Journal Articles

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*[https://academic.oup.com/abbs/article-lookup/doi/10.1093/abbs/gmx018 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.
 
*[https://academic.oup.com/abbs/article-lookup/doi/10.1093/abbs/gmx018 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.
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*[https://www.nature.com/articles/s41598-017-05614-4?WT.feed_name=subjects_neurochemistry 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.
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*[https://link.springer.com/article/10.1007%2Fs00429-017-1583-z 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==
 
==ETC Technology==
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*[http://mbio.asm.org/content/7/5/e00796-16 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.
 
*[http://mbio.asm.org/content/7/5/e00796-16 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.
   
==Analysis Using CLARITY==
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==Nanoparticle detection with CLARITY==
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*[http://pubs.acs.org/doi/abs/10.1021/acsnano.6b01879 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.
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*[http://pubs.acs.org/doi/abs/10.1021/acs.bioconjchem.6b00500 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.
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*[http://pubs.acs.org/doi/abs/10.1021/jacs.7b04022 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.
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==Neural Analysis Using CLARITY==
 
*[http://clarityresourcecenter.org/pdfs/spence.pdf 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.
 
*[http://clarityresourcecenter.org/pdfs/spence.pdf 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.
   
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*[http://www.sciencedirect.com/science/article/pii/S0969996114002848 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.
 
*[http://www.sciencedirect.com/science/article/pii/S0969996114002848 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.
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*[http://www.pnas.org/content/112/36/E5068.full#T1 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.
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*[https://www.nature.com/nature/journal/v530/n7590/full/nature16964.html#affil-auth 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.
   
 
*[http://clarityresourcecenter.org/pdfs/ye-allen2016.pdf 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.
 
*[http://clarityresourcecenter.org/pdfs/ye-allen2016.pdf 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.
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*[https://www.nature.com/neuro/journal/v20/n6/full/nn.4523.html 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.
 
*[https://www.nature.com/neuro/journal/v20/n6/full/nn.4523.html 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.
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*[http://www.nature.com/neuro/journal/v20/n2/full/nn.4462.html 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.
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*[https://elifesciences.org/articles/21886 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.
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*[http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001392 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.
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*[https://www.jci.org/articles/view/92300 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.
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*[https://www.frontiersin.org/articles/10.3389/fimmu.2019.02675/full 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==
 
==CLARITY of rat tissue==
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*[http://onlinelibrary.wiley.com/doi/10.1113/JP271992/full 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.
 
*[http://onlinelibrary.wiley.com/doi/10.1113/JP271992/full 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.
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*[https://www.nature.com/articles/srep42209 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==
 
==CLARITY of liver tissue==
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==CLARITY of the pancreas==
 
==CLARITY of the pancreas==
 
*[http://www.nature.com/articles/ncomms12685 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.
 
*[http://www.nature.com/articles/ncomms12685 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.
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==CLARITY of the spleen==
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*[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0182416 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==
 
==CLARITY of mammary glands==
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==CLARITY of skeletal muscle==
 
==CLARITY of skeletal muscle==
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*[https://link.springer.com/protocol/10.1007%2F978-1-4939-3810-0_10 Skeletal muscle tissue clearing for LacZ and fluorescent reporters, and immunofluorescence staining] M Verma, BSR Murkonda, Y Asakura, and A Asakura. <u>Skeletal Muscle Regeneration in the Mouse: Methods and Protocols</u> (2016) M. Kyba, New York, NY, Springer New York: 129-140.
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*[http://onlinelibrary.wiley.com.ezproxy.stanford.edu/doi/10.1002/cbin.10578/abstract Clearing skeletal muscle with CLARITY for light microscopy imaging] A Milgroom and E Ralston. ''Cell Biology International'' 2016, 40(4): 478-483.
 
*[http://onlinelibrary.wiley.com.ezproxy.stanford.edu/doi/10.1002/cbin.10578/abstract 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==
 
==CLARITY of bone tissue==
 
*[http://stm.sciencemag.org/content/9/387/eaah6518 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.
 
*[http://stm.sciencemag.org/content/9/387/eaah6518 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.
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==CLARITY of eye tissue==
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*[https://www.spiedigitallibrary.org/journals/Journal-of-Biomedical-Optics/volume-22/issue-07/076011/Quantifying-three-dimensional-rodent-retina-vascular-development-using-optical-tissue/10.1117/1.JBO.22.7.076011.full?SSO=1 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==
 
==CLARITY of mouse limbs==
 
*[https://peerj.com/articles/3519/ 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.
 
*[https://peerj.com/articles/3519/ 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.
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==CLARITY of mouse skin tissue==
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*[http://www.sciencedirect.com/science/article/pii/S0142961216301442 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==
 
==CLARITY of embryonic tissue==
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*[http://www.nature.com/articles/srep43786 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.
 
*[http://www.nature.com/articles/srep43786 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.
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*[http://onlinelibrary.wiley.com/doi/10.1002/jez.b.22697/full 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==
 
==CLARITY of human brain tissue==
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*[http://onlinelibrary.wiley.com/doi/10.1002/cne.24204/full 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.
 
*[http://onlinelibrary.wiley.com/doi/10.1002/cne.24204/full 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.
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*[http://dmm.biologists.org/content/10/7/847 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==
 
==CLARITY of sea lamprey tissue==
 
*[https://www.jove.com/video/51648/a-new-clarification-method-to-visualize-biliary-degeneration-during 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.
 
*[https://www.jove.com/video/51648/a-new-clarification-method-to-visualize-biliary-degeneration-during 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.
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*[https://elifesciences.org/articles/16472 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==
 
==CLARITY of plants==
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*[http://www.nature.com/npp/journal/v42/n3/full/npp2016156a.html 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.
 
*[http://www.nature.com/npp/journal/v42/n3/full/npp2016156a.html 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==
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==CLARITY Extensions and Variations: Hydrogel-Tissue Chemistry Techniques==
*[http://pubs.acs.org/doi/abs/10.1021/acsnano.6b01879 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.
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*[http://clarityresourcecenter.org/pdfs/gr.pdf 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.
   
*[http://pubs.acs.org/doi/abs/10.1021/acs.bioconjchem.6b00500 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.
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*[http://science.sciencemag.org/content/347/6221/543 Expansion microscopy] F Chen, PW Tillberg, ES Boyden. ''Science'' 2015, 347: 543-548.
   
==CLARITY extensions, variations, and new directions==
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*[http://www.cell.com/cell/abstract/S0092-8674(15)01505-6 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.
*[http://www.nature.com/neuro/journal/v16/n8/full/nn.3447.html 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.
 
   
*[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0084321 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.
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*[http://www.nature.com/nprot/journal/v10/n11/full/nprot.2015.122.html 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.
   
*[http://clarityresourcecenter.org/pdfs/gr.pdf 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.
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*[http://www.pnas.org/content/113/52/14915 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.
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*[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5192069/ 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.
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*[http://www.nature.com/nbt/journal/v34/n9/full/nbt.3641.html?foxtrotcallback=true 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.
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*[http://www.nature.com/articles/srep38848 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.
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==Other Tissue Clearing Techniques==
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*[http://www.nature.com/neuro/journal/v16/n8/full/nn.3447.html 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.
   
 
*[http://clarityresourcecenter.org/pdfs/cubic.pdf 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.
 
*[http://clarityresourcecenter.org/pdfs/cubic.pdf 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.
   
 
*[http://www.cell.com/abstract/S0092-8674(14)01297-5 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.
 
*[http://www.cell.com/abstract/S0092-8674(14)01297-5 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.
 
*[http://science.sciencemag.org/content/347/6221/543 Expansion microscopy] F Chen, PW Tillberg, ES Boyden. ''Science'' 2015, 347: 543-548.
 
   
 
*[http://clarityresourcecenter.org/pdfs/Constantini2015.pdf 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
 
*[http://clarityresourcecenter.org/pdfs/Constantini2015.pdf 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
   
 
*[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0116280 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.
 
*[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0116280 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.
 
*[http://www.cell.com/cell/abstract/S0092-8674(15)01505-6 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.
 
   
 
*[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4338786/ 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.
 
*[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4338786/ 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.
   
 
*[http://dev.biologists.org/content/142/23/4168 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.
 
*[http://dev.biologists.org/content/142/23/4168 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.
 
*[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0142974 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.
 
   
 
*[http://www.nature.com/neuro/journal/v18/n10/full/nn.4107.html Sca''l''eS: 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.
 
*[http://www.nature.com/neuro/journal/v18/n10/full/nn.4107.html Sca''l''eS: 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.
 
*[http://www.nature.com/nprot/journal/v10/n11/full/nprot.2015.122.html 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.
 
   
 
*[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0124650 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.
 
*[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0124650 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.
 
*[http://www.pnas.org/content/113/52/14915 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.
 
   
 
*[http://www.nature.com/articles/srep30736 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.
 
*[http://www.nature.com/articles/srep30736 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.
   
 
*[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4928791/ 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.
 
*[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4928791/ 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.
 
*[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5192069/ 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.
 
   
 
*[http://www.nature.com/articles/srep35606 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.
 
*[http://www.nature.com/articles/srep35606 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.
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*[http://pubs.acs.org/doi/full/10.1021/acsnano.6b00142 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.
 
*[http://pubs.acs.org/doi/full/10.1021/acsnano.6b00142 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.
 
*[http://www.nature.com/articles/srep38848 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.
 
   
 
*[http://onlinelibrary.wiley.com/doi/10.1111/nan.12361/abstract 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.
 
*[http://onlinelibrary.wiley.com/doi/10.1111/nan.12361/abstract 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.
   
 
*[http://jasn.asnjournals.org/content/28/2/452.full 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.
 
*[http://jasn.asnjournals.org/content/28/2/452.full 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.
  +
  +
*[http://www.sciencedirect.com/science/article/pii/S2211124717308069 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.
  +
  +
*[https://www.osapublishing.org/boe/fulltext.cfm?uri=boe-8-8-3583&id=369101 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.
  +
  +
*[https://www.nature.com/articles/s41598-017-10204-5 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.
  +
  +
*[http://www.pnas.org/content/114/35/E7321.full 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==
  +
*[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0084321 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.
  +
  +
*[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0142974 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==
 
==Combined CLARITY and MRI/diffusion tensor imaging==
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*[https://www.nature.com/articles/srep46306 Label-free volumetric optical imaging of intact murine brains] J Ren, H Choi, K Chung, and BE Bouma. ''Scientific Reports'' 2017, 7: 46306.
 
*[https://www.nature.com/articles/srep46306 Label-free volumetric optical imaging of intact murine brains] J Ren, H Choi, K Chung, and BE Bouma. ''Scientific Reports'' 2017, 7: 46306.
  +
  +
*[https://www.nature.com/articles/s41551-017-0084 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.
  +
  +
*[https://biologicalproceduresonline.biomedcentral.com/articles/10.1186/s12575-017-0057-2 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==
  +
*[http://proceedings.spiedigitallibrary.org/proceeding.aspx?articleid=2520352 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.
  +
  +
*[https://www.nature.com/nmeth/journal/v13/n3/full/nmeth.3767.html#affil-auth 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.
  +
  +
*[http://journal.frontiersin.org/article/10.3389/fninf.2017.00036/full A manual segmentation tool for three-dimensional neuron datasets] C Magliaro, AL Callara, N Vanello, and A Ahluwalia. ''Frontiers in Neuroinformatics'' 2017, 11: 36.
  +
  +
*[https://www.nature.com/articles/s41593-017-0027-7 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==
 
==Tissue clearing review articles==
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*[http://www.molcells.org/journal/view.html?doi=10.14348/molcells.2016.0088&sort=&scale=10&key=&keyword=&s_v=39&s_n=6&pn=vol&TG=vol&year=2016 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.
 
*[http://www.molcells.org/journal/view.html?doi=10.14348/molcells.2016.0088&sort=&scale=10&key=&keyword=&s_v=39&s_n=6&pn=vol&TG=vol&year=2016 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.
  +
  +
*[https://www.sciencedirect.com/science/article/pii/S0891061817300984 Advances and perspectives in tissue clearing using CLARITY] KHR Jensen and RW Berg. ''Journal of Chemical Neuroanatomy'' 2017, 86: 19-34.

Latest revision as of 20:09, 22 November 2019

Contents

[edit] CLARITY Technique

[edit] ETC Technology

[edit] RNA detection with CLARITY

[edit] Nanoparticle detection with CLARITY

[edit] Neural Analysis Using CLARITY

  • 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.

[edit] CLARITY of rat tissue

[edit] CLARITY of spinal cord

[edit] CLARITY of lung tissue

[edit] CLARITY of heart tissue

[edit] CLARITY of liver tissue

[edit] CLARITY of kidney tissue

[edit] CLARITY of intestines

[edit] CLARITY of the pancreas

[edit] CLARITY of the spleen

[edit] CLARITY of mammary glands

[edit] CLARITY of ovarian tissue

[edit] CLARITY of skeletal muscle

[edit] CLARITY of bone tissue

[edit] CLARITY of eye tissue

[edit] CLARITY of mouse limbs

[edit] CLARITY of mouse skin tissue

[edit] CLARITY of embryonic tissue

[edit] CLARITY of human brain tissue

[edit] CLARITY of zebrafish

[edit] CLARITY of sea lamprey tissue

[edit] CLARITY of plants

[edit] CLARITY of organoids

[edit] CLARITY Extensions and Variations: Hydrogel-Tissue Chemistry Techniques

[edit] Other Tissue Clearing Techniques

[edit] Combined CLARITY and MicroCT Imaging

[edit] Combined CLARITY and MRI/diffusion tensor imaging

[edit] Microscopy

[edit] Data Analysis Tools

[edit] Tissue clearing review articles