Hydrogel-Tissue Chemistry: Principles and Applications

Literature Cited

1. 1.  Adhikari A, Lerner TN, Finkelstein J, Pak S, Jennings JH et al. 2015. Basomedial amygdala mediates top-down control of anxiety and fear. Nature 527:179–85
   [Google Scholar]
2. 2.  Anderson R, Maga AM 2015. A novel procedure for rapid imaging of adult mouse brains with microCT using iodine-based contrast. PLOS ONE 10:e0142974
   [Google Scholar]
3. 3.  Ando K, Laborde Q, Lazar A, Godefroy D, Youssef I et al. 2014. Inside Alzheimer brain with CLARITY: senile plaques, neurofibrillary tangles and axons in 3-D. Acta Neuropathol 128:457–59
   [Google Scholar]
4. 4.  Aoyagi Y, Kawakami R, Osanai H, Hibi T, Nemoto T 2015. A rapid optical clearing protocol using 2,2′-thiodiethanol for microscopic observation of fixed mouse brain. PLOS ONE 10:e0116280
   [Google Scholar]
5. 5.  Bastrup J, Larsen PH 2017. Optimized CLARITY technique detects reduced parvalbumin density in a genetic model of schizophrenia. J. Neurosci. Methods 283:23–32
   [Google Scholar]
6. 6.  Botelho JF, Smith-Paredes D, Soto-Acuna S, Nunez-Leon D, Palma V, Vargas AO 2017. Greater growth of proximal metatarsals in bird embryos and the evolution of hallux position in the grasping foot. J. Exp. Zool. B Mol. Dev. Evol. 328:106–18
   [Google Scholar]
7. 7.  Bria A, Iannello G, Onofri L, Peng H 2016. TeraFly: real-time three-dimensional visualization and annotation of terabytes of multidimensional volumetric images. Nat. Methods 13:192–94
   [Google Scholar]
8. 8.  Chan KY, Jang MJ, Yoo BB, Greenbaum A, Ravi N et al. 2017. Engineered AAVs for efficient noninvasive gene delivery to the central and peripheral nervous systems. Nat. Neurosci. 20:1172–79
   [Google Scholar]
9. 9.  Chang EH, Argyelan M, Aggarwal M, Chandon TS, Karlsgodt KH et al. 2017. The role of myelination in measures of white matter integrity: combination of diffusion tensor imaging and two-photon microscopy of CLARITY intact brains. Neuroimage 147:253–61
   [Google Scholar]
10. 10.  Chang JB, Chen F, Yoon YG, Jung EE, Babcock H et al. 2017. Iterative expansion microscopy. Nat. Methods 14:593–99
    [Google Scholar]
11. 11.  Chen F, Tillberg PW, Boyden ES 2015. Expansion microscopy. Science 347:543
    [Google Scholar]
12. 12.  Chen F, Wassie AT, Cote AJ, Sinha A, Alon S et al. 2016. Nanoscale imaging of RNA with expansion microscopy. Nat. Methods 13:679–84
    [Google Scholar]
13. 13.  Chen YY, Silva PN, Syed AM, Sindhwani S, Rocheleau JV, Chan WC 2016. Clarifying intact 3D tissues on a microfluidic chip for high-throughput structural analysis. PNAS 113:14915–20
    [Google Scholar]
14. 14.  Chung-Davidson YW, Davidson PJ, Scott AM, Walaszczyk EJ, Brant CO et al. 2014. A new clarification method to visualize biliary degeneration during liver metamorphosis in Sea Lamprey (Petromyzon marinus). J. Vis. Exp. 6:88
    [Google Scholar]
15. 15.  Chung K, Deisseroth K 2013. CLARITY for mapping the nervous system. Nat. Methods 10:508–13
    [Google Scholar]
16. 16.  Chung K, Wallace J, Kim SY, Kalyanasundaram S, Andalman AS et al. 2013. Structural and molecular interrogation of intact biological systems. Nature 497:332–37
    [Google Scholar]
17. 17.  Collette JC, Choubey L, Smith KM 2017. Glial and stem cell expression of murine Fibroblast Growth Factor Receptor 1 in the embryonic and perinatal nervous system. PeerJ 5:e3519
    [Google Scholar]
18. 18.  Costantini I, Ghobril JP, Di Giovanna AP, Allegra Mascaro AL, Silvestri L et al. 2015. A versatile clearing agent for multi-modal brain imaging. Sci. Rep. 5:9808
    [Google Scholar]
19. 19.  Cronan MR, Beerman RW, Rosenberg AF, Saelens JW, Johnson MG et al. 2016. Macrophage epithelial reprogramming underlies mycobacterial granuloma formation and promotes infection. Immunity 45:861–76
    [Google Scholar]
20. 20.  Cronan MR, Rosenberg AF, Oehlers SH, Saelens JW, Sisk DM et al. 2015. CLARITY and PACT-based imaging of adult zebrafish and mouse for whole-animal analysis of infections. Dis. Model. Mech. 8:1643–50
    [Google Scholar]
21. 21.  Cui Y, Wang X, Ren W, Liu J, Irudayaraj J 2016. Optical clearing delivers ultrasensitive hyperspectral dark-field imaging for single-cell evaluation. ACS Nano 10:3132–43
    [Google Scholar]
22. 22.  d'Esposito A, Nikitichev D, Desjardins A, Walker-Samuel S, Lythgoe MF 2015. Quantification of light attenuation in optically cleared mouse brains. J. Biomed. Opt. 20:80503
    [Google Scholar]
23. 23.  Deisseroth K. 2016. A look inside the brain. Sci. Am. 315:30–37
    [Google Scholar]
24. 24.  Deisseroth K. 2017. Optical and chemical discoveries recognized for impact on biology and psychiatry. EMBO Rep 18:859–60
    [Google Scholar]
25. 25.  Deisseroth KA, Chung K 2015. Methods and compositions for preparing biological specimens for microscopic analysis www.google.com/patents/US20150144490. Filing date: March 13, 2013. US Patent Appl. No. US20150144490
26. 26.  Deisseroth KA, Gradinaru V 2014. Functional targeted brain endoskeletonization www.google.com/patents/US20140030192. Filing date: Jan 26, 2012. US Patent Appl. No. US20140030192
27. 27.  DePas WH, Starwalt-Lee R, Van Sambeek L, Ravindra Kumar S, Gradinaru V, Newman DK 2016. Exposing the three-dimensional biogeography and metabolic states of pathogens in cystic fibrosis sputum via hydrogel embedding, clearing, and rRNA labeling. mBio 7:5e00796–16
    [Google Scholar]
28. 28.  Deverman BE, Pravdo PL, Simpson BP, Kumar SR, Chan KY et al. 2016. Cre-dependent selection yields AAV variants for widespread gene transfer to the adult brain. Nat. Biotech. 34:204–9
    [Google Scholar]
29. 29.  Ding Y, Lee J, Ma J, Sung K, Yokota T et al. 2017. Light-sheet fluorescence imaging to localize cardiac lineage and protein distribution. Sci. Rep. 7:42209
    [Google Scholar]
30. 30.  Dodt H-U. 2015. The superresolved brain. Science 347:474–75
    [Google Scholar]
31. 31.  Dodt H-U, Leischner U, Schierloh A, Jahrling N, Mauch CP et al. 2007. Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain. Nat. Methods 4:331–36
    [Google Scholar]
32. 32.  Epp JR, Niibori Y, Liz Hsiang HL, Mercaldo V, Deisseroth K et al. 2015. Optimization of CLARITY for clearing whole-brain and other intact organs. eNeuro 2:1–15
    [Google Scholar]
33. 33.  Ertürk A, Becker K, Jährling N, Mauch CP, Hojer CD et al. 2012. Three-dimensional imaging of solvent-cleared organs using 3DISCO. Nat. Protoc. 7:1983–95
    [Google Scholar]
34. 34.  Feldman MY. 1973. Reactions of nucleic acids and nucleoproteins with formaldehyde. Prog. Nucl. Acid Res. Mol. Biol. 13:1–49
    [Google Scholar]
35. 35.  Feng Y, Cui P, Lu X, Hsueh B, Möller Billig F et al. 2017. CLARITY reveals dynamics of ovarian follicular architecture and vasculature in three-dimensions. Sci. Rep. 7:44810
    [Google Scholar]
36. 36.  Fini JB, Mughal BB, Le Mevel S, Leemans M, Lettmann M et al. 2017. Human amniotic fluid contaminants alter thyroid hormone signalling and early brain development in Xenopus embryos. Sci. Rep. 7:43786
    [Google Scholar]
37. 37.  Font-Burgada J, Shalapour S, Ramaswamy S, Hsueh B, Rossell D et al. 2015. Hybrid periportal hepatocytes regenerate the injured liver without giving rise to cancer. Cell 162:766–79
    [Google Scholar]
38. 38.  Fourgeaud L, Traves PG, Tufail Y, Leal-Bailey H, Lew ED et al. 2016. TAM receptors regulate multiple features of microglial physiology. Nature 532:240–44
    [Google Scholar]
39. 39.  Fretaud M, Riviere L, Job E, Gay S, Lareyre JJ et al. 2017. High-resolution 3D imaging of whole organ after clearing: taking a new look at the zebrafish testis. Sci. Rep. 7:43012
    [Google Scholar]
40. 40.  Fürth D, Vaissière T, Tzortzi O, Xuan Y, Märtin A et al. 2017. An interactive framework for whole-brain maps at cellular resolution. Nat. Neurosci. 21:139–49
    [Google Scholar]
41. 41.  Glaser AK, Reder NP, Chen Y, McCarty EF, Yin C et al. 2017. Light-sheet microscopy for slide-free non-destructive pathology of large clinical specimens. Nat. Biomed. Eng. 1:0084
    [Google Scholar]
42. 42.  Gloschat CR, Koppel AC, Aras KK, Brennan JA, Holzem KM, Efimov IR 2016. Arrhythmogenic and metabolic remodelling of failing human heart. J. Physiol. 594:3963–80
    [Google Scholar]
43. 43.  Gonzalez-Gonzalez MA, Gomez-Gonzalez GB, Becerra-Gonzalez M, Martinez-Torres A 2017. Identification of novel cellular clusters define a specialized area in the cerebellar periventricular zone. Sci. Rep. 7:40768
    [Google Scholar]
44. 44.  Greenbaum A, Chan KY, Dobreva T, Brown D, Balani DH et al. 2017. Bone CLARITY: clearing, imaging, and computational analysis of osteoprogenitors within intact bone marrow. Sci. Transl. Med. 9:387
    [Google Scholar]
45. 45.  Hama H, Hioki H, Namiki K, Hoshida T, Kurokawa H et al. 2015. ScaleS: an optical clearing palette for biological imaging. Nat. Neurosci. 18:1518–29
    [Google Scholar]
46. 46.  Hama H, Kurokawa H, Kawano H, Ando R, Shimogori T et al. 2011. Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain. Nat. Neurosci. 14:1481–88
    [Google Scholar]
47. 47.  Hilscher MM, Leao RN, Edwards SJ, Leao KE, Kullander K 2017. Chrna2-Martinotti cells synchronize layer 5 type A pyramidal cells via rebound excitation. PLOS Biol 15:e2001392
    [Google Scholar]
48. 48.  Hirashima T, Adachi T 2015. Procedures for the quantification of whole-tissue immunofluorescence images obtained at single-cell resolution during murine tubular organ development. PLOS ONE 10:e0135343
    [Google Scholar]
49. 49.  Hou B, Zhang D, Zhao S, Wei M, Yang Z et al. 2015. Scalable and DiI-compatible optical clearance of the mammalian brain. Front. Neuroanat 9:19
    [Google Scholar]
50. 50.  Hsiang HL, Epp JR, van den Oever MC, Yan C, Rashid AJ et al. 2014. Manipulating a “cocaine engram” in mice. J. Neurosci. 34:14115–27
    [Google Scholar]
51. 51.  Hsueh B, Burns VM, Pauerstein P, Holzem K, Ye L et al. 2017. Pathways to clinical CLARITY: volumetric analysis of irregular, soft, and heterogeneous tissues in development and disease. Sci. Rep. 7:5899
    [Google Scholar]
52. 52.  Jensen KHR, Berg RW 2016. CLARITY-compatible lipophilic dyes for electrode marking and neuronal tracing. Sci. Rep. 6:32674
    [Google Scholar]
53. 53.  Jensen KHR, Berg RW 2017. Advances and perspectives in tissue clearing using CLARITY. J. Chem. Neuroanat. 86:19–34
    [Google Scholar]
54. 54.  Joshi NS, Akama-Garren EH, Lu Y, Lee DY, Chang GP et al. 2015. Regulatory T cells in tumor-associated tertiary lymphoid structures suppress anti-tumor T cell responses. Immunity 43:579–90
    [Google Scholar]
55. 55.  Kardamakis AA, Pérez-Fernández J, Grillner S 2016. Spatiotemporal interplay between multisensory excitation and recruited inhibition in the lamprey optic tectum. eLife 5:e16472
    [Google Scholar]
56. 56.  Ke MT, Fujimoto S, Imai T 2013. SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction. Nat. Neurosci. 16:1154–61
    [Google Scholar]
57. 57.  Kellner M, Heidrich M, Lorbeer RA, Antonopoulos GC, Knudsen L et al. 2016. A combined method for correlative 3D imaging of biological samples from macro to nano scale. Sci. Rep. 6:35606
    [Google Scholar]
58. 58.  Kieffer C, Ladinsky MS, Ninh A, Galimidi RP, Bjorkman PJ 2017. Longitudinal imaging of HIV-1 spread in humanized mice with parallel 3D immunofluorescence and electron tomography. eLife 6:e23282
    [Google Scholar]
59. 59.  Kim S-Y, Cho JH, Murray E, Bakh N, Choi H et al. 2015. Stochastic electrotransport selectively enhances the transport of highly electromobile molecules. PNAS 112:E6274–83
    [Google Scholar]
60. 60.  Klavir O, Prigge M, Sarel A, Paz R, Yizhar O 2017. Manipulating fear associations via optogenetic modulation of amygdala inputs to prefrontal cortex. Nat. Neurosci. 20:836–44
    [Google Scholar]
61. 61.  Klingberg A, Hasenberg A, Ludwig-Portugall I, Medyukhina A, Mann L et al. 2017. Fully automated evaluation of total glomerular number and capillary tuft size in nephritic kidneys using lightsheet microscopy. J. Am. Soc. Nephrol. 28:452–59
    [Google Scholar]
62. 62.  Kolesova H, Capek M, Radochova B, Janacek J, Sedmera D 2016. Comparison of different tissue clearing methods and 3D imaging techniques for visualization of GFP-expressing mouse embryos and embryonic hearts. Histochem. Cell Biol. 146:141–52
    [Google Scholar]
63. 63.  Krolewski DM, Kumar V, Martin B, Tomer R, Deisseroth K et al. 2018. Quantitative validation of immunofluorescence and lectin staining using reduced CLARITY acrylamide formulations. Brain Struct. Funct. 223:987–99
    [Google Scholar]
64. 64.  Ku T, Swaney J, Park JY, Albanese A, Murray E et al. 2016. Multiplexed and scalable super-resolution imaging of three-dimensional protein localization in size-adjustable tissues. Nat. Biotechnol. 34:973–81
    [Google Scholar]
65. 65.  Kubota SI, Takahashi K, Nishida J, Morishita Y, Ehata S et al. 2017. Whole-body profiling of cancer metastasis with single-cell resolution. Cell Rep 20:236–50
    [Google Scholar]
66. 66.  Kurihara D, Mizuta Y, Sato Y, Higashiyama T 2015. ClearSee: a rapid optical clearing reagent for whole-plant fluorescence imaging. Development 142:4168–79
    [Google Scholar]
67. 67.  Kutten KS, Vogelstein JT, Charon N, Ye L, Deisseroth K, Miller MI 2016. Deformably registering and annotating whole CLARITY brains to an atlas via masked LDDMM Presented at Proc. SPIE Opt., Photonics, Digit Technol. for Imaging Appl. IV Brussels, Belg:
68. 68.  Lai HM, Liu AKL, Ng W-L, DeFelice J, Lee WS et al. 2016. Rationalisation and validation of an acrylamide-free procedure in three-dimensional histological imaging. PLOS ONE 11:e0158628
    [Google Scholar]
69. 69.  Lai M, Li X, Li J, Hu Y, Czajkowsky DM, Shao Z 2017. Improved clearing of lipid droplet-rich tissues for three-dimensional structural elucidation. Acta Biochim. Biophys. Sin. 49:465–67
    [Google Scholar]
70. 70.  Lee CT, Chen J, Kindberg AA, Bendriem RM, Spivak CE et al. 2017. CYP3A5 mediates effects of cocaine on human neocorticogenesis: studies using an in vitro 3D self-organized hPSC model with a single cortex-like unit. Neuropsychopharmacology 42:774–84
    [Google Scholar]
71. 71.  Lee E, Choi J, Jo Y, Kim JY, Jang YJ et al. 2016. ACT-PRESTO: rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging. Sci. Rep. 6:18631
    [Google Scholar]
72. 72.  Lee H, Park JH, Seo I, Park SH, Kim S 2014. Improved application of the electrophoretic tissue clearing technology, CLARITY, to intact solid organs including brain, pancreas, liver, kidney, lung, and intestine. BMC Dev. Biol. 14:48
    [Google Scholar]
73. 73.  Lerner TN, Shilyansky C, Davidson TJ, Evans KE, Beier KT et al. 2015. Intact-brain analyses reveal distinct information carried by SNc dopamine subcircuits. Cell 162:635–47
    [Google Scholar]
74. 74.  Leuze C, Aswendt M, Ferenczi E, Liu CW, Hsueh B et al. 2017. The separate effects of lipids and proteins on brain MRI contrast revealed through tissue clearing. Neuroimage 156:412–22
    [Google Scholar]
75. 75.  Li J, Czajkowsky DM, Li X, Shao Z 2015. Fast immuno-labeling by electrophoretically driven infiltration for intact tissue imaging. Sci. Rep. 5:10640
    [Google Scholar]
76. 76.  Li P, Janczewski WA, Yackle K, Kam K, Pagliardini S et al. 2016. The peptidergic control circuit for sighing. Nature 530:293–97
    [Google Scholar]
77. 77.  Liang H, Schofield E, Paxinos G 2016. Imaging serotonergic fibers in the mouse spinal cord using the CLARITY/CUBIC technique. J. Vis. Exp. 108:53673
    [Google Scholar]
78. 78.  Liang H, Wang S, Francis R, Whan R, Watson C, Paxinos G 2015. Distribution of raphespinal fibers in the mouse spinal cord. Mol. Pain 11:42
    [Google Scholar]
79. 79.  Lisovsky A, Zhang DK, Sefton MV 2016. Effect of methacrylic acid beads on the sonic hedgehog signaling pathway and macrophage polarization in a subcutaneous injection mouse model. Biomaterials 98:203–14
    [Google Scholar]
80. 80.  Liu AKL, Hurry MED, Ng OTW, DeFelice J, Lai HM et al. 2016. Bringing CLARITY to the human brain: visualization of Lewy pathology in three dimensions. Neuropathol. Appl. Neurobiol. 42:573–87
    [Google Scholar]
81. 81.  Liu AKL, Lai HM, Chang RCC, Gentleman SM 2017. 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. Neuropathol. Appl. Neurobiol. 43:346–51
    [Google Scholar]
82. 82.  Lloyd-Lewis B, Davis FM, Harris OB, Hitchcock JR, Lourenco FC et al. 2016. Imaging the mammary gland and mammary tumours in 3D: optical tissue clearing and immunofluorescence methods. Breast Cancer Res 18:127
    [Google Scholar]
83. 83.  Lu X, Guo S, Cheng Y, Kim J-h, Feng Y, Feng Y 2017. Stimulation of ovarian follicle growth after AMPK inhibition. Reproduction 153:683–94
    [Google Scholar]
84. 84.  Magliaro C, Callara AL, Mattei G, Morcinelli M, Viaggi C et al. 2016. Clarifying CLARITY: quantitative optimization of the diffusion based delipidation protocol for genetically labeled tissue. Front. Neurosci. 10:179
    [Google Scholar]
85. 85.  Magliaro C, Callara AL, Vanello N, Ahluwalia A 2017. A manual segmentation tool for three-dimensional neuron datasets. Front. Neuroinform. 11:36
    [Google Scholar]
86. 86.  Mann AP, Scodeller P, Hussain S, Joo J, Kwon E et al. 2016. A peptide for targeted, systemic delivery of imaging and therapeutic compounds into acute brain injuries. Nat. Commun. 7:11980
    [Google Scholar]
87. 87.  Marx V. 2014. Microscopy: seeing through tissue. Nat. Methods 11:1209–14
    [Google Scholar]
88. 88.  Mayrhofer M, Gourain V, Reischl M, Affaticati P, Jenett A et al. 2017. A novel brain tumour model in zebrafish reveals the role of YAP activation in MAPK- and PI3K-induced malignant growth. Dis. Model. Mech. 10:15–28
    [Google Scholar]
89. 89.  Menegas W, Babayan BM, Uchida N, Watabe-Uchida M 2017. Opposite initialization to novel cues in dopamine signaling in ventral and posterior striatum in mice. eLife 6:e21886
    [Google Scholar]
90. 90.  Menegas W, Bergan JF, Ogawa SK, Isogai Y, Umadevi Venkataraju K et al. 2015. Dopamine neurons projecting to the posterior striatum form an anatomically distinct subclass. eLife 4:e10032
    [Google Scholar]
91. 91.  Milgroom A, Ralston E 2016. Clearing skeletal muscle with CLARITY for light microscopy imaging. Cell Biol. Int. 40:478–83
    [Google Scholar]
92. 92.  Miller SJ, Rothstein JD 2016. Astroglia in thick tissue with super resolution and cellular reconstruction. PLOS ONE 11:e0160391
    [Google Scholar]
93. 93.  Miller SJ, Rothstein JD 2017. 3D printer generated tissue iMolds for cleared tissue using single- and multi-photon microscopy for deep tissue evaluation. Biol. Proced. Online 19:7
    [Google Scholar]
94. 94.  Murray E, Cho JH, Goodwin D, Ku T, Swaney J et al. 2015. Simple, scalable proteomic imaging for high-dimensional profiling of intact systems. Cell 163:1500–14
    [Google Scholar]
95. 95.  Muzumdar MD, Dorans KJ, Chung KM, Robbins R, Tammela T et al. 2016. Clonal dynamics following p53 loss of heterozygosity in Kras-driven cancers. Nat. Commun. 7:12685
    [Google Scholar]
96. 96.  Neckel PH, Mattheus U, Hirt B, Just L, Mack AF 2016. Large-scale tissue clearing (PACT): technical evaluation and new perspectives in immunofluorescence, histology, and ultrastructure. Sci. Rep. 6:34331
    [Google Scholar]
97. 97.  Nordströma U, Beauvais G, Ghosh A, Pulikkaparambil Sasidharan BC, Lundblad M et al. 2015. Progressive nigrostriatal terminal dysfunction and degeneration in the engrailed1 heterozygous mouse model of Parkinson's disease. Neurobiol. Dis. 73:70–82
    [Google Scholar]
98. 98.  Palmer WM, Martin AP, Flynn JR, Reed SL, White RG et al. 2015. PEA-CLARITY: 3D molecular imaging of whole plant organs. Sci. Rep. 5:13492
    [Google Scholar]
99. 99.  Pan C, Cai R, Quacquarelli FP, Ghasemigharagoz A, Lourbopoulos A et al. 2016. Shrinkage-mediated imaging of entire organs and organisms using uDISCO. Nat. Methods 13:859–67
    [Google Scholar]
100. 100.  Pan M, Reid MA, Lowman XH, Kulkarni RP, Tran TQ et al. 2016. Regional glutamine deficiency in tumours promotes dedifferentiation through inhibition of histone demethylation. Nat. Cell Biol. 18:1090–101
     [Google Scholar]
101. 101.  Phillips AT, Rico AB, Stauft CB, Hammond SL, Aboellail TA et al. 2016. Entry sites of Venezuelan and western equine encephalitis viruses in the mouse central nervous system following peripheral infection. J. Virol. 90:5785–96
     [Google Scholar]
102. 102.  Phillips J, Laude A, Lightowlers R, Morris CM, Turnbull DM, Lax NZ 2016. Development of passive CLARITY and immunofluorescent labelling of multiple proteins in human cerebellum: understanding mechanisms of neurodegeneration in mitochondrial disease. Sci. Rep. 6:26013
     [Google Scholar]
103. 103.  Plummer NW, Evsyukova IY, Robertson SD, de Marchena J, Tucker CJ, Jensen P 2015. Expanding the power of recombinase-based labeling to uncover cellular diversity. Development 142:4385–93
     [Google Scholar]
104. 104.  Poguzhelskaya E, Artamonov D, Bolshakova A, Vlasova O, Bezprozvanny I 2014. Simplified method to perform CLARITY imaging. Mol. Neurodegener. 9:19
     [Google Scholar]
105. 105.  Reinig MR, Novak SW, Tao X, Bentolila LA, Roberts DG et al. 2016. Enhancing image quality in cleared tissue with adaptive optics. J. Biomed. Opt. 21:121508
     [Google Scholar]
106. 106.  Ren J, Choi H, Chung K, Bouma BE 2017. Label-free volumetric optical imaging of intact murine brains. Sci. Rep. 7:46306
     [Google Scholar]
107. 107.  Renier N, Wu Z, Simon DJ, Yang J, Ariel P, Tessier-Lavigne M 2014. iDISCO: a simple, rapid method to immunolabel large tissue samples for volume imaging.. Cell 159:896–910
     [Google Scholar]
108. 108.  Roberts DG, Johnsonbaugh HB, Spence RD, MacKenzie-Graham A 2016. Optical clearing of the mouse central nervous system using passive CLARITY. J. Vis. Exp. 112:e54025
     [Google Scholar]
109. 109.  Romanov RA, Zeisel A, Bakker J, Girach F, Hellysaz A et al. 2017. Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes. Nat. Neurosci. 20:176–88
     [Google Scholar]
110. 110.  Saboor F, Reckmann AN, Tomczyk CU, Peters DM, Weissmann N et al. 2016. Nestin-expressing vascular wall cells drive development of pulmonary hypertension. Eur. Respir. J. 47:876–88
     [Google Scholar]
111. 111.  Saul MC, Seward CH, Troy JM, Zhang H, Sloofman LG et al. 2017. Transcriptional regulatory dynamics drive coordinated metabolic and neural response to social challenge in mice. Genome Res 27:959–72
     [Google Scholar]
112. 112.  Schnittke N, Herrick DB, Lin B, Peterson J, Coleman JH et al. 2015. Transcription factor p63 controls the reserve status but not the stemness of horizontal basal cells in the olfactory epithelium. PNAS 112:E5068–77
     [Google Scholar]
113. 113.  Schwarz MK, Scherbarth A, Sprengel R, Engelhardt J, Theer P, Giese G 2015. Fluorescent-protein stabilization and high-resolution imaging of cleared, intact mouse brains. PLOS ONE 10:e0124650
     [Google Scholar]
114. 114.  Serita T, Fukushima H, Kida S 2017. Constitutive activation of CREB in mice enhances temporal association learning and increases hippocampal CA1 neuronal spine density and complexity. Sci. Rep. 7:42528
     [Google Scholar]
115. 115.  Shah S, Lubeck E, Schwarzkopf M, He TF, Greenbaum A et al. 2016. Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing. Development 143:2862–67
     [Google Scholar]
116. 116.  Sindhwani S, Syed AM, Wilhelm S, Chan WC 2017. Exploring passive clearing for 3D optical imaging of nanoparticles in intact tissues. Bioconjug. Chem. 28:253–59
     [Google Scholar]
117. 117.  Sindhwani S, Syed AM, Wilhelm S, Glancy DR, Chen YY et al. 2016. Three-dimensional optical mapping of nanoparticle distribution in intact tissues. ACS Nano 10:5468–78
     [Google Scholar]
118. 118.  Spence RD, Kurth F, Itoh N, Mongerson CR, Wailes SH et al. 2014. Bringing CLARITY to gray matter atrophy. Neuroimage 101:625–32
     [Google Scholar]
119. 119.  Stefaniuk M, Gualda EJ, Pawlowska M, Legutko D, Matryba P et al. 2016. Light-sheet microscopy imaging of a whole cleared rat brain with Thy1-GFP transgene. Sci. Rep. 6:28209
     [Google Scholar]
120. 120.  Stout KA, Dunn AR, Lohr KM, Alter SP, Cliburn RA et al. 2016. Selective enhancement of dopamine release in the ventral pallidum of methamphetamine-sensitized mice. ACS Chem. Neurosci. 7:1364–73
     [Google Scholar]
121. 121.  Sulkin MS, Widder E, Shao C, Holzem KM, Gloschat C et al. 2013. Three-dimensional printing physiology laboratory technology. Am. J. Physiol. Heart Circ. Physiol. 305:H1569–73
     [Google Scholar]
122. 122.  Sung K, Ding Y, Ma J, Chen H, Huang V et al. 2016. Simplified three-dimensional tissue clearing and incorporation of colorimetric phenotyping. Sci. Rep. 6:30736
     [Google Scholar]
123. 123.  Susaki EA, Tainaka K, Perrin D, Kishino F, Tawara T et al. 2014. Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis. Cell 157:726–39
     [Google Scholar]
124. 124.  Susaki EA, Tainaka K, Perrin D, Yukinaga H, Kuno A, Ueda HR 2015. Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging. Nat. Protoc. 10:1709–27
     [Google Scholar]
125. 125.  Sylwestrak EL, Rajasethupathy P, Wright MA, Jaffe A, Deisseroth K 2016. Multiplexed intact-tissue transcriptional analysis at cellular resolution. Cell 164:792–804
     [Google Scholar]
126. 126.  Tainaka K, Kubota SI, Suyama TQ, Susaki EA, Perrin D et al. 2014. Whole-body imaging with single-cell resolution by tissue decolorization. Cell 159:911–24
     [Google Scholar]
127. 127.  Tillberg PW, Chen F, Piatkevich KD, Zhao Y, Yu C-C et al. 2016. Protein-retention expansion microscopy of cells and tissues labeled using standard fluorescent proteins and antibodies. Nat. Biotechnol. 34:987–92
     [Google Scholar]
128. 128.  Timmers AC. 2016. Light microscopy of whole plant organs. J. Microsc. 263:165–70
     [Google Scholar]
129. 129.  Todhunter ME, Jee NY, Hughes AJ, Coyle MC, Cerchiari A et al. 2015. Programmed synthesis of three-dimensional tissues. Nat. Methods 12:975–81
     [Google Scholar]
130. 130.  Tomer R, Lovett-Barron M, Kauvar I, Andalman A, Burns VM et al. 2015. SPED light sheet microscopy: fast mapping of biological system structure and function. Cell 163:1796–806
     [Google Scholar]
131. 131.  Tomer R, Ye L, Hsueh B, Deisseroth K 2014. Advanced CLARITY for rapid and high-resolution imaging of intact tissues. Nat. Protoc. 9:1682–97
     [Google Scholar]
132. 132.  Tran E, Hellebust A, Wu J, Gillenwater A, Vigneswaran N, Richards-Kortum RR 2016. Optically cleared mouse tongues for three-dimensional investigation of oral neoplasia Presented at Optical Tomogr. Spectrosc Fort Lauderdale, FL:
133. 133.  Treweek JB, Chan KY, Flytzanis NC, Yang B, Deverman BE et al. 2015. Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping. Nat. Protoc. 10:1860–96
     [Google Scholar]
134. 134.  Treweek JB, Gradinaru V 2016. Extracting structural and functional features of widely distributed biological circuits with single cell resolution via tissue clearing and delivery vectors. Curr. Opin. Biotechnol. 40:193–207
     [Google Scholar]
135. 135.  Tyson AL, Hilton ST, Andreae LC 2015. Rapid, simple and inexpensive production of custom 3D printed equipment for large-volume fluorescence microscopy. Int. J. Pharm. 494:651–56
     [Google Scholar]
136. 136.  Unal G, Joshi A, Viney TJ, Kis V, Somogyi P 2015. Synaptic targets of medial septal projections in the hippocampus and extrahippocampal cortices of the mouse. J. Neurosci. 35:15812–26
     [Google Scholar]
137. 137.  Unnersjo-Jess D, Scott L, Blom H, Brismar H 2016. Super-resolution stimulated emission depletion imaging of slit diaphragm proteins in optically cleared kidney tissue. Kidney Int 89:243–47
     [Google Scholar]
138. 138.  Uribe-Marino A, Gassen NC, Wiesbeck MF, Balsevich G, Santarelli S et al. 2016. Prefrontal cortex corticotropin-releasing factor receptor 1 conveys acute stress-induced executive dysfunction. Biol. Psychiatry 80:743–53
     [Google Scholar]
139. 139.  Wong MD, Spring S, Henkelman RM 2014. Structural stabilization of tissue for embryo phenotyping using micro-CT with iodine staining. PLOS ONE 8:e84321
     [Google Scholar]
140. 140.  Woo J, Lee M, Seo JM, Park HS, Cho YE 2016. Optimization of the optical transparency of rodent tissues by modified PACT-based passive clearing. Exp. Mol. Med. 48:e274
     [Google Scholar]
141. 141.  Xavier AL, Fontaine R, Bloch S, Affaticati P, Jenett A et al. 2017. Comparative analysis of monoaminergic cerebrospinal fluid-contacting cells in Osteichthyes (bony vertebrates). J. Comp. Neurol. 525:2265–83
     [Google Scholar]
142. 142.  Yang B, Treweek JB, Kulkarni RP, Deverman BE, Chen CK et al. 2014. Single-cell phenotyping within transparent intact tissue through whole-body clearing. Cell 158:945–58
     [Google Scholar]
143. 143.  Ye L, Allen WE, Thompson KR, Tian Q, Hsueh B et al. 2016. Wiring and molecular features of prefrontal ensembles representing distinct experiences. Cell 165:1776–88
     [Google Scholar]
144. 144.  Yu T, Qi Y, Wang J, Feng W, Xu J et al. 2016. Rapid and Prodium iodide-compatible optical clearing method for brain tissue based on sugar/sugar-alcohol. J. Biomed. Opt. 21:081203
     [Google Scholar]
145. 145.  Yu T, Qi Y, Zhu J, Xu J, Gong H et al. 2017. Elevated-temperature-induced acceleration of PACT clearing process of mouse brain tissue. Sci. Rep. 7:38848
     [Google Scholar]
146. 146.  Yuan M, Meyer T, Benkowitz C, Savanthrapadian S, Ansel-Bollepalli L et al. 2017. Somatostatin-positive interneurons in the dentate gyrus of mice provide local- and long-range septal synaptic inhibition. eLife 6:e21105
     [Google Scholar]
147. 147.  Zhang MD, Tortoriello G, Hsueh B, Tomer R, Ye L et al. 2014. Neuronal calcium-binding proteins 1/2 localize to dorsal root ganglia and excitatory spinal neurons and are regulated by nerve injury. PNAS 111:E1149–58
     [Google Scholar]
148. 148.  Zhao Y, Bucur O, Irshad H, Chen F, Weins A et al. 2017. Nanoscale imaging of clinical specimens using pathology-optimized expansion microscopy. Nat. Biotechnol. 35:757–64
     [Google Scholar]
149. 149.  Zheng H, Rinaman L 2016. Simplified CLARITY for visualizing immunofluorescence labeling in the developing rat brain. Brain Struct. Funct. 221:2375–83
     [Google Scholar]
150. 150.  Zygelyte E, Bernard ME, Tomlinson JE, Martin MJ, Terhorst A et al. 2016. RetroDISCO: clearing technique to improve quantification of retrograde labeled motor neurons of intact mouse spinal cords. J. Neurosci. Methods 271:34–42
     [Google Scholar]