized mice KA Stout, AR Dunn, KM Lohr, SP Alter, RA Cliburn, TS Guillot, and GW Miller. ACS Chemical Neuroscience 2016, 7(10): 1364-1373.

• A peptide for targeted, systemic delivery of imaging and therapeutic compounds into acute brain injuries AP Mann, P Scodeller, S Hussain, J Joo, E Kwon, GB Braun, T Molder, Z-G She, VR Kotamraju, B Ranscht, S Krajewski, T Teesalu, S Bhatia, MJ Sailor, and E Ruoslahti. Nature Communications 2016, 7: 11980.

• Entry sites of venezuelan and western equine encephalitis viruses in the mouse central nervous system following peripheral infection AT Phillips, AB Rico, CB Stauft, SL Hammond, TA Aboellail, RB Tjalkens, and KE Olson. Journal of Virology 2016, 90(12): 5785-5796.

• TAM receptors regulate multiple features of microglial physiology L Fourgeaud, PG Traves, Y Tufail, H Leal-Bailey, ED Lew, PG Burrola, P Callaway, A Zagorska, CV Rothlin, A Nimmerjahn, and G Lemke. Nature 2016, 532: 240-244.

• Identification of novel cellular clusters define a specialized area in the cerebellar periventricular zone MA Gonzalez-Gonzalez, GB Gomez-Gonzalez, M Becerra-Gonzalez, and A Martinez-Torres. Scientific Reports 2017, 7: 40768.

• Constitutive activation of CREB in mice enhances temporal association learning and increases hippocampal CA1 neuronal spine density and complexity T Serita, H Fukushima, and S Kida. Scientific Reports 2017, 7: 42528.

• Somatostatin-positive interneurons in the dentate gyrus of mice provide local- and long-range septal synaptic inhibition M Yuan, T Meyer, C Benkowitz, S Savanthrapadian, L Ansel-Bollepalli, A Foggetti, P Wulff, P Alcami, C Elgueta, and M Bartos. eLife 2017, 6: e21105.

• Transcriptional regulatory dynamics drive coordinated metabolic and neural response to social challenge in mice MC Saul, CH Seward, JM Troy, H Zhang, LG Sloofman, X Lu, PA Weisner, D Caetano-Anolles, H Sun, SD Zhao, S Chandrasekaran, S Sinha, and L Stubbs. Genome Research 2017, 27: 959-972.

• A manual segmentation tool for three-dimensional neuron datasets C Magliaro, AL Callara, N Vanello, and A Ahluwalia. Frontiers in Neuroinformatics 2017, 11: 36.

• Manipulating fear associations via optogenetic modulation of amygdala inputs to prefrontal cortex O Klavir, M Prigge, A Sarel, R Paz, and O Yizhar. Nature Neuroscience 2017, 20(6): 836-844.

• Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes RA Romanov, A Zeisel, J Bakker, F Girach, A Hellysaz, R Tomer, A Alpar, J Mulder, F Clotman, E Keimpema, B Hsueh, AK Crow, H Martens, C Schwindling, D Calvigioni, JS Bains, Z Mate, G Szabo, Y Yanagawa, M-D Zhang, A Rendeiro, M Farlik, M Uhlen, P Wulff, C Bock, C Broberger, K Deisseroth, T Hokfelt, S Linnarsson, TL Horvath, and T Harkany. Nature Neuroscience 2017, 20(2): 176-188.

• Opposite initialization to novel cues in dopamine signaling in ventral and posterior striatum in mice W Menegas, BM Babayan, N Uchida, and M Watabe-Uchida. eLife 2017, 6: e21886.

• Chrna2-Martinotti cells synchronize layer 5 type A pyramidal cells via rebound excitation MM Hilscher, RN Leao, SJ Edwards, KE Leao, and K Kullander. PLoS Biology 2017, 15(2): e2001392.

• Enhanced astrocytic D-serine underlies synaptic damage after traumatic brain injury EJ Perez, SA Tapanes, ZB Loris, DT Balu, TJ Sick, JT Coyle, and DJ Liebl. Journal of Clinical Investigation 2017, 127(8):3114–3125.

• Orthopedic surgery triggers attention deficits in a delirium-like mouse model R Velagapudi, S Subramaniyan, C Xiong, F Porkka, RM Rodriguiz, WC Wetsel, and N Terrando. Frontiers in Immunology 2019, 10(2675).

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.

• Distribution of raphespinal fibers in the mouse spinal cord H Liang, S Wang, R Francis, R Whan, C Watson, and G Paxinos. Molecular Pain 2015, 11:42.

• 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.

• Arrhythmogenic and metabolic remodeling of failing human heart CR Gloschat, AC Koppel, KK Aras, JA Brennan, KM Holzem, and IR Efimov. Journal of Physiology 2016, 594(14): 3963-3980.

• Light-sheet fluorescence imaging to localize cardiac lineage and protein distribution Y Ding, J Lee, J Ma, K Sung, T Yokata, N Singh, M Dooraghi, P Abiri, Y Wang, RP Kulkarni, A Nakano, TP Nguyen, P Fei, and TK Hsiai. Scientific Reports 2017, 7: 42209.

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 kidney tissue

• Super-resolution stimulated emission depletion imaging of slit diaphragm proteins in optically cleared kidney tissue D Unnersjo-Jess, L Scott, H Blom, and H Brismar. Kidney International 2016, 89(1): 243-247.

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.

• Longitudinal imaging of HIV-1 spread in humanized mice with parallel 3D immunofluorescence and electron tomography C Kieffer, MS Ladinsky, A Ninh, RP Galimidi, and PJ Bjorkman. eLife 2017, 6: e23282.

CLARITY of the pancreas

• Clonal dynamics following p53 loss of heterozygosity in Kras-driven cancers MD Muzumdar, KJ Dorans, KM Chung, R Robbins, T Tammela, V Gocheva, CM-C Li, and T Jacks. Nature Communications 2016, 7: 12685.

CLARITY of the spleen

• Neuroanatomy of the spleen: mapping the relationship between sympathetic neurons and lymphocytes K Murray, DR Godinez, I Brust-Mascher, EN Miller, MG Gareau, C Reardon. PLoS One 2017, 12(7): e0182416.

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 ovarian tissue

• CLARITY reveals dynamics of ovarian follicular architecture and vasculature in three-dimensions Y Feng, P Cui, X Lu, B Hsueh, FM Billig, LZ Yanez, R Tomer, D Boerboom, P Carmeliet, K Deisseroth, and AJW Hsueh. Scientific Reports 2017, 7: 44810.

• Stimulation of ovarian follicle growth after AMPK inhibition X Lu, S Guo, Y Cheng, J-H Kim, Y Feng, and Y Feng. Reproduction 2017, 153: 683-694.

CLARITY of skeletal muscle

• Skeletal muscle tissue clearing for LacZ and fluorescent reporters, and immunofluorescence staining M Verma, BSR Murkonda, Y Asakura, and A Asakura. Skeletal Muscle Regeneration in the Mouse: Methods and Protocols (2016) M. Kyba, New York, NY, Springer New York: 129-140.

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

CLARITY of bone tissue

• Bone CLARITY: Clearing, imaging, and computational analysis of osteoprogenitors within intact bone marrow A Greenbaum, KY Chan, T Dobreva, D Brown, DH Balani, R Boyce, HM Kronenberg, HJ McBride, and V Gradinaru. Science Translational Medicine 2017, 9(387): eaah6518.

CLARITY of eye tissue

• Quantifying three-dimensional rodent retina vascular development using optical tissue clearing and light-sheet microscopy JN Singh, TM Nowlin, GJ Seedorf, SH Abman, and DP Shepherd. Journal of Biomedical Optics 2017, 22(7): 076011.

CLARITY of mouse limbs

• Glial and stem cell expression of murine Fibroblast Growth Factor Receptor 1 in the embryonic and perinatal nervous system JC Collette, L Choubey, and K Muller Smith. PeerJ 2017, 5: e3519.

CLARITY of mouse skin tissue

• Effect of methacrylic acid beads on the sonic hedgehog signaling pathway and macrophage polarization in a subcutaneous injection mouse model A Lisovsky, DKY Zhang, and MV Sefton. Biomaterials 2016, 98: 203-214.

CLARITY of embryonic tissue

• Procedures for the quantification of whole-tissue immunofluorescence images obtained at single-cell resolution during murine tubular organ development T Hirashima and T Adachi. PLoS One 2015, 10(8): e0135343.

• Human amniotic fluid contaminants alter thyroid hormone signalling and early brain development in Xenopus embryos J-B Fini, BB Mughal, S Le Mevel, M Leemans, M Lettmann, P Spirhanzlova, P Affaticati, A Jenett, and BA Demeneix. Scientific Reports 2017, 7: 43786.

• Greater growth of proximal metatarsals in bird embryos and the evolution of hallux position in the grasping foot JF Botelho, D Smith-Paredes, S Soto-Acuna, D Nunez-Leon, V Palma, and AO Vargas. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 2017, 328B: 106-118.

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.

• Development of passive CLARITY and immunofluorescent labelling of multiple proteins in human cerebellum: Understanding mechanisms of neurodegeneration in mitochondrial disease J Phillips, A Laude, R Lightowlers, CM Morris, DM Turnbull, and NZ Lax. Scientific Reports 2016, 6: 26013.

CLARITY of zebrafish

• Macrophage epithelial reprogramming underlies mycobacterial granuloma formation and promotes infection MR Cronan, RW Beerman, AF Rosenberg, JW Saelens, MG Johnson, SH Oehlers, DM Sisk, KL Jurcic Smith, NA Medvitz, SE Miller, LA Trinh, SE Fraser, JF Madden, J Turner, JE Stout, S Lee, and DM Tobin. Immunity 2016, 45: 861-876.

• High-resolution 3D imaging of whole organ after clearing: taking a new look at the zebrafish testis M Fretaud, L Riviere, E De Job, S Gay, J-J Lareyre, J-S Joly, P Affaticati, and V Thermes. Scientific Reports 2017, 7:43012.

• A novel brain tumour model in zebrafish reveals the role of YAP activation in MAPK- and PI3K-induced malignant growth M Mayrhofer, V Gourain, M Reischl, P Affaticati, A Jenett, J-S Joly, M Benelli, F Demichelis, PL Poliani, D Sieger, and M Mione. Disease Models & Mechanisms 2017, 10: 15-28.

• Comparative analysis of monoaminergic cerebrospinal fluid-contacting cells in Osteichthyes (bony vertebrates) AL Xavier, R Fontaine, S Bloch, P Affaticati, A Jenett, M Demarque, P Vernier, and K Yamamoto. Journal of Comparative Neurology 2017, 525: 2265-2283.

• Imaging of viral neuroinvasion in the zebrafish reveals that Sindbis and chikungunya viruses favour different entry routes G Passoni, C Langevin, N Palha, BC Mounce, V Briolat, P Affaticati, E De Job, J-S Joly, M Vignuzzi, M-C Saleh, P Herbomel, P Boudinot, and J-P Levraud. Disease Models and Mechanisms 2017, 10: 847-857.

CLARITY of sea lamprey tissue

• A new clarification method to visualize biliary degeneration during liver metamorphosis in sea lamprey (petromyzon marinus) Y-W Chung-Davidson, PJ Davidson, AM Scott, EJ Walaszczyk, CO Brant, T Buchinger, NS Johnson, and W Li. Journal of Visualized Experiments 2014, 88: e51648.

• Spatiotemporal interplay between multisensory excitation and recruited inhibition in the lamprey optic tectum AA Kardamakis, J Perez-Fernandez, and S Grillner. eLife 2016, 5: e16472.

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.

• Light microscopy of whole plant organs ACJ Timmers. Journal of Microscopy 2016, 263(2): 165-170.

CLARITY of organoids

• Programmed synthesis of three-dimensional tissues ME Todhunter, NY Jee, AJ Hughes, MC Coyle, A Cerchiari, J Farlow, JC Garbe, MA LaBarge, TA Desai, and ZJ Gartner. Nature Methods 2015, 12(10): 975-981.

• 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.

CLARITY Extensions and Variations: Hydrogel-Tissue Chemistry Techniques

• 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.

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

• 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.

• Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping JB Treweek, KY Chan, NC Flytzanis, B Yang, BE Deverman, A Greenbaum, A Lignell, C Xiao, L Cai, MS Ladinsky, PJ Bjorkman, CC Fowlkes, and V Gradinaru. Nature Protocols 2015, 10: 1860-1896.

• 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.

• 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.

• Multiplexed and scalable super-resolution imaging of three-dimensional protein localization in size-adjustable tissues T Ku, J Swaney, J-Y Park, A Albanese, E Murray, JH Cho, Y-G Park, V Mangena, J Chen, and K Chung. Nature Biotechnology 2016, 34(9): 973-981.

• 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.

Other Tissue Clearing Techniques

• SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction M-T Ke, S Fujimoto, and T Imai. Nature Neuroscience 2013, 16: 1154-1161.

• 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.

• 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

• A rapid optical clearing protocol using 2,2'-thiodiethanol for microscopic observation of fixed mouse brain Y Aoyagi, R Kawakami, H Osanai, T Hibi, and T Nemoto. PLoS One 2015, 10(1): e0116280.

• 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.

• ClearSee: A rapid optical clearing reagent for whole-plant fluorescence imaging D Kurihara, Y Mizuta, Y Sato, and T Higashiyama. Development 2015, 142: 4168-4179.

• ScaleS: An optical clearing palette for biological imaging H Hama, H Hioki, K Namiki, T Hoshida, H Kurokawa, F Ishidate, T Kaneko, T Akagi, T Saito, T Saido, and A Miyawaki. Nature Neuroscience 2015, 18: 1518-1529.

• Fluorescent-protein stabilization and high-resolution imaging of cleared, intact mouse brains MK Schwarz, A Scherbarth, R Sprengel, J Engelhardt, P Theer, G Giese. PLoS One 2015, 10(5): e0124650.

• 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.

• A combined method for correlative 3D imaging of biological samples from macro to nano scale M Kellner, M Heidrich, R-A Lorbeer, GC Antonopoulos, L Knudsen, C Wrede, N Izykowski, R Grothausmann, D Jonigk, M Ochs, T Ripken, MP Kuhnel, and H Meyer. Scientific Reports 2016, 6: 35606.

• Shrinkage-mediated imaging of entire organs and organisms using uDISCO C Pan, R Cai, RP Quacquarelli, A Ghasemigharagoz, A Lourbopoulos, P Matryba, N Plesnila, M Dichgans, F Hellal, and A Erturk. Nature Methods 2016, 13(10): 859-867.

• RetroDISCO: Clearing technique to improve quantification of retrograde labeled motor neurons of intact mouse spinal cords E Zygelyte, ME Bernard, JE Tomlinson, MJ Martin, A Terhorst, HE Bradford, SA Lundquist, M Sledziona, and J Cheetham. Journal of Neuroscience Methods 2016, 271: 34-42.

• Rapid and prodium iodide-compatible optical clearing method for brain tissue based on sugar/sugar-alcohol T Yu, Y Qi, J Wang, W Feng, J Xu, J Zhu, Y Yao, H Gong, Q Luo, and D Zhu. Journal of Biomedical Optics 2016, 21(8): 081203.

• Optical clearing delivers ultrasensitive hyperspectral dark-field imaging for single-cell evaluation Y Cui, X Wang, W Ren, J Liu, and J Irudayaraj. ACS Nano 2016, 10: 3132-3143.

• Free of acrylamide sodium dodecyl sulphate (SDS)-based tissue clearing (FASTClear): a novel protocol of tissue clearing for three-dimensional visualization of human brain tissues AKL Liu, HM Lai, RC-C Chang, and SM Gentleman. Neuropathology and Applied Neurobiology 2017, 43(4): 346-351.

• Fully automated evaluation of total glomerular number and capillary tuft size in nephritic kidneys using lightsheet microscopy A Klingberg, A Hasenberg, I Ludwig-Portugall, A Medyukhina, L Mann, A Brenzel, DR Engel, MT Figge, C Kurts, and M Gunzer. Journal of the American Society of Nephrology 2017, 28: 452-459.

• Whole-body profiling of cancer metastasis with single-cell resolution SI Kubota, K Takahashi, J Nishida, Y Morishita, S Ehata, K Tainaka, K Miyazono, and HR Ueda. Cell Reports 2017, 20: 236-250.

• Plastic embedding immunolabeled large-volume samples for three-dimensional high-resolution imaging Y Gang, X Liu, X Wang, Q Zhang, H Zhou, R Chen, L Liu, Y Jia, F Yin, G Rao, J Chen, and S Zeng. Biomedical Optics Express 2017, 8(8): 3583-3596.

• Fast free-of-acrylamide clearing tissue (FACT) - an optimized new protocol for rapid, high-resolution imaging of three-dimensional brain tissue N Xu, A Tamadon, Y Liu, T Ma, RK Leak, J Chen, Y Gao, and Y Feng. Scientific Reports 2017, 7: 9895.

• Multiplex, quantitative cellular analysis in large tissue volumes with clearing-enhanced 3D microscopy (Ce3D) W Li, RN Germain, and MY Gerner. PNAS 2017, 114(35): E7321-E7330.

Combined CLARITY and MicroCT Imaging

• Structural stabilization of tissue for embryo phenotyping using micro-CT with iodine staining MD Wong, S Spring, and RM Henkelman. PLoS One 2013, 8(12): e84321.

• A novel procedure for rapid imaging of adult mouse brains with MicroCT using iodine-based contrast R Anderson and A Murat Maga. PLoS One 2015, 10(11): e0142974.

Combined CLARITY and MRI/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.

• The separate effects of lipids and proteins on brain MRI contrast revealed through tissue clearing C Leuze, M Aswendt, E Ferenczi, CW Liu, B Hsueh, M Goubran, Q Tian, G Steinberg, MM Zeineh, K Deisseroth, and JA McNab. NeuroImage 2017.

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.

• Label-free volumetric optical imaging of intact murine brains J Ren, H Choi, K Chung, and BE Bouma. Scientific Reports 2017, 7: 46306.

• Light-sheet microscopy for slide-free non-destructive pathology of large clinical specimens AK Glaser, NP Reder, Y Chen, EF McCarty, C Yin, L Wei, Y Wang, LD True, and JTC Liu. Nature Biomedical Engineering 2017, 1: 0084.

• 3D printer generated tissue iMolds for cleared tissue using single- and multi-photon microscopy for deep tissue evaluation SJ Miller and JD Rothstein. Biological Procedures Online 2017, 19:7.

Data Analysis Tools

• Deformably registering and annotating whole CLARITY brains to an atlas via Masked LDDMM KS Kutten, JT Vogelstein, N Charon, L Ye, K Deisseroth, and MI Miller. Proceedings of SPIE 2016, 9896: 989616.

• TeraFly: real-time three-dimensional visualization and annotation of terabytes of multidimensional volumetric images A Bria, G Iannello, L Onofri, and H Peng. Nature Methods 2016, 13(3): 192-194.

• A manual segmentation tool for three-dimensional neuron datasets C Magliaro, AL Callara, N Vanello, and A Ahluwalia. Frontiers in Neuroinformatics 2017, 11: 36.

• An interactive framework for whole-brain maps at cellular resolution D Furth, T Vaissiere, O Tzortzi, Y Xuan, A Martin, I Lazaridis, G Spigolon, G Fisone, R Tomer, K Deisseroth, M Carlen, CA Miller, G Rumbaugh, and K Meletis. Nature Neuroscience 2017, 21: 139-149.

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.

• Advances and perspectives in tissue clearing using CLARITY KHR Jensen and RW Berg. Journal of Chemical Neuroanatomy 2017, 86: 19-34.