Abstract

High-resolution three-dimensional biomolecule distribution information of large samples is essential to understanding their biological structure and function. Here, we proposed a method combining large sample resin embedding with iDISCO immunofluorescence staining to acquire the profile of biomolecules with high spatial resolution. We evaluated the compatibility of plastic embedding with an iDISCO staining technique and found that the fluorophores and the neuronal fine structures could be well preserved in the Lowicryl HM20 resin, and that numerous antibodies and fluorescent tracers worked well upon Lowicryl HM20 resin embedding. Further, using fluorescence Micro-Optical sectioning tomography (fMOST) technology combined with ultra-thin slicing and imaging, we were able to image the immunolabeled large-volume tissues with high resolution.

© 2017 Optical Society of America

Full Article  |  PDF Article
OSA Recommended Articles
Chemical reactivation of resin-embedded pHuji adds red for simultaneous two-color imaging with EGFP

Wenyan Guo, Xiuli Liu, Yurong Liu, Yadong Gang, Xiaobin He, Yao Jia, Fangfang Yin, Pei Li, Fei Huang, Hongfu Zhou, Xiaojun Wang, Hui Gong, Qingming Luo, Fuqiang Xu, and Shaoqun Zeng
Biomed. Opt. Express 8(7) 3281-3288 (2017)

Human iris three-dimensional imaging at micron resolution by a micro-plenoptic camera

Hao Chen, Maria A. Woodward, David T. Burke, V. Swetha E. Jeganathan, Hakan Demirci, and Volker Sick
Biomed. Opt. Express 8(10) 4514-4522 (2017)

Multiphoton in vivo imaging with a femtosecond semiconductor disk laser

Fabian F. Voigt, Florian Emaury, Philipp Bethge, Dominik Waldburger, Sandro M. Link, Stefano Carta, Alexander van der Bourg, Fritjof Helmchen, and Ursula Keller
Biomed. Opt. Express 8(7) 3213-3231 (2017)

More Recommended Articles

References

  • View by:
  • Article Order
  • |
  • Year
  • |
  • Author
  • |
  • Publication
  1. T. Alanentalo, A. Asayesh, H. Morrison, C. E. Lorén, D. Holmberg, J. Sharpe, and U. Ahlgren, “Tomographic molecular imaging and 3D quantification within adult mouse organs,” Nat. Methods 4(1), 31–33 (2007).
    [Crossref] [PubMed]
  2. K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
    [Crossref] [PubMed]
  3. A. H. Coons, H. J. Creech, R. N. Jones, and E. Berliner, “The demonstration of pneumococcal antigen in tissues by the use of fluorescent antibody,” J. Immunol. 45(3), 159–170 (1942).
  4. A. H. Coons and M. H. Kaplan, “Localization of antigen in tissue cells; improvements in a method for the detection of antigen by means of fluorescent antibody,” J. Exp. Med. 91(1), 1–13 (1949).
    [Crossref] [PubMed]
  5. N. Renier, Z. Wu, D. J. Simon, J. Yang, P. Ariel, and M. Tessier-Lavigne, “iDISCO: a simple, rapid method to immunolabel large tissue samples for volume imaging,” Cell 159(4), 896–910 (2014).
    [Crossref] [PubMed]
  6. S. Karma, J. Homan, C. Stoianovici, and B. Choi, “Enhanced fluorescence imaging with DMSO-mediated optical clearing,” J. Innov. Opt. Health Sci. 3(3), 153–158 (2010).
    [Crossref]
  7. B. Yang, J. B. Treweek, R. P. Kulkarni, B. E. Deverman, C. K. Chen, E. Lubeck, S. Shah, L. Cai, and V. Gradinaru, “Single-cell phenotyping within transparent intact tissue through whole-body clearing,” Cell 158(4), 945–958 (2014).
    [Crossref] [PubMed]
  8. E. Murray, J. H. 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, M. P. Frosch, V. J. Wedeen, H. S. Seung, and K. Chung, “Simple, scalable proteomic imaging for high-dimensional profiling of intact systems,” Cell 163(6), 1500–1514 (2015).
    [Crossref] [PubMed]
  9. E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
    [Crossref] [PubMed]
  10. H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
    [Crossref] [PubMed]
  11. J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
    [Crossref] [PubMed]
  12. L. Silvestri, A. L. Allegra Mascaro, J. Lotti, L. Sacconi, and F. S. Pavone, “Advanced optical techniques to explore brain structure and function,” J. Innov. Opt. Health Sci. 6(1), 1230002 (2013).
    [Crossref]
  13. B. A. Wilt, L. D. Burns, E. T. Wei Ho, K. K. Ghosh, E. A. Mukamel, and M. J. Schnitzer, “Advances in light microscopy for neuroscience,” Annu. Rev. Neurosci. 32(1), 435–506 (2009).
    [Crossref] [PubMed]
  14. W. J. Weninger, S. H. Geyer, T. J. Mohun, D. Rasskin-Gutman, T. Matsui, I. Ribeiro, L. F. Costa, J. C. Izpisúa-Belmonte, and G. B. Müller, “High-resolution episcopic microscopy: a rapid technique for high detailed 3D analysis of gene activity in the context of tissue architecture and morphology,” Anat. Embryol. (Berl.) 211(3), 213–221 (2006).
    [Crossref] [PubMed]
  15. A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
    [Crossref] [PubMed]
  16. T. Zheng, Z. Yang, A. Li, X. Lv, Z. Zhou, X. Wang, X. Qi, S. Li, Q. Luo, H. Gong, and S. Zeng, “Visualization of brain circuits using two-photon fluorescence micro-optical sectioning tomography,” Opt. Express 21(8), 9839–9850 (2013).
    [Crossref] [PubMed]
  17. H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013).
    [Crossref] [PubMed]
  18. B. Zhang, A. Li, Z. Yang, J. Wu, Q. Luo, and H. Gong, “Modified Golgi-Cox method for micrometer scale sectioning of the whole mouse brain,” J. Neurosci. Methods 197(1), 1–5 (2011).
    [Crossref] [PubMed]
  19. S. S. Biel, K. Kawaschinski, K. P. Wittern, U. Hintze, and R. Wepf, “From tissue to cellular ultrastructure: closing the gap between micro- and nanostructural imaging,” J. Microsc. 212(1), 91–99 (2003).
    [Crossref] [PubMed]
  20. S. Wessel, S. Pagel, M. Ritter, H. Hohenberg, and R. Wepf, “Topographic Measurements of Real Structures in reflection Confocal Laser Scanning Microscope (CLSM),” Microsc. Microanal. 9(S03), 162–163 (2003).
  21. M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V. V. Hodirnau, M. P. Scheffer, A. Seybert, S. Malkusch, E. M. Schuman, M. Heilemann, and A. S. Frangakis, “Correlative light- and electron microscopy with chemical tags,” J. Struct. Biol. 186(2), 205–213 (2014).
    [Crossref] [PubMed]
  22. D. Kim, T. J. Deerinck, Y. M. Sigal, H. P. Babcock, M. H. Ellisman, and X. Zhuang, “Correlative stochastic optical reconstruction microscopy and electron microscopy,” PLoS One 10(4), e0124581 (2015).
    [Crossref] [PubMed]
  23. A. Burette, L. Khatri, M. Wyszynski, M. Sheng, E. B. Ziff, and R. J. Weinberg, “Differential cellular and subcellular localization of ampa receptor-binding protein and glutamate receptor-interacting protein,” J. Neurosci. 21(2), 495–503 (2001).
    [PubMed]
  24. Y. Gang, H. Zhou, Y. Jia, L. Liu, X. Liu, G. Rao, L. Li, X. Wang, X. Lv, H. Xiong, Z. Yang, Q. Luo, H. Gong, and S. Zeng, “Embedding and chemical reactivation of green fluorescent protein in the whole mouse brain for optical micro-imaging,” Front. Neurosci. 11, 121 (2017).
    [Crossref] [PubMed]
  25. Y. Sun, H. Yu, D. Zheng, Q. Cao, Y. Wang, D. Harris, and Y. Wang, “Sudan black B reduces autofluorescence in murine renal tissue,” Arch. Pathol. Lab. Med. 135(10), 1335–1342 (2011).
    [Crossref] [PubMed]
  26. H. Gong, D. Xu, J. Yuan, X. Li, C. Guo, J. Peng, Y. Li, L. A. Schwarz, A. Li, B. Hu, B. Xiong, Q. Sun, Y. Zhang, J. Liu, Q. Zhong, T. Xu, S. Zeng, and Q. Luo, “High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level,” Nat. Commun. 7, 12142 (2016).
    [Crossref] [PubMed]
  27. T. Yang, T. Zheng, Z. Shang, X. Wang, X. Lv, J. Yuan, and S. Zeng, “Rapid imaging of large tissues using high-resolution stage-scanning microscopy,” Biomed. Opt. Express 6(5), 1867–1875 (2015).
    [Crossref] [PubMed]
  28. J. Wu, Y. He, Z. Yang, C. Guo, Q. Luo, W. Zhou, S. Chen, A. Li, B. Xiong, T. Jiang, and H. Gong, “3D BrainCV: simultaneous visualization and analysis of cells and capillaries in a whole mouse brain with one-micron voxel resolution,” Neuroimage 87, 199–208 (2014).
    [Crossref] [PubMed]
  29. T. Quan, H. Zhou, J. Li, S. Li, A. Li, Y. Li, X. Lv, Q. Luo, H. Gong, and S. Zeng, “NeuroGPS-Tree: automatic reconstruction of large-scale neuronal populations with dense neurites,” Nat. Methods 13(1), 51–54 (2016).
    [PubMed]
  30. J. Li, T. Quan, S. Li, H. Zhou, Q. Luo, H. Gong, and S. Zeng, “Reconstruction of micron resolution mouse brain surface from large-scale imaging dataset using resampling-based variational model,” Sci. Rep. 5(1), 12782 (2015).
    [Crossref] [PubMed]
  31. T. Quan, T. Zheng, Z. Yang, W. Ding, S. Li, J. Li, H. Zhou, Q. Luo, H. Gong, and S. Zeng, “NeuroGPS: automated localization of neurons for brain circuits using L1 minimization model,” Sci. Rep. 3(1), 1414 (2013).
    [Crossref] [PubMed]
  32. S. Li, H. Zhou, T. Quan, J. Li, Y. Li, A. Li, Q. Luo, H. Gong, and S. Zeng, “SparseTracer: the reconstruction of discontinuous neuronal morphology in noisy images,” Neuroinformatics 15(2), 133–149 (2017).
    [Crossref] [PubMed]
  33. S. B. Newman, E. Borysko, and M. Swerdlow, “New sectioning techniques for light and electron microscopy,” Science 110(2846), 66–68 (1949).
    [Crossref] [PubMed]
  34. G. R. Newman and J. A. Hobot, “Resins for combined light and electron microscopy: a half century of development,” Histochem. J. 31(8), 495–505 (1999).
    [Crossref] [PubMed]
  35. Z. Yang, B. Hu, Y. Zhang, Q. Luo, and H. Gong, “Development of a plastic embedding method for large-volume and fluorescent-protein-expressing tissues,” PLoS One 8(4), e60877 (2013).
    [Crossref] [PubMed]
  36. H. Xiong, Z. Zhou, M. Zhu, X. Lv, A. Li, S. Li, L. Li, T. Yang, S. Wang, Z. Yang, T. Xu, Q. Luo, H. Gong, and S. Zeng, “Chemical reactivation of quenched fluorescent protein molecules enables resin-embedded fluorescence microimaging,” Nat. Commun. 5, 3992 (2014).
    [Crossref] [PubMed]
  37. M. A. Karreman, A. V. Agronskaia, E. G. van Donselaar, K. Vocking, F. Fereidouni, B. M. Humbel, C. T. Verrips, A. J. Verkleij, and H. C. Gerritsen, “Optimizing immuno-labeling for correlative fluorescence and electron microscopy on a single specimen,” J. Struct. Biol. 180(2), 382–386 (2012).
    [Crossref] [PubMed]
  38. J. A. Ramos-Vara, “Technical aspects of immunohistochemistry,” Vet. Pathol. 42(4), 405–426 (2005).
    [Crossref] [PubMed]
  39. F. Collman, J. Buchanan, K. D. Phend, K. D. Micheva, R. J. Weinberg, and S. J. Smith, “Mapping synapses by conjugate light-electron array tomography,” J. Neurosci. 35(14), 5792–5807 (2015).
    [Crossref] [PubMed]

2017 (2)

Y. Gang, H. Zhou, Y. Jia, L. Liu, X. Liu, G. Rao, L. Li, X. Wang, X. Lv, H. Xiong, Z. Yang, Q. Luo, H. Gong, and S. Zeng, “Embedding and chemical reactivation of green fluorescent protein in the whole mouse brain for optical micro-imaging,” Front. Neurosci. 11, 121 (2017).
[Crossref] [PubMed]

S. Li, H. Zhou, T. Quan, J. Li, Y. Li, A. Li, Q. Luo, H. Gong, and S. Zeng, “SparseTracer: the reconstruction of discontinuous neuronal morphology in noisy images,” Neuroinformatics 15(2), 133–149 (2017).
[Crossref] [PubMed]

2016 (2)

T. Quan, H. Zhou, J. Li, S. Li, A. Li, Y. Li, X. Lv, Q. Luo, H. Gong, and S. Zeng, “NeuroGPS-Tree: automatic reconstruction of large-scale neuronal populations with dense neurites,” Nat. Methods 13(1), 51–54 (2016).
[PubMed]

H. Gong, D. Xu, J. Yuan, X. Li, C. Guo, J. Peng, Y. Li, L. A. Schwarz, A. Li, B. Hu, B. Xiong, Q. Sun, Y. Zhang, J. Liu, Q. Zhong, T. Xu, S. Zeng, and Q. Luo, “High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level,” Nat. Commun. 7, 12142 (2016).
[Crossref] [PubMed]

2015 (5)

T. Yang, T. Zheng, Z. Shang, X. Wang, X. Lv, J. Yuan, and S. Zeng, “Rapid imaging of large tissues using high-resolution stage-scanning microscopy,” Biomed. Opt. Express 6(5), 1867–1875 (2015).
[Crossref] [PubMed]

D. Kim, T. J. Deerinck, Y. M. Sigal, H. P. Babcock, M. H. Ellisman, and X. Zhuang, “Correlative stochastic optical reconstruction microscopy and electron microscopy,” PLoS One 10(4), e0124581 (2015).
[Crossref] [PubMed]

J. Li, T. Quan, S. Li, H. Zhou, Q. Luo, H. Gong, and S. Zeng, “Reconstruction of micron resolution mouse brain surface from large-scale imaging dataset using resampling-based variational model,” Sci. Rep. 5(1), 12782 (2015).
[Crossref] [PubMed]

E. Murray, J. H. 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, M. P. Frosch, V. J. Wedeen, H. S. Seung, and K. Chung, “Simple, scalable proteomic imaging for high-dimensional profiling of intact systems,” Cell 163(6), 1500–1514 (2015).
[Crossref] [PubMed]

F. Collman, J. Buchanan, K. D. Phend, K. D. Micheva, R. J. Weinberg, and S. J. Smith, “Mapping synapses by conjugate light-electron array tomography,” J. Neurosci. 35(14), 5792–5807 (2015).
[Crossref] [PubMed]

2014 (6)

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
[Crossref] [PubMed]

N. Renier, Z. Wu, D. J. Simon, J. Yang, P. Ariel, and M. Tessier-Lavigne, “iDISCO: a simple, rapid method to immunolabel large tissue samples for volume imaging,” Cell 159(4), 896–910 (2014).
[Crossref] [PubMed]

M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V. V. Hodirnau, M. P. Scheffer, A. Seybert, S. Malkusch, E. M. Schuman, M. Heilemann, and A. S. Frangakis, “Correlative light- and electron microscopy with chemical tags,” J. Struct. Biol. 186(2), 205–213 (2014).
[Crossref] [PubMed]

H. Xiong, Z. Zhou, M. Zhu, X. Lv, A. Li, S. Li, L. Li, T. Yang, S. Wang, Z. Yang, T. Xu, Q. Luo, H. Gong, and S. Zeng, “Chemical reactivation of quenched fluorescent protein molecules enables resin-embedded fluorescence microimaging,” Nat. Commun. 5, 3992 (2014).
[Crossref] [PubMed]

B. Yang, J. B. Treweek, R. P. Kulkarni, B. E. Deverman, C. K. Chen, E. Lubeck, S. Shah, L. Cai, and V. Gradinaru, “Single-cell phenotyping within transparent intact tissue through whole-body clearing,” Cell 158(4), 945–958 (2014).
[Crossref] [PubMed]

J. Wu, Y. He, Z. Yang, C. Guo, Q. Luo, W. Zhou, S. Chen, A. Li, B. Xiong, T. Jiang, and H. Gong, “3D BrainCV: simultaneous visualization and analysis of cells and capillaries in a whole mouse brain with one-micron voxel resolution,” Neuroimage 87, 199–208 (2014).
[Crossref] [PubMed]

2013 (6)

T. Quan, T. Zheng, Z. Yang, W. Ding, S. Li, J. Li, H. Zhou, Q. Luo, H. Gong, and S. Zeng, “NeuroGPS: automated localization of neurons for brain circuits using L1 minimization model,” Sci. Rep. 3(1), 1414 (2013).
[Crossref] [PubMed]

L. Silvestri, A. L. Allegra Mascaro, J. Lotti, L. Sacconi, and F. S. Pavone, “Advanced optical techniques to explore brain structure and function,” J. Innov. Opt. Health Sci. 6(1), 1230002 (2013).
[Crossref]

T. Zheng, Z. Yang, A. Li, X. Lv, Z. Zhou, X. Wang, X. Qi, S. Li, Q. Luo, H. Gong, and S. Zeng, “Visualization of brain circuits using two-photon fluorescence micro-optical sectioning tomography,” Opt. Express 21(8), 9839–9850 (2013).
[Crossref] [PubMed]

H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013).
[Crossref] [PubMed]

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
[Crossref] [PubMed]

Z. Yang, B. Hu, Y. Zhang, Q. Luo, and H. Gong, “Development of a plastic embedding method for large-volume and fluorescent-protein-expressing tissues,” PLoS One 8(4), e60877 (2013).
[Crossref] [PubMed]

2012 (1)

M. A. Karreman, A. V. Agronskaia, E. G. van Donselaar, K. Vocking, F. Fereidouni, B. M. Humbel, C. T. Verrips, A. J. Verkleij, and H. C. Gerritsen, “Optimizing immuno-labeling for correlative fluorescence and electron microscopy on a single specimen,” J. Struct. Biol. 180(2), 382–386 (2012).
[Crossref] [PubMed]

2011 (3)

Y. Sun, H. Yu, D. Zheng, Q. Cao, Y. Wang, D. Harris, and Y. Wang, “Sudan black B reduces autofluorescence in murine renal tissue,” Arch. Pathol. Lab. Med. 135(10), 1335–1342 (2011).
[Crossref] [PubMed]

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
[Crossref] [PubMed]

B. Zhang, A. Li, Z. Yang, J. Wu, Q. Luo, and H. Gong, “Modified Golgi-Cox method for micrometer scale sectioning of the whole mouse brain,” J. Neurosci. Methods 197(1), 1–5 (2011).
[Crossref] [PubMed]

2010 (2)

S. Karma, J. Homan, C. Stoianovici, and B. Choi, “Enhanced fluorescence imaging with DMSO-mediated optical clearing,” J. Innov. Opt. Health Sci. 3(3), 153–158 (2010).
[Crossref]

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

2009 (1)

B. A. Wilt, L. D. Burns, E. T. Wei Ho, K. K. Ghosh, E. A. Mukamel, and M. J. Schnitzer, “Advances in light microscopy for neuroscience,” Annu. Rev. Neurosci. 32(1), 435–506 (2009).
[Crossref] [PubMed]

2007 (1)

T. Alanentalo, A. Asayesh, H. Morrison, C. E. Lorén, D. Holmberg, J. Sharpe, and U. Ahlgren, “Tomographic molecular imaging and 3D quantification within adult mouse organs,” Nat. Methods 4(1), 31–33 (2007).
[Crossref] [PubMed]

2006 (1)

W. J. Weninger, S. H. Geyer, T. J. Mohun, D. Rasskin-Gutman, T. Matsui, I. Ribeiro, L. F. Costa, J. C. Izpisúa-Belmonte, and G. B. Müller, “High-resolution episcopic microscopy: a rapid technique for high detailed 3D analysis of gene activity in the context of tissue architecture and morphology,” Anat. Embryol. (Berl.) 211(3), 213–221 (2006).
[Crossref] [PubMed]

2005 (1)

J. A. Ramos-Vara, “Technical aspects of immunohistochemistry,” Vet. Pathol. 42(4), 405–426 (2005).
[Crossref] [PubMed]

2003 (2)

S. S. Biel, K. Kawaschinski, K. P. Wittern, U. Hintze, and R. Wepf, “From tissue to cellular ultrastructure: closing the gap between micro- and nanostructural imaging,” J. Microsc. 212(1), 91–99 (2003).
[Crossref] [PubMed]

S. Wessel, S. Pagel, M. Ritter, H. Hohenberg, and R. Wepf, “Topographic Measurements of Real Structures in reflection Confocal Laser Scanning Microscope (CLSM),” Microsc. Microanal. 9(S03), 162–163 (2003).

2002 (1)

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

2001 (1)

A. Burette, L. Khatri, M. Wyszynski, M. Sheng, E. B. Ziff, and R. J. Weinberg, “Differential cellular and subcellular localization of ampa receptor-binding protein and glutamate receptor-interacting protein,” J. Neurosci. 21(2), 495–503 (2001).
[PubMed]

1999 (1)

G. R. Newman and J. A. Hobot, “Resins for combined light and electron microscopy: a half century of development,” Histochem. J. 31(8), 495–505 (1999).
[Crossref] [PubMed]

1949 (2)

S. B. Newman, E. Borysko, and M. Swerdlow, “New sectioning techniques for light and electron microscopy,” Science 110(2846), 66–68 (1949).
[Crossref] [PubMed]

A. H. Coons and M. H. Kaplan, “Localization of antigen in tissue cells; improvements in a method for the detection of antigen by means of fluorescent antibody,” J. Exp. Med. 91(1), 1–13 (1949).
[Crossref] [PubMed]

1942 (1)

A. H. Coons, H. J. Creech, R. N. Jones, and E. Berliner, “The demonstration of pneumococcal antigen in tissues by the use of fluorescent antibody,” J. Immunol. 45(3), 159–170 (1942).

Abe, T.

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
[Crossref] [PubMed]

Agronskaia, A. V.

M. A. Karreman, A. V. Agronskaia, E. G. van Donselaar, K. Vocking, F. Fereidouni, B. M. Humbel, C. T. Verrips, A. J. Verkleij, and H. C. Gerritsen, “Optimizing immuno-labeling for correlative fluorescence and electron microscopy on a single specimen,” J. Struct. Biol. 180(2), 382–386 (2012).
[Crossref] [PubMed]

Ahlgren, U.

T. Alanentalo, A. Asayesh, H. Morrison, C. E. Lorén, D. Holmberg, J. Sharpe, and U. Ahlgren, “Tomographic molecular imaging and 3D quantification within adult mouse organs,” Nat. Methods 4(1), 31–33 (2007).
[Crossref] [PubMed]

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

Alanentalo, T.

T. Alanentalo, A. Asayesh, H. Morrison, C. E. Lorén, D. Holmberg, J. Sharpe, and U. Ahlgren, “Tomographic molecular imaging and 3D quantification within adult mouse organs,” Nat. Methods 4(1), 31–33 (2007).
[Crossref] [PubMed]

Allegra Mascaro, A. L.

L. Silvestri, A. L. Allegra Mascaro, J. Lotti, L. Sacconi, and F. S. Pavone, “Advanced optical techniques to explore brain structure and function,” J. Innov. Opt. Health Sci. 6(1), 1230002 (2013).
[Crossref]

Andalman, A. S.

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
[Crossref] [PubMed]

Ando, R.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
[Crossref] [PubMed]

Ariel, P.

N. Renier, Z. Wu, D. J. Simon, J. Yang, P. Ariel, and M. Tessier-Lavigne, “iDISCO: a simple, rapid method to immunolabel large tissue samples for volume imaging,” Cell 159(4), 896–910 (2014).
[Crossref] [PubMed]

Asayesh, A.

T. Alanentalo, A. Asayesh, H. Morrison, C. E. Lorén, D. Holmberg, J. Sharpe, and U. Ahlgren, “Tomographic molecular imaging and 3D quantification within adult mouse organs,” Nat. Methods 4(1), 31–33 (2007).
[Crossref] [PubMed]

Babcock, H. P.

D. Kim, T. J. Deerinck, Y. M. Sigal, H. P. Babcock, M. H. Ellisman, and X. Zhuang, “Correlative stochastic optical reconstruction microscopy and electron microscopy,” PLoS One 10(4), e0124581 (2015).
[Crossref] [PubMed]

Bakh, N.

E. Murray, J. H. 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, M. P. Frosch, V. J. Wedeen, H. S. Seung, and K. Chung, “Simple, scalable proteomic imaging for high-dimensional profiling of intact systems,” Cell 163(6), 1500–1514 (2015).
[Crossref] [PubMed]

Baldock, R.

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

Berliner, E.

A. H. Coons, H. J. Creech, R. N. Jones, and E. Berliner, “The demonstration of pneumococcal antigen in tissues by the use of fluorescent antibody,” J. Immunol. 45(3), 159–170 (1942).

Bernstein, H.

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
[Crossref] [PubMed]

Biel, S. S.

S. S. Biel, K. Kawaschinski, K. P. Wittern, U. Hintze, and R. Wepf, “From tissue to cellular ultrastructure: closing the gap between micro- and nanostructural imaging,” J. Microsc. 212(1), 91–99 (2003).
[Crossref] [PubMed]

Borysko, E.

S. B. Newman, E. Borysko, and M. Swerdlow, “New sectioning techniques for light and electron microscopy,” Science 110(2846), 66–68 (1949).
[Crossref] [PubMed]

Buchanan, J.

F. Collman, J. Buchanan, K. D. Phend, K. D. Micheva, R. J. Weinberg, and S. J. Smith, “Mapping synapses by conjugate light-electron array tomography,” J. Neurosci. 35(14), 5792–5807 (2015).
[Crossref] [PubMed]

Bunse, S.

M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V. V. Hodirnau, M. P. Scheffer, A. Seybert, S. Malkusch, E. M. Schuman, M. Heilemann, and A. S. Frangakis, “Correlative light- and electron microscopy with chemical tags,” J. Struct. Biol. 186(2), 205–213 (2014).
[Crossref] [PubMed]

Burette, A.

A. Burette, L. Khatri, M. Wyszynski, M. Sheng, E. B. Ziff, and R. J. Weinberg, “Differential cellular and subcellular localization of ampa receptor-binding protein and glutamate receptor-interacting protein,” J. Neurosci. 21(2), 495–503 (2001).
[PubMed]

Burns, L. D.

B. A. Wilt, L. D. Burns, E. T. Wei Ho, K. K. Ghosh, E. A. Mukamel, and M. J. Schnitzer, “Advances in light microscopy for neuroscience,” Annu. Rev. Neurosci. 32(1), 435–506 (2009).
[Crossref] [PubMed]

Cai, L.

B. Yang, J. B. Treweek, R. P. Kulkarni, B. E. Deverman, C. K. Chen, E. Lubeck, S. Shah, L. Cai, and V. Gradinaru, “Single-cell phenotyping within transparent intact tissue through whole-body clearing,” Cell 158(4), 945–958 (2014).
[Crossref] [PubMed]

Cao, Q.

Y. Sun, H. Yu, D. Zheng, Q. Cao, Y. Wang, D. Harris, and Y. Wang, “Sudan black B reduces autofluorescence in murine renal tissue,” Arch. Pathol. Lab. Med. 135(10), 1335–1342 (2011).
[Crossref] [PubMed]

Chen, C. K.

B. Yang, J. B. Treweek, R. P. Kulkarni, B. E. Deverman, C. K. Chen, E. Lubeck, S. Shah, L. Cai, and V. Gradinaru, “Single-cell phenotyping within transparent intact tissue through whole-body clearing,” Cell 158(4), 945–958 (2014).
[Crossref] [PubMed]

Chen, S.

J. Wu, Y. He, Z. Yang, C. Guo, Q. Luo, W. Zhou, S. Chen, A. Li, B. Xiong, T. Jiang, and H. Gong, “3D BrainCV: simultaneous visualization and analysis of cells and capillaries in a whole mouse brain with one-micron voxel resolution,” Neuroimage 87, 199–208 (2014).
[Crossref] [PubMed]

Cho, J. H.

E. Murray, J. H. 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, M. P. Frosch, V. J. Wedeen, H. S. Seung, and K. Chung, “Simple, scalable proteomic imaging for high-dimensional profiling of intact systems,” Cell 163(6), 1500–1514 (2015).
[Crossref] [PubMed]

Choi, B.

S. Karma, J. Homan, C. Stoianovici, and B. Choi, “Enhanced fluorescence imaging with DMSO-mediated optical clearing,” J. Innov. Opt. Health Sci. 3(3), 153–158 (2010).
[Crossref]

Choi, H.

E. Murray, J. H. 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, M. P. Frosch, V. J. Wedeen, H. S. Seung, and K. Chung, “Simple, scalable proteomic imaging for high-dimensional profiling of intact systems,” Cell 163(6), 1500–1514 (2015).
[Crossref] [PubMed]

Chung, K.

E. Murray, J. H. 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, M. P. Frosch, V. J. Wedeen, H. S. Seung, and K. Chung, “Simple, scalable proteomic imaging for high-dimensional profiling of intact systems,” Cell 163(6), 1500–1514 (2015).
[Crossref] [PubMed]

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
[Crossref] [PubMed]

Collman, F.

F. Collman, J. Buchanan, K. D. Phend, K. D. Micheva, R. J. Weinberg, and S. J. Smith, “Mapping synapses by conjugate light-electron array tomography,” J. Neurosci. 35(14), 5792–5807 (2015).
[Crossref] [PubMed]

Coons, A. H.

A. H. Coons and M. H. Kaplan, “Localization of antigen in tissue cells; improvements in a method for the detection of antigen by means of fluorescent antibody,” J. Exp. Med. 91(1), 1–13 (1949).
[Crossref] [PubMed]

A. H. Coons, H. J. Creech, R. N. Jones, and E. Berliner, “The demonstration of pneumococcal antigen in tissues by the use of fluorescent antibody,” J. Immunol. 45(3), 159–170 (1942).

Costa, L. F.

W. J. Weninger, S. H. Geyer, T. J. Mohun, D. Rasskin-Gutman, T. Matsui, I. Ribeiro, L. F. Costa, J. C. Izpisúa-Belmonte, and G. B. Müller, “High-resolution episcopic microscopy: a rapid technique for high detailed 3D analysis of gene activity in the context of tissue architecture and morphology,” Anat. Embryol. (Berl.) 211(3), 213–221 (2006).
[Crossref] [PubMed]

Creech, H. J.

A. H. Coons, H. J. Creech, R. N. Jones, and E. Berliner, “The demonstration of pneumococcal antigen in tissues by the use of fluorescent antibody,” J. Immunol. 45(3), 159–170 (1942).

Davidson, D.

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

Davidson, T. J.

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
[Crossref] [PubMed]

Deerinck, T. J.

D. Kim, T. J. Deerinck, Y. M. Sigal, H. P. Babcock, M. H. Ellisman, and X. Zhuang, “Correlative stochastic optical reconstruction microscopy and electron microscopy,” PLoS One 10(4), e0124581 (2015).
[Crossref] [PubMed]

Deisseroth, K.

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
[Crossref] [PubMed]

Denisin, A. K.

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
[Crossref] [PubMed]

Deverman, B. E.

B. Yang, J. B. Treweek, R. P. Kulkarni, B. E. Deverman, C. K. Chen, E. Lubeck, S. Shah, L. Cai, and V. Gradinaru, “Single-cell phenotyping within transparent intact tissue through whole-body clearing,” Cell 158(4), 945–958 (2014).
[Crossref] [PubMed]

Ding, W.

T. Quan, T. Zheng, Z. Yang, W. Ding, S. Li, J. Li, H. Zhou, Q. Luo, H. Gong, and S. Zeng, “NeuroGPS: automated localization of neurons for brain circuits using L1 minimization model,” Sci. Rep. 3(1), 1414 (2013).
[Crossref] [PubMed]

H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013).
[Crossref] [PubMed]

Eguchi, M.

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
[Crossref] [PubMed]

Ellisman, M. H.

D. Kim, T. J. Deerinck, Y. M. Sigal, H. P. Babcock, M. H. Ellisman, and X. Zhuang, “Correlative stochastic optical reconstruction microscopy and electron microscopy,” PLoS One 10(4), e0124581 (2015).
[Crossref] [PubMed]

Endesfelder, U.

M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V. V. Hodirnau, M. P. Scheffer, A. Seybert, S. Malkusch, E. M. Schuman, M. Heilemann, and A. S. Frangakis, “Correlative light- and electron microscopy with chemical tags,” J. Struct. Biol. 186(2), 205–213 (2014).
[Crossref] [PubMed]

Feng, Z.

H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013).
[Crossref] [PubMed]

Fereidouni, F.

M. A. Karreman, A. V. Agronskaia, E. G. van Donselaar, K. Vocking, F. Fereidouni, B. M. Humbel, C. T. Verrips, A. J. Verkleij, and H. C. Gerritsen, “Optimizing immuno-labeling for correlative fluorescence and electron microscopy on a single specimen,” J. Struct. Biol. 180(2), 382–386 (2012).
[Crossref] [PubMed]

Frangakis, A. S.

M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V. V. Hodirnau, M. P. Scheffer, A. Seybert, S. Malkusch, E. M. Schuman, M. Heilemann, and A. S. Frangakis, “Correlative light- and electron microscopy with chemical tags,” J. Struct. Biol. 186(2), 205–213 (2014).
[Crossref] [PubMed]

Frosch, M. P.

E. Murray, J. H. 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, M. P. Frosch, V. J. Wedeen, H. S. Seung, and K. Chung, “Simple, scalable proteomic imaging for high-dimensional profiling of intact systems,” Cell 163(6), 1500–1514 (2015).
[Crossref] [PubMed]

Fukami, K.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
[Crossref] [PubMed]

Gang, Y.

Y. Gang, H. Zhou, Y. Jia, L. Liu, X. Liu, G. Rao, L. Li, X. Wang, X. Lv, H. Xiong, Z. Yang, Q. Luo, H. Gong, and S. Zeng, “Embedding and chemical reactivation of green fluorescent protein in the whole mouse brain for optical micro-imaging,” Front. Neurosci. 11, 121 (2017).
[Crossref] [PubMed]

Gerritsen, H. C.

M. A. Karreman, A. V. Agronskaia, E. G. van Donselaar, K. Vocking, F. Fereidouni, B. M. Humbel, C. T. Verrips, A. J. Verkleij, and H. C. Gerritsen, “Optimizing immuno-labeling for correlative fluorescence and electron microscopy on a single specimen,” J. Struct. Biol. 180(2), 382–386 (2012).
[Crossref] [PubMed]

Geyer, S. H.

W. J. Weninger, S. H. Geyer, T. J. Mohun, D. Rasskin-Gutman, T. Matsui, I. Ribeiro, L. F. Costa, J. C. Izpisúa-Belmonte, and G. B. Müller, “High-resolution episcopic microscopy: a rapid technique for high detailed 3D analysis of gene activity in the context of tissue architecture and morphology,” Anat. Embryol. (Berl.) 211(3), 213–221 (2006).
[Crossref] [PubMed]

Ghosh, K. K.

B. A. Wilt, L. D. Burns, E. T. Wei Ho, K. K. Ghosh, E. A. Mukamel, and M. J. Schnitzer, “Advances in light microscopy for neuroscience,” Annu. Rev. Neurosci. 32(1), 435–506 (2009).
[Crossref] [PubMed]

Gong, H.

Y. Gang, H. Zhou, Y. Jia, L. Liu, X. Liu, G. Rao, L. Li, X. Wang, X. Lv, H. Xiong, Z. Yang, Q. Luo, H. Gong, and S. Zeng, “Embedding and chemical reactivation of green fluorescent protein in the whole mouse brain for optical micro-imaging,” Front. Neurosci. 11, 121 (2017).
[Crossref] [PubMed]

S. Li, H. Zhou, T. Quan, J. Li, Y. Li, A. Li, Q. Luo, H. Gong, and S. Zeng, “SparseTracer: the reconstruction of discontinuous neuronal morphology in noisy images,” Neuroinformatics 15(2), 133–149 (2017).
[Crossref] [PubMed]

T. Quan, H. Zhou, J. Li, S. Li, A. Li, Y. Li, X. Lv, Q. Luo, H. Gong, and S. Zeng, “NeuroGPS-Tree: automatic reconstruction of large-scale neuronal populations with dense neurites,” Nat. Methods 13(1), 51–54 (2016).
[PubMed]

H. Gong, D. Xu, J. Yuan, X. Li, C. Guo, J. Peng, Y. Li, L. A. Schwarz, A. Li, B. Hu, B. Xiong, Q. Sun, Y. Zhang, J. Liu, Q. Zhong, T. Xu, S. Zeng, and Q. Luo, “High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level,” Nat. Commun. 7, 12142 (2016).
[Crossref] [PubMed]

J. Li, T. Quan, S. Li, H. Zhou, Q. Luo, H. Gong, and S. Zeng, “Reconstruction of micron resolution mouse brain surface from large-scale imaging dataset using resampling-based variational model,” Sci. Rep. 5(1), 12782 (2015).
[Crossref] [PubMed]

J. Wu, Y. He, Z. Yang, C. Guo, Q. Luo, W. Zhou, S. Chen, A. Li, B. Xiong, T. Jiang, and H. Gong, “3D BrainCV: simultaneous visualization and analysis of cells and capillaries in a whole mouse brain with one-micron voxel resolution,” Neuroimage 87, 199–208 (2014).
[Crossref] [PubMed]

H. Xiong, Z. Zhou, M. Zhu, X. Lv, A. Li, S. Li, L. Li, T. Yang, S. Wang, Z. Yang, T. Xu, Q. Luo, H. Gong, and S. Zeng, “Chemical reactivation of quenched fluorescent protein molecules enables resin-embedded fluorescence microimaging,” Nat. Commun. 5, 3992 (2014).
[Crossref] [PubMed]

Z. Yang, B. Hu, Y. Zhang, Q. Luo, and H. Gong, “Development of a plastic embedding method for large-volume and fluorescent-protein-expressing tissues,” PLoS One 8(4), e60877 (2013).
[Crossref] [PubMed]

H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013).
[Crossref] [PubMed]

T. Zheng, Z. Yang, A. Li, X. Lv, Z. Zhou, X. Wang, X. Qi, S. Li, Q. Luo, H. Gong, and S. Zeng, “Visualization of brain circuits using two-photon fluorescence micro-optical sectioning tomography,” Opt. Express 21(8), 9839–9850 (2013).
[Crossref] [PubMed]

T. Quan, T. Zheng, Z. Yang, W. Ding, S. Li, J. Li, H. Zhou, Q. Luo, H. Gong, and S. Zeng, “NeuroGPS: automated localization of neurons for brain circuits using L1 minimization model,” Sci. Rep. 3(1), 1414 (2013).
[Crossref] [PubMed]

B. Zhang, A. Li, Z. Yang, J. Wu, Q. Luo, and H. Gong, “Modified Golgi-Cox method for micrometer scale sectioning of the whole mouse brain,” J. Neurosci. Methods 197(1), 1–5 (2011).
[Crossref] [PubMed]

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

Goodwin, D.

E. Murray, J. H. 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, M. P. Frosch, V. J. Wedeen, H. S. Seung, and K. Chung, “Simple, scalable proteomic imaging for high-dimensional profiling of intact systems,” Cell 163(6), 1500–1514 (2015).
[Crossref] [PubMed]

Gradinaru, V.

B. Yang, J. B. Treweek, R. P. Kulkarni, B. E. Deverman, C. K. Chen, E. Lubeck, S. Shah, L. Cai, and V. Gradinaru, “Single-cell phenotyping within transparent intact tissue through whole-body clearing,” Cell 158(4), 945–958 (2014).
[Crossref] [PubMed]

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
[Crossref] [PubMed]

Grosenick, L.

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
[Crossref] [PubMed]

Guo, C.

H. Gong, D. Xu, J. Yuan, X. Li, C. Guo, J. Peng, Y. Li, L. A. Schwarz, A. Li, B. Hu, B. Xiong, Q. Sun, Y. Zhang, J. Liu, Q. Zhong, T. Xu, S. Zeng, and Q. Luo, “High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level,” Nat. Commun. 7, 12142 (2016).
[Crossref] [PubMed]

J. Wu, Y. He, Z. Yang, C. Guo, Q. Luo, W. Zhou, S. Chen, A. Li, B. Xiong, T. Jiang, and H. Gong, “3D BrainCV: simultaneous visualization and analysis of cells and capillaries in a whole mouse brain with one-micron voxel resolution,” Neuroimage 87, 199–208 (2014).
[Crossref] [PubMed]

Hama, H.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
[Crossref] [PubMed]

Harris, D.

Y. Sun, H. Yu, D. Zheng, Q. Cao, Y. Wang, D. Harris, and Y. Wang, “Sudan black B reduces autofluorescence in murine renal tissue,” Arch. Pathol. Lab. Med. 135(10), 1335–1342 (2011).
[Crossref] [PubMed]

He, Y.

J. Wu, Y. He, Z. Yang, C. Guo, Q. Luo, W. Zhou, S. Chen, A. Li, B. Xiong, T. Jiang, and H. Gong, “3D BrainCV: simultaneous visualization and analysis of cells and capillaries in a whole mouse brain with one-micron voxel resolution,” Neuroimage 87, 199–208 (2014).
[Crossref] [PubMed]

Hecksher-Sørensen, J.

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

Heilemann, M.

M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V. V. Hodirnau, M. P. Scheffer, A. Seybert, S. Malkusch, E. M. Schuman, M. Heilemann, and A. S. Frangakis, “Correlative light- and electron microscopy with chemical tags,” J. Struct. Biol. 186(2), 205–213 (2014).
[Crossref] [PubMed]

Hill, B.

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

Hintze, U.

S. S. Biel, K. Kawaschinski, K. P. Wittern, U. Hintze, and R. Wepf, “From tissue to cellular ultrastructure: closing the gap between micro- and nanostructural imaging,” J. Microsc. 212(1), 91–99 (2003).
[Crossref] [PubMed]

Hobot, J. A.

G. R. Newman and J. A. Hobot, “Resins for combined light and electron microscopy: a half century of development,” Histochem. J. 31(8), 495–505 (1999).
[Crossref] [PubMed]

Hodirnau, V. V.

M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V. V. Hodirnau, M. P. Scheffer, A. Seybert, S. Malkusch, E. M. Schuman, M. Heilemann, and A. S. Frangakis, “Correlative light- and electron microscopy with chemical tags,” J. Struct. Biol. 186(2), 205–213 (2014).
[Crossref] [PubMed]

Hohenberg, H.

S. Wessel, S. Pagel, M. Ritter, H. Hohenberg, and R. Wepf, “Topographic Measurements of Real Structures in reflection Confocal Laser Scanning Microscope (CLSM),” Microsc. Microanal. 9(S03), 162–163 (2003).

Holmberg, D.

T. Alanentalo, A. Asayesh, H. Morrison, C. E. Lorén, D. Holmberg, J. Sharpe, and U. Ahlgren, “Tomographic molecular imaging and 3D quantification within adult mouse organs,” Nat. Methods 4(1), 31–33 (2007).
[Crossref] [PubMed]

Homan, J.

S. Karma, J. Homan, C. Stoianovici, and B. Choi, “Enhanced fluorescence imaging with DMSO-mediated optical clearing,” J. Innov. Opt. Health Sci. 3(3), 153–158 (2010).
[Crossref]

Hu, B.

H. Gong, D. Xu, J. Yuan, X. Li, C. Guo, J. Peng, Y. Li, L. A. Schwarz, A. Li, B. Hu, B. Xiong, Q. Sun, Y. Zhang, J. Liu, Q. Zhong, T. Xu, S. Zeng, and Q. Luo, “High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level,” Nat. Commun. 7, 12142 (2016).
[Crossref] [PubMed]

Z. Yang, B. Hu, Y. Zhang, Q. Luo, and H. Gong, “Development of a plastic embedding method for large-volume and fluorescent-protein-expressing tissues,” PLoS One 8(4), e60877 (2013).
[Crossref] [PubMed]

Hubbert, A.

E. Murray, J. H. 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, M. P. Frosch, V. J. Wedeen, H. S. Seung, and K. Chung, “Simple, scalable proteomic imaging for high-dimensional profiling of intact systems,” Cell 163(6), 1500–1514 (2015).
[Crossref] [PubMed]

Humbel, B. M.

M. A. Karreman, A. V. Agronskaia, E. G. van Donselaar, K. Vocking, F. Fereidouni, B. M. Humbel, C. T. Verrips, A. J. Verkleij, and H. C. Gerritsen, “Optimizing immuno-labeling for correlative fluorescence and electron microscopy on a single specimen,” J. Struct. Biol. 180(2), 382–386 (2012).
[Crossref] [PubMed]

Izpisúa-Belmonte, J. C.

W. J. Weninger, S. H. Geyer, T. J. Mohun, D. Rasskin-Gutman, T. Matsui, I. Ribeiro, L. F. Costa, J. C. Izpisúa-Belmonte, and G. B. Müller, “High-resolution episcopic microscopy: a rapid technique for high detailed 3D analysis of gene activity in the context of tissue architecture and morphology,” Anat. Embryol. (Berl.) 211(3), 213–221 (2006).
[Crossref] [PubMed]

Jia, Y.

Y. Gang, H. Zhou, Y. Jia, L. Liu, X. Liu, G. Rao, L. Li, X. Wang, X. Lv, H. Xiong, Z. Yang, Q. Luo, H. Gong, and S. Zeng, “Embedding and chemical reactivation of green fluorescent protein in the whole mouse brain for optical micro-imaging,” Front. Neurosci. 11, 121 (2017).
[Crossref] [PubMed]

Jiang, T.

J. Wu, Y. He, Z. Yang, C. Guo, Q. Luo, W. Zhou, S. Chen, A. Li, B. Xiong, T. Jiang, and H. Gong, “3D BrainCV: simultaneous visualization and analysis of cells and capillaries in a whole mouse brain with one-micron voxel resolution,” Neuroimage 87, 199–208 (2014).
[Crossref] [PubMed]

Jones, R. N.

A. H. Coons, H. J. Creech, R. N. Jones, and E. Berliner, “The demonstration of pneumococcal antigen in tissues by the use of fluorescent antibody,” J. Immunol. 45(3), 159–170 (1942).

Kalyanasundaram, S.

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
[Crossref] [PubMed]

Kaplan, M. H.

A. H. Coons and M. H. Kaplan, “Localization of antigen in tissue cells; improvements in a method for the detection of antigen by means of fluorescent antibody,” J. Exp. Med. 91(1), 1–13 (1949).
[Crossref] [PubMed]

Karma, S.

S. Karma, J. Homan, C. Stoianovici, and B. Choi, “Enhanced fluorescence imaging with DMSO-mediated optical clearing,” J. Innov. Opt. Health Sci. 3(3), 153–158 (2010).
[Crossref]

Karreman, M. A.

M. A. Karreman, A. V. Agronskaia, E. G. van Donselaar, K. Vocking, F. Fereidouni, B. M. Humbel, C. T. Verrips, A. J. Verkleij, and H. C. Gerritsen, “Optimizing immuno-labeling for correlative fluorescence and electron microscopy on a single specimen,” J. Struct. Biol. 180(2), 382–386 (2012).
[Crossref] [PubMed]

Kawano, H.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
[Crossref] [PubMed]

Kawaschinski, K.

S. S. Biel, K. Kawaschinski, K. P. Wittern, U. Hintze, and R. Wepf, “From tissue to cellular ultrastructure: closing the gap between micro- and nanostructural imaging,” J. Microsc. 212(1), 91–99 (2003).
[Crossref] [PubMed]

Khatri, L.

A. Burette, L. Khatri, M. Wyszynski, M. Sheng, E. B. Ziff, and R. J. Weinberg, “Differential cellular and subcellular localization of ampa receptor-binding protein and glutamate receptor-interacting protein,” J. Neurosci. 21(2), 495–503 (2001).
[PubMed]

Kim, D.

D. Kim, T. J. Deerinck, Y. M. Sigal, H. P. Babcock, M. H. Ellisman, and X. Zhuang, “Correlative stochastic optical reconstruction microscopy and electron microscopy,” PLoS One 10(4), e0124581 (2015).
[Crossref] [PubMed]

Kim, S. Y.

E. Murray, J. H. 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, M. P. Frosch, V. J. Wedeen, H. S. Seung, and K. Chung, “Simple, scalable proteomic imaging for high-dimensional profiling of intact systems,” Cell 163(6), 1500–1514 (2015).
[Crossref] [PubMed]

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
[Crossref] [PubMed]

Kishino, F.

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
[Crossref] [PubMed]

Kiyonari, H.

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
[Crossref] [PubMed]

Ku, T.

E. Murray, J. H. 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, M. P. Frosch, V. J. Wedeen, H. S. Seung, and K. Chung, “Simple, scalable proteomic imaging for high-dimensional profiling of intact systems,” Cell 163(6), 1500–1514 (2015).
[Crossref] [PubMed]

Kulkarni, R. P.

B. Yang, J. B. Treweek, R. P. Kulkarni, B. E. Deverman, C. K. Chen, E. Lubeck, S. Shah, L. Cai, and V. Gradinaru, “Single-cell phenotyping within transparent intact tissue through whole-body clearing,” Cell 158(4), 945–958 (2014).
[Crossref] [PubMed]

Kunz, M.

M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V. V. Hodirnau, M. P. Scheffer, A. Seybert, S. Malkusch, E. M. Schuman, M. Heilemann, and A. S. Frangakis, “Correlative light- and electron microscopy with chemical tags,” J. Struct. Biol. 186(2), 205–213 (2014).
[Crossref] [PubMed]

Kurokawa, H.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
[Crossref] [PubMed]

Li, A.

S. Li, H. Zhou, T. Quan, J. Li, Y. Li, A. Li, Q. Luo, H. Gong, and S. Zeng, “SparseTracer: the reconstruction of discontinuous neuronal morphology in noisy images,” Neuroinformatics 15(2), 133–149 (2017).
[Crossref] [PubMed]

T. Quan, H. Zhou, J. Li, S. Li, A. Li, Y. Li, X. Lv, Q. Luo, H. Gong, and S. Zeng, “NeuroGPS-Tree: automatic reconstruction of large-scale neuronal populations with dense neurites,” Nat. Methods 13(1), 51–54 (2016).
[PubMed]

H. Gong, D. Xu, J. Yuan, X. Li, C. Guo, J. Peng, Y. Li, L. A. Schwarz, A. Li, B. Hu, B. Xiong, Q. Sun, Y. Zhang, J. Liu, Q. Zhong, T. Xu, S. Zeng, and Q. Luo, “High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level,” Nat. Commun. 7, 12142 (2016).
[Crossref] [PubMed]

J. Wu, Y. He, Z. Yang, C. Guo, Q. Luo, W. Zhou, S. Chen, A. Li, B. Xiong, T. Jiang, and H. Gong, “3D BrainCV: simultaneous visualization and analysis of cells and capillaries in a whole mouse brain with one-micron voxel resolution,” Neuroimage 87, 199–208 (2014).
[Crossref] [PubMed]

H. Xiong, Z. Zhou, M. Zhu, X. Lv, A. Li, S. Li, L. Li, T. Yang, S. Wang, Z. Yang, T. Xu, Q. Luo, H. Gong, and S. Zeng, “Chemical reactivation of quenched fluorescent protein molecules enables resin-embedded fluorescence microimaging,” Nat. Commun. 5, 3992 (2014).
[Crossref] [PubMed]

H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013).
[Crossref] [PubMed]

T. Zheng, Z. Yang, A. Li, X. Lv, Z. Zhou, X. Wang, X. Qi, S. Li, Q. Luo, H. Gong, and S. Zeng, “Visualization of brain circuits using two-photon fluorescence micro-optical sectioning tomography,” Opt. Express 21(8), 9839–9850 (2013).
[Crossref] [PubMed]

B. Zhang, A. Li, Z. Yang, J. Wu, Q. Luo, and H. Gong, “Modified Golgi-Cox method for micrometer scale sectioning of the whole mouse brain,” J. Neurosci. Methods 197(1), 1–5 (2011).
[Crossref] [PubMed]

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

Li, J.

S. Li, H. Zhou, T. Quan, J. Li, Y. Li, A. Li, Q. Luo, H. Gong, and S. Zeng, “SparseTracer: the reconstruction of discontinuous neuronal morphology in noisy images,” Neuroinformatics 15(2), 133–149 (2017).
[Crossref] [PubMed]

T. Quan, H. Zhou, J. Li, S. Li, A. Li, Y. Li, X. Lv, Q. Luo, H. Gong, and S. Zeng, “NeuroGPS-Tree: automatic reconstruction of large-scale neuronal populations with dense neurites,” Nat. Methods 13(1), 51–54 (2016).
[PubMed]

J. Li, T. Quan, S. Li, H. Zhou, Q. Luo, H. Gong, and S. Zeng, “Reconstruction of micron resolution mouse brain surface from large-scale imaging dataset using resampling-based variational model,” Sci. Rep. 5(1), 12782 (2015).
[Crossref] [PubMed]

T. Quan, T. Zheng, Z. Yang, W. Ding, S. Li, J. Li, H. Zhou, Q. Luo, H. Gong, and S. Zeng, “NeuroGPS: automated localization of neurons for brain circuits using L1 minimization model,” Sci. Rep. 3(1), 1414 (2013).
[Crossref] [PubMed]

Li, L.

Y. Gang, H. Zhou, Y. Jia, L. Liu, X. Liu, G. Rao, L. Li, X. Wang, X. Lv, H. Xiong, Z. Yang, Q. Luo, H. Gong, and S. Zeng, “Embedding and chemical reactivation of green fluorescent protein in the whole mouse brain for optical micro-imaging,” Front. Neurosci. 11, 121 (2017).
[Crossref] [PubMed]

H. Xiong, Z. Zhou, M. Zhu, X. Lv, A. Li, S. Li, L. Li, T. Yang, S. Wang, Z. Yang, T. Xu, Q. Luo, H. Gong, and S. Zeng, “Chemical reactivation of quenched fluorescent protein molecules enables resin-embedded fluorescence microimaging,” Nat. Commun. 5, 3992 (2014).
[Crossref] [PubMed]

Li, S.

S. Li, H. Zhou, T. Quan, J. Li, Y. Li, A. Li, Q. Luo, H. Gong, and S. Zeng, “SparseTracer: the reconstruction of discontinuous neuronal morphology in noisy images,” Neuroinformatics 15(2), 133–149 (2017).
[Crossref] [PubMed]

T. Quan, H. Zhou, J. Li, S. Li, A. Li, Y. Li, X. Lv, Q. Luo, H. Gong, and S. Zeng, “NeuroGPS-Tree: automatic reconstruction of large-scale neuronal populations with dense neurites,” Nat. Methods 13(1), 51–54 (2016).
[PubMed]

J. Li, T. Quan, S. Li, H. Zhou, Q. Luo, H. Gong, and S. Zeng, “Reconstruction of micron resolution mouse brain surface from large-scale imaging dataset using resampling-based variational model,” Sci. Rep. 5(1), 12782 (2015).
[Crossref] [PubMed]

H. Xiong, Z. Zhou, M. Zhu, X. Lv, A. Li, S. Li, L. Li, T. Yang, S. Wang, Z. Yang, T. Xu, Q. Luo, H. Gong, and S. Zeng, “Chemical reactivation of quenched fluorescent protein molecules enables resin-embedded fluorescence microimaging,” Nat. Commun. 5, 3992 (2014).
[Crossref] [PubMed]

T. Zheng, Z. Yang, A. Li, X. Lv, Z. Zhou, X. Wang, X. Qi, S. Li, Q. Luo, H. Gong, and S. Zeng, “Visualization of brain circuits using two-photon fluorescence micro-optical sectioning tomography,” Opt. Express 21(8), 9839–9850 (2013).
[Crossref] [PubMed]

T. Quan, T. Zheng, Z. Yang, W. Ding, S. Li, J. Li, H. Zhou, Q. Luo, H. Gong, and S. Zeng, “NeuroGPS: automated localization of neurons for brain circuits using L1 minimization model,” Sci. Rep. 3(1), 1414 (2013).
[Crossref] [PubMed]

Li, X.

H. Gong, D. Xu, J. Yuan, X. Li, C. Guo, J. Peng, Y. Li, L. A. Schwarz, A. Li, B. Hu, B. Xiong, Q. Sun, Y. Zhang, J. Liu, Q. Zhong, T. Xu, S. Zeng, and Q. Luo, “High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level,” Nat. Commun. 7, 12142 (2016).
[Crossref] [PubMed]

Li, Y.

S. Li, H. Zhou, T. Quan, J. Li, Y. Li, A. Li, Q. Luo, H. Gong, and S. Zeng, “SparseTracer: the reconstruction of discontinuous neuronal morphology in noisy images,” Neuroinformatics 15(2), 133–149 (2017).
[Crossref] [PubMed]

T. Quan, H. Zhou, J. Li, S. Li, A. Li, Y. Li, X. Lv, Q. Luo, H. Gong, and S. Zeng, “NeuroGPS-Tree: automatic reconstruction of large-scale neuronal populations with dense neurites,” Nat. Methods 13(1), 51–54 (2016).
[PubMed]

H. Gong, D. Xu, J. Yuan, X. Li, C. Guo, J. Peng, Y. Li, L. A. Schwarz, A. Li, B. Hu, B. Xiong, Q. Sun, Y. Zhang, J. Liu, Q. Zhong, T. Xu, S. Zeng, and Q. Luo, “High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level,” Nat. Commun. 7, 12142 (2016).
[Crossref] [PubMed]

Liu, J.

H. Gong, D. Xu, J. Yuan, X. Li, C. Guo, J. Peng, Y. Li, L. A. Schwarz, A. Li, B. Hu, B. Xiong, Q. Sun, Y. Zhang, J. Liu, Q. Zhong, T. Xu, S. Zeng, and Q. Luo, “High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level,” Nat. Commun. 7, 12142 (2016).
[Crossref] [PubMed]

Liu, L.

Y. Gang, H. Zhou, Y. Jia, L. Liu, X. Liu, G. Rao, L. Li, X. Wang, X. Lv, H. Xiong, Z. Yang, Q. Luo, H. Gong, and S. Zeng, “Embedding and chemical reactivation of green fluorescent protein in the whole mouse brain for optical micro-imaging,” Front. Neurosci. 11, 121 (2017).
[Crossref] [PubMed]

Liu, Q.

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

Liu, X.

Y. Gang, H. Zhou, Y. Jia, L. Liu, X. Liu, G. Rao, L. Li, X. Wang, X. Lv, H. Xiong, Z. Yang, Q. Luo, H. Gong, and S. Zeng, “Embedding and chemical reactivation of green fluorescent protein in the whole mouse brain for optical micro-imaging,” Front. Neurosci. 11, 121 (2017).
[Crossref] [PubMed]

Lorén, C. E.

T. Alanentalo, A. Asayesh, H. Morrison, C. E. Lorén, D. Holmberg, J. Sharpe, and U. Ahlgren, “Tomographic molecular imaging and 3D quantification within adult mouse organs,” Nat. Methods 4(1), 31–33 (2007).
[Crossref] [PubMed]

Lotti, J.

L. Silvestri, A. L. Allegra Mascaro, J. Lotti, L. Sacconi, and F. S. Pavone, “Advanced optical techniques to explore brain structure and function,” J. Innov. Opt. Health Sci. 6(1), 1230002 (2013).
[Crossref]

Lubeck, E.

B. Yang, J. B. Treweek, R. P. Kulkarni, B. E. Deverman, C. K. Chen, E. Lubeck, S. Shah, L. Cai, and V. Gradinaru, “Single-cell phenotyping within transparent intact tissue through whole-body clearing,” Cell 158(4), 945–958 (2014).
[Crossref] [PubMed]

Luo, Q.

S. Li, H. Zhou, T. Quan, J. Li, Y. Li, A. Li, Q. Luo, H. Gong, and S. Zeng, “SparseTracer: the reconstruction of discontinuous neuronal morphology in noisy images,” Neuroinformatics 15(2), 133–149 (2017).
[Crossref] [PubMed]

Y. Gang, H. Zhou, Y. Jia, L. Liu, X. Liu, G. Rao, L. Li, X. Wang, X. Lv, H. Xiong, Z. Yang, Q. Luo, H. Gong, and S. Zeng, “Embedding and chemical reactivation of green fluorescent protein in the whole mouse brain for optical micro-imaging,” Front. Neurosci. 11, 121 (2017).
[Crossref] [PubMed]

T. Quan, H. Zhou, J. Li, S. Li, A. Li, Y. Li, X. Lv, Q. Luo, H. Gong, and S. Zeng, “NeuroGPS-Tree: automatic reconstruction of large-scale neuronal populations with dense neurites,” Nat. Methods 13(1), 51–54 (2016).
[PubMed]

H. Gong, D. Xu, J. Yuan, X. Li, C. Guo, J. Peng, Y. Li, L. A. Schwarz, A. Li, B. Hu, B. Xiong, Q. Sun, Y. Zhang, J. Liu, Q. Zhong, T. Xu, S. Zeng, and Q. Luo, “High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level,” Nat. Commun. 7, 12142 (2016).
[Crossref] [PubMed]

J. Li, T. Quan, S. Li, H. Zhou, Q. Luo, H. Gong, and S. Zeng, “Reconstruction of micron resolution mouse brain surface from large-scale imaging dataset using resampling-based variational model,” Sci. Rep. 5(1), 12782 (2015).
[Crossref] [PubMed]

J. Wu, Y. He, Z. Yang, C. Guo, Q. Luo, W. Zhou, S. Chen, A. Li, B. Xiong, T. Jiang, and H. Gong, “3D BrainCV: simultaneous visualization and analysis of cells and capillaries in a whole mouse brain with one-micron voxel resolution,” Neuroimage 87, 199–208 (2014).
[Crossref] [PubMed]

H. Xiong, Z. Zhou, M. Zhu, X. Lv, A. Li, S. Li, L. Li, T. Yang, S. Wang, Z. Yang, T. Xu, Q. Luo, H. Gong, and S. Zeng, “Chemical reactivation of quenched fluorescent protein molecules enables resin-embedded fluorescence microimaging,” Nat. Commun. 5, 3992 (2014).
[Crossref] [PubMed]

Z. Yang, B. Hu, Y. Zhang, Q. Luo, and H. Gong, “Development of a plastic embedding method for large-volume and fluorescent-protein-expressing tissues,” PLoS One 8(4), e60877 (2013).
[Crossref] [PubMed]

H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013).
[Crossref] [PubMed]

T. Zheng, Z. Yang, A. Li, X. Lv, Z. Zhou, X. Wang, X. Qi, S. Li, Q. Luo, H. Gong, and S. Zeng, “Visualization of brain circuits using two-photon fluorescence micro-optical sectioning tomography,” Opt. Express 21(8), 9839–9850 (2013).
[Crossref] [PubMed]

T. Quan, T. Zheng, Z. Yang, W. Ding, S. Li, J. Li, H. Zhou, Q. Luo, H. Gong, and S. Zeng, “NeuroGPS: automated localization of neurons for brain circuits using L1 minimization model,” Sci. Rep. 3(1), 1414 (2013).
[Crossref] [PubMed]

B. Zhang, A. Li, Z. Yang, J. Wu, Q. Luo, and H. Gong, “Modified Golgi-Cox method for micrometer scale sectioning of the whole mouse brain,” J. Neurosci. Methods 197(1), 1–5 (2011).
[Crossref] [PubMed]

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

Lv, X.

Y. Gang, H. Zhou, Y. Jia, L. Liu, X. Liu, G. Rao, L. Li, X. Wang, X. Lv, H. Xiong, Z. Yang, Q. Luo, H. Gong, and S. Zeng, “Embedding and chemical reactivation of green fluorescent protein in the whole mouse brain for optical micro-imaging,” Front. Neurosci. 11, 121 (2017).
[Crossref] [PubMed]

T. Quan, H. Zhou, J. Li, S. Li, A. Li, Y. Li, X. Lv, Q. Luo, H. Gong, and S. Zeng, “NeuroGPS-Tree: automatic reconstruction of large-scale neuronal populations with dense neurites,” Nat. Methods 13(1), 51–54 (2016).
[PubMed]

T. Yang, T. Zheng, Z. Shang, X. Wang, X. Lv, J. Yuan, and S. Zeng, “Rapid imaging of large tissues using high-resolution stage-scanning microscopy,” Biomed. Opt. Express 6(5), 1867–1875 (2015).
[Crossref] [PubMed]

H. Xiong, Z. Zhou, M. Zhu, X. Lv, A. Li, S. Li, L. Li, T. Yang, S. Wang, Z. Yang, T. Xu, Q. Luo, H. Gong, and S. Zeng, “Chemical reactivation of quenched fluorescent protein molecules enables resin-embedded fluorescence microimaging,” Nat. Commun. 5, 3992 (2014).
[Crossref] [PubMed]

H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013).
[Crossref] [PubMed]

T. Zheng, Z. Yang, A. Li, X. Lv, Z. Zhou, X. Wang, X. Qi, S. Li, Q. Luo, H. Gong, and S. Zeng, “Visualization of brain circuits using two-photon fluorescence micro-optical sectioning tomography,” Opt. Express 21(8), 9839–9850 (2013).
[Crossref] [PubMed]

Malkusch, S.

M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V. V. Hodirnau, M. P. Scheffer, A. Seybert, S. Malkusch, E. M. Schuman, M. Heilemann, and A. S. Frangakis, “Correlative light- and electron microscopy with chemical tags,” J. Struct. Biol. 186(2), 205–213 (2014).
[Crossref] [PubMed]

Matsui, T.

W. J. Weninger, S. H. Geyer, T. J. Mohun, D. Rasskin-Gutman, T. Matsui, I. Ribeiro, L. F. Costa, J. C. Izpisúa-Belmonte, and G. B. Müller, “High-resolution episcopic microscopy: a rapid technique for high detailed 3D analysis of gene activity in the context of tissue architecture and morphology,” Anat. Embryol. (Berl.) 211(3), 213–221 (2006).
[Crossref] [PubMed]

Mattis, J.

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
[Crossref] [PubMed]

McCue, M.

E. Murray, J. H. 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, M. P. Frosch, V. J. Wedeen, H. S. Seung, and K. Chung, “Simple, scalable proteomic imaging for high-dimensional profiling of intact systems,” Cell 163(6), 1500–1514 (2015).
[Crossref] [PubMed]

Micheva, K. D.

F. Collman, J. Buchanan, K. D. Phend, K. D. Micheva, R. J. Weinberg, and S. J. Smith, “Mapping synapses by conjugate light-electron array tomography,” J. Neurosci. 35(14), 5792–5807 (2015).
[Crossref] [PubMed]

Mirzabekov, J. J.

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
[Crossref] [PubMed]

Miyawaki, A.

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
[Crossref] [PubMed]

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
[Crossref] [PubMed]

Mohun, T. J.

W. J. Weninger, S. H. Geyer, T. J. Mohun, D. Rasskin-Gutman, T. Matsui, I. Ribeiro, L. F. Costa, J. C. Izpisúa-Belmonte, and G. B. Müller, “High-resolution episcopic microscopy: a rapid technique for high detailed 3D analysis of gene activity in the context of tissue architecture and morphology,” Anat. Embryol. (Berl.) 211(3), 213–221 (2006).
[Crossref] [PubMed]

Morrison, H.

T. Alanentalo, A. Asayesh, H. Morrison, C. E. Lorén, D. Holmberg, J. Sharpe, and U. Ahlgren, “Tomographic molecular imaging and 3D quantification within adult mouse organs,” Nat. Methods 4(1), 31–33 (2007).
[Crossref] [PubMed]

Mukamel, E. A.

B. A. Wilt, L. D. Burns, E. T. Wei Ho, K. K. Ghosh, E. A. Mukamel, and M. J. Schnitzer, “Advances in light microscopy for neuroscience,” Annu. Rev. Neurosci. 32(1), 435–506 (2009).
[Crossref] [PubMed]

Müller, G. B.

W. J. Weninger, S. H. Geyer, T. J. Mohun, D. Rasskin-Gutman, T. Matsui, I. Ribeiro, L. F. Costa, J. C. Izpisúa-Belmonte, and G. B. Müller, “High-resolution episcopic microscopy: a rapid technique for high detailed 3D analysis of gene activity in the context of tissue architecture and morphology,” Anat. Embryol. (Berl.) 211(3), 213–221 (2006).
[Crossref] [PubMed]

Murray, E.

E. Murray, J. H. 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, M. P. Frosch, V. J. Wedeen, H. S. Seung, and K. Chung, “Simple, scalable proteomic imaging for high-dimensional profiling of intact systems,” Cell 163(6), 1500–1514 (2015).
[Crossref] [PubMed]

Newman, G. R.

G. R. Newman and J. A. Hobot, “Resins for combined light and electron microscopy: a half century of development,” Histochem. J. 31(8), 495–505 (1999).
[Crossref] [PubMed]

Newman, S. B.

S. B. Newman, E. Borysko, and M. Swerdlow, “New sectioning techniques for light and electron microscopy,” Science 110(2846), 66–68 (1949).
[Crossref] [PubMed]

Noda, H.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
[Crossref] [PubMed]

Onoe, H.

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
[Crossref] [PubMed]

Pagel, S.

S. Wessel, S. Pagel, M. Ritter, H. Hohenberg, and R. Wepf, “Topographic Measurements of Real Structures in reflection Confocal Laser Scanning Microscope (CLSM),” Microsc. Microanal. 9(S03), 162–163 (2003).

Pak, S.

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
[Crossref] [PubMed]

Park, J. Y.

E. Murray, J. H. 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, M. P. Frosch, V. J. Wedeen, H. S. Seung, and K. Chung, “Simple, scalable proteomic imaging for high-dimensional profiling of intact systems,” Cell 163(6), 1500–1514 (2015).
[Crossref] [PubMed]

Park, Y. G.

E. Murray, J. H. 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, M. P. Frosch, V. J. Wedeen, H. S. Seung, and K. Chung, “Simple, scalable proteomic imaging for high-dimensional profiling of intact systems,” Cell 163(6), 1500–1514 (2015).
[Crossref] [PubMed]

Pavone, F. S.

L. Silvestri, A. L. Allegra Mascaro, J. Lotti, L. Sacconi, and F. S. Pavone, “Advanced optical techniques to explore brain structure and function,” J. Innov. Opt. Health Sci. 6(1), 1230002 (2013).
[Crossref]

Peng, J.

H. Gong, D. Xu, J. Yuan, X. Li, C. Guo, J. Peng, Y. Li, L. A. Schwarz, A. Li, B. Hu, B. Xiong, Q. Sun, Y. Zhang, J. Liu, Q. Zhong, T. Xu, S. Zeng, and Q. Luo, “High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level,” Nat. Commun. 7, 12142 (2016).
[Crossref] [PubMed]

Perkovic, M.

M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V. V. Hodirnau, M. P. Scheffer, A. Seybert, S. Malkusch, E. M. Schuman, M. Heilemann, and A. S. Frangakis, “Correlative light- and electron microscopy with chemical tags,” J. Struct. Biol. 186(2), 205–213 (2014).
[Crossref] [PubMed]

Perrin, D.

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
[Crossref] [PubMed]

Perry, P.

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

Phend, K. D.

F. Collman, J. Buchanan, K. D. Phend, K. D. Micheva, R. J. Weinberg, and S. J. Smith, “Mapping synapses by conjugate light-electron array tomography,” J. Neurosci. 35(14), 5792–5807 (2015).
[Crossref] [PubMed]

Qi, X.

T. Zheng, Z. Yang, A. Li, X. Lv, Z. Zhou, X. Wang, X. Qi, S. Li, Q. Luo, H. Gong, and S. Zeng, “Visualization of brain circuits using two-photon fluorescence micro-optical sectioning tomography,” Opt. Express 21(8), 9839–9850 (2013).
[Crossref] [PubMed]

H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013).
[Crossref] [PubMed]

Quan, T.

S. Li, H. Zhou, T. Quan, J. Li, Y. Li, A. Li, Q. Luo, H. Gong, and S. Zeng, “SparseTracer: the reconstruction of discontinuous neuronal morphology in noisy images,” Neuroinformatics 15(2), 133–149 (2017).
[Crossref] [PubMed]

T. Quan, H. Zhou, J. Li, S. Li, A. Li, Y. Li, X. Lv, Q. Luo, H. Gong, and S. Zeng, “NeuroGPS-Tree: automatic reconstruction of large-scale neuronal populations with dense neurites,” Nat. Methods 13(1), 51–54 (2016).
[PubMed]

J. Li, T. Quan, S. Li, H. Zhou, Q. Luo, H. Gong, and S. Zeng, “Reconstruction of micron resolution mouse brain surface from large-scale imaging dataset using resampling-based variational model,” Sci. Rep. 5(1), 12782 (2015).
[Crossref] [PubMed]

T. Quan, T. Zheng, Z. Yang, W. Ding, S. Li, J. Li, H. Zhou, Q. Luo, H. Gong, and S. Zeng, “NeuroGPS: automated localization of neurons for brain circuits using L1 minimization model,” Sci. Rep. 3(1), 1414 (2013).
[Crossref] [PubMed]

Ramakrishnan, C.

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
[Crossref] [PubMed]

Ramos-Vara, J. A.

J. A. Ramos-Vara, “Technical aspects of immunohistochemistry,” Vet. Pathol. 42(4), 405–426 (2005).
[Crossref] [PubMed]

Rao, G.

Y. Gang, H. Zhou, Y. Jia, L. Liu, X. Liu, G. Rao, L. Li, X. Wang, X. Lv, H. Xiong, Z. Yang, Q. Luo, H. Gong, and S. Zeng, “Embedding and chemical reactivation of green fluorescent protein in the whole mouse brain for optical micro-imaging,” Front. Neurosci. 11, 121 (2017).
[Crossref] [PubMed]

Rasskin-Gutman, D.

W. J. Weninger, S. H. Geyer, T. J. Mohun, D. Rasskin-Gutman, T. Matsui, I. Ribeiro, L. F. Costa, J. C. Izpisúa-Belmonte, and G. B. Müller, “High-resolution episcopic microscopy: a rapid technique for high detailed 3D analysis of gene activity in the context of tissue architecture and morphology,” Anat. Embryol. (Berl.) 211(3), 213–221 (2006).
[Crossref] [PubMed]

Renier, N.

N. Renier, Z. Wu, D. J. Simon, J. Yang, P. Ariel, and M. Tessier-Lavigne, “iDISCO: a simple, rapid method to immunolabel large tissue samples for volume imaging,” Cell 159(4), 896–910 (2014).
[Crossref] [PubMed]

Ribeiro, I.

W. J. Weninger, S. H. Geyer, T. J. Mohun, D. Rasskin-Gutman, T. Matsui, I. Ribeiro, L. F. Costa, J. C. Izpisúa-Belmonte, and G. B. Müller, “High-resolution episcopic microscopy: a rapid technique for high detailed 3D analysis of gene activity in the context of tissue architecture and morphology,” Anat. Embryol. (Berl.) 211(3), 213–221 (2006).
[Crossref] [PubMed]

Ritter, M.

S. Wessel, S. Pagel, M. Ritter, H. Hohenberg, and R. Wepf, “Topographic Measurements of Real Structures in reflection Confocal Laser Scanning Microscope (CLSM),” Microsc. Microanal. 9(S03), 162–163 (2003).

Ross, A.

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

Sacconi, L.

L. Silvestri, A. L. Allegra Mascaro, J. Lotti, L. Sacconi, and F. S. Pavone, “Advanced optical techniques to explore brain structure and function,” J. Innov. Opt. Health Sci. 6(1), 1230002 (2013).
[Crossref]

Sakaue-Sawano, A.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
[Crossref] [PubMed]

Scheffer, M. P.

M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V. V. Hodirnau, M. P. Scheffer, A. Seybert, S. Malkusch, E. M. Schuman, M. Heilemann, and A. S. Frangakis, “Correlative light- and electron microscopy with chemical tags,” J. Struct. Biol. 186(2), 205–213 (2014).
[Crossref] [PubMed]

Schnitzer, M. J.

B. A. Wilt, L. D. Burns, E. T. Wei Ho, K. K. Ghosh, E. A. Mukamel, and M. J. Schnitzer, “Advances in light microscopy for neuroscience,” Annu. Rev. Neurosci. 32(1), 435–506 (2009).
[Crossref] [PubMed]

Schuman, E. M.

M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V. V. Hodirnau, M. P. Scheffer, A. Seybert, S. Malkusch, E. M. Schuman, M. Heilemann, and A. S. Frangakis, “Correlative light- and electron microscopy with chemical tags,” J. Struct. Biol. 186(2), 205–213 (2014).
[Crossref] [PubMed]

Schwarz, L. A.

H. Gong, D. Xu, J. Yuan, X. Li, C. Guo, J. Peng, Y. Li, L. A. Schwarz, A. Li, B. Hu, B. Xiong, Q. Sun, Y. Zhang, J. Liu, Q. Zhong, T. Xu, S. Zeng, and Q. Luo, “High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level,” Nat. Commun. 7, 12142 (2016).
[Crossref] [PubMed]

Seung, H. S.

E. Murray, J. H. 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, M. P. Frosch, V. J. Wedeen, H. S. Seung, and K. Chung, “Simple, scalable proteomic imaging for high-dimensional profiling of intact systems,” Cell 163(6), 1500–1514 (2015).
[Crossref] [PubMed]

Seybert, A.

M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V. V. Hodirnau, M. P. Scheffer, A. Seybert, S. Malkusch, E. M. Schuman, M. Heilemann, and A. S. Frangakis, “Correlative light- and electron microscopy with chemical tags,” J. Struct. Biol. 186(2), 205–213 (2014).
[Crossref] [PubMed]

Shah, S.

B. Yang, J. B. Treweek, R. P. Kulkarni, B. E. Deverman, C. K. Chen, E. Lubeck, S. Shah, L. Cai, and V. Gradinaru, “Single-cell phenotyping within transparent intact tissue through whole-body clearing,” Cell 158(4), 945–958 (2014).
[Crossref] [PubMed]

Shang, Z.

Sharpe, J.

T. Alanentalo, A. Asayesh, H. Morrison, C. E. Lorén, D. Holmberg, J. Sharpe, and U. Ahlgren, “Tomographic molecular imaging and 3D quantification within adult mouse organs,” Nat. Methods 4(1), 31–33 (2007).
[Crossref] [PubMed]

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

Sheng, M.

A. Burette, L. Khatri, M. Wyszynski, M. Sheng, E. B. Ziff, and R. J. Weinberg, “Differential cellular and subcellular localization of ampa receptor-binding protein and glutamate receptor-interacting protein,” J. Neurosci. 21(2), 495–503 (2001).
[PubMed]

Shimizu, Y.

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
[Crossref] [PubMed]

Shimogori, T.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
[Crossref] [PubMed]

Sigal, Y. M.

D. Kim, T. J. Deerinck, Y. M. Sigal, H. P. Babcock, M. H. Ellisman, and X. Zhuang, “Correlative stochastic optical reconstruction microscopy and electron microscopy,” PLoS One 10(4), e0124581 (2015).
[Crossref] [PubMed]

Silvestri, L.

L. Silvestri, A. L. Allegra Mascaro, J. Lotti, L. Sacconi, and F. S. Pavone, “Advanced optical techniques to explore brain structure and function,” J. Innov. Opt. Health Sci. 6(1), 1230002 (2013).
[Crossref]

Simon, D. J.

N. Renier, Z. Wu, D. J. Simon, J. Yang, P. Ariel, and M. Tessier-Lavigne, “iDISCO: a simple, rapid method to immunolabel large tissue samples for volume imaging,” Cell 159(4), 896–910 (2014).
[Crossref] [PubMed]

Smith, S. J.

F. Collman, J. Buchanan, K. D. Phend, K. D. Micheva, R. J. Weinberg, and S. J. Smith, “Mapping synapses by conjugate light-electron array tomography,” J. Neurosci. 35(14), 5792–5807 (2015).
[Crossref] [PubMed]

Stoianovici, C.

S. Karma, J. Homan, C. Stoianovici, and B. Choi, “Enhanced fluorescence imaging with DMSO-mediated optical clearing,” J. Innov. Opt. Health Sci. 3(3), 153–158 (2010).
[Crossref]

Sun, Q.

H. Gong, D. Xu, J. Yuan, X. Li, C. Guo, J. Peng, Y. Li, L. A. Schwarz, A. Li, B. Hu, B. Xiong, Q. Sun, Y. Zhang, J. Liu, Q. Zhong, T. Xu, S. Zeng, and Q. Luo, “High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level,” Nat. Commun. 7, 12142 (2016).
[Crossref] [PubMed]

Sun, Y.

Y. Sun, H. Yu, D. Zheng, Q. Cao, Y. Wang, D. Harris, and Y. Wang, “Sudan black B reduces autofluorescence in murine renal tissue,” Arch. Pathol. Lab. Med. 135(10), 1335–1342 (2011).
[Crossref] [PubMed]

Susaki, E. A.

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
[Crossref] [PubMed]

Swaney, J.

E. Murray, J. H. 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, M. P. Frosch, V. J. Wedeen, H. S. Seung, and K. Chung, “Simple, scalable proteomic imaging for high-dimensional profiling of intact systems,” Cell 163(6), 1500–1514 (2015).
[Crossref] [PubMed]

Swerdlow, M.

S. B. Newman, E. Borysko, and M. Swerdlow, “New sectioning techniques for light and electron microscopy,” Science 110(2846), 66–68 (1949).
[Crossref] [PubMed]

Tainaka, K.

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
[Crossref] [PubMed]

Tawara, T.

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
[Crossref] [PubMed]

Tessier-Lavigne, M.

N. Renier, Z. Wu, D. J. Simon, J. Yang, P. Ariel, and M. Tessier-Lavigne, “iDISCO: a simple, rapid method to immunolabel large tissue samples for volume imaging,” Cell 159(4), 896–910 (2014).
[Crossref] [PubMed]

Treweek, J. B.

B. Yang, J. B. Treweek, R. P. Kulkarni, B. E. Deverman, C. K. Chen, E. Lubeck, S. Shah, L. Cai, and V. Gradinaru, “Single-cell phenotyping within transparent intact tissue through whole-body clearing,” Cell 158(4), 945–958 (2014).
[Crossref] [PubMed]

Ueda, H. R.

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
[Crossref] [PubMed]

van Donselaar, E. G.

M. A. Karreman, A. V. Agronskaia, E. G. van Donselaar, K. Vocking, F. Fereidouni, B. M. Humbel, C. T. Verrips, A. J. Verkleij, and H. C. Gerritsen, “Optimizing immuno-labeling for correlative fluorescence and electron microscopy on a single specimen,” J. Struct. Biol. 180(2), 382–386 (2012).
[Crossref] [PubMed]

Vassallo, S.

E. Murray, J. H. 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, M. P. Frosch, V. J. Wedeen, H. S. Seung, and K. Chung, “Simple, scalable proteomic imaging for high-dimensional profiling of intact systems,” Cell 163(6), 1500–1514 (2015).
[Crossref] [PubMed]

Verkleij, A. J.

M. A. Karreman, A. V. Agronskaia, E. G. van Donselaar, K. Vocking, F. Fereidouni, B. M. Humbel, C. T. Verrips, A. J. Verkleij, and H. C. Gerritsen, “Optimizing immuno-labeling for correlative fluorescence and electron microscopy on a single specimen,” J. Struct. Biol. 180(2), 382–386 (2012).
[Crossref] [PubMed]

Verrips, C. T.

M. A. Karreman, A. V. Agronskaia, E. G. van Donselaar, K. Vocking, F. Fereidouni, B. M. Humbel, C. T. Verrips, A. J. Verkleij, and H. C. Gerritsen, “Optimizing immuno-labeling for correlative fluorescence and electron microscopy on a single specimen,” J. Struct. Biol. 180(2), 382–386 (2012).
[Crossref] [PubMed]

Vocking, K.

M. A. Karreman, A. V. Agronskaia, E. G. van Donselaar, K. Vocking, F. Fereidouni, B. M. Humbel, C. T. Verrips, A. J. Verkleij, and H. C. Gerritsen, “Optimizing immuno-labeling for correlative fluorescence and electron microscopy on a single specimen,” J. Struct. Biol. 180(2), 382–386 (2012).
[Crossref] [PubMed]

Wallace, J.

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
[Crossref] [PubMed]

Wang, Q.

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

Wang, S.

H. Xiong, Z. Zhou, M. Zhu, X. Lv, A. Li, S. Li, L. Li, T. Yang, S. Wang, Z. Yang, T. Xu, Q. Luo, H. Gong, and S. Zeng, “Chemical reactivation of quenched fluorescent protein molecules enables resin-embedded fluorescence microimaging,” Nat. Commun. 5, 3992 (2014).
[Crossref] [PubMed]

Wang, X.

Wang, Y.

Y. Sun, H. Yu, D. Zheng, Q. Cao, Y. Wang, D. Harris, and Y. Wang, “Sudan black B reduces autofluorescence in murine renal tissue,” Arch. Pathol. Lab. Med. 135(10), 1335–1342 (2011).
[Crossref] [PubMed]

Y. Sun, H. Yu, D. Zheng, Q. Cao, Y. Wang, D. Harris, and Y. Wang, “Sudan black B reduces autofluorescence in murine renal tissue,” Arch. Pathol. Lab. Med. 135(10), 1335–1342 (2011).
[Crossref] [PubMed]

Watanabe, T. M.

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
[Crossref] [PubMed]

Wedeen, V. J.

E. Murray, J. H. 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, M. P. Frosch, V. J. Wedeen, H. S. Seung, and K. Chung, “Simple, scalable proteomic imaging for high-dimensional profiling of intact systems,” Cell 163(6), 1500–1514 (2015).
[Crossref] [PubMed]

Wei Ho, E. T.

B. A. Wilt, L. D. Burns, E. T. Wei Ho, K. K. Ghosh, E. A. Mukamel, and M. J. Schnitzer, “Advances in light microscopy for neuroscience,” Annu. Rev. Neurosci. 32(1), 435–506 (2009).
[Crossref] [PubMed]

Weinberg, R. J.

F. Collman, J. Buchanan, K. D. Phend, K. D. Micheva, R. J. Weinberg, and S. J. Smith, “Mapping synapses by conjugate light-electron array tomography,” J. Neurosci. 35(14), 5792–5807 (2015).
[Crossref] [PubMed]

A. Burette, L. Khatri, M. Wyszynski, M. Sheng, E. B. Ziff, and R. J. Weinberg, “Differential cellular and subcellular localization of ampa receptor-binding protein and glutamate receptor-interacting protein,” J. Neurosci. 21(2), 495–503 (2001).
[PubMed]

Weninger, W. J.

W. J. Weninger, S. H. Geyer, T. J. Mohun, D. Rasskin-Gutman, T. Matsui, I. Ribeiro, L. F. Costa, J. C. Izpisúa-Belmonte, and G. B. Müller, “High-resolution episcopic microscopy: a rapid technique for high detailed 3D analysis of gene activity in the context of tissue architecture and morphology,” Anat. Embryol. (Berl.) 211(3), 213–221 (2006).
[Crossref] [PubMed]

Wepf, R.

S. S. Biel, K. Kawaschinski, K. P. Wittern, U. Hintze, and R. Wepf, “From tissue to cellular ultrastructure: closing the gap between micro- and nanostructural imaging,” J. Microsc. 212(1), 91–99 (2003).
[Crossref] [PubMed]

S. Wessel, S. Pagel, M. Ritter, H. Hohenberg, and R. Wepf, “Topographic Measurements of Real Structures in reflection Confocal Laser Scanning Microscope (CLSM),” Microsc. Microanal. 9(S03), 162–163 (2003).

Wessel, S.

S. Wessel, S. Pagel, M. Ritter, H. Hohenberg, and R. Wepf, “Topographic Measurements of Real Structures in reflection Confocal Laser Scanning Microscope (CLSM),” Microsc. Microanal. 9(S03), 162–163 (2003).

Wigge, C.

M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V. V. Hodirnau, M. P. Scheffer, A. Seybert, S. Malkusch, E. M. Schuman, M. Heilemann, and A. S. Frangakis, “Correlative light- and electron microscopy with chemical tags,” J. Struct. Biol. 186(2), 205–213 (2014).
[Crossref] [PubMed]

Wilt, B. A.

B. A. Wilt, L. D. Burns, E. T. Wei Ho, K. K. Ghosh, E. A. Mukamel, and M. J. Schnitzer, “Advances in light microscopy for neuroscience,” Annu. Rev. Neurosci. 32(1), 435–506 (2009).
[Crossref] [PubMed]

Wittern, K. P.

S. S. Biel, K. Kawaschinski, K. P. Wittern, U. Hintze, and R. Wepf, “From tissue to cellular ultrastructure: closing the gap between micro- and nanostructural imaging,” J. Microsc. 212(1), 91–99 (2003).
[Crossref] [PubMed]

Wu, J.

J. Wu, Y. He, Z. Yang, C. Guo, Q. Luo, W. Zhou, S. Chen, A. Li, B. Xiong, T. Jiang, and H. Gong, “3D BrainCV: simultaneous visualization and analysis of cells and capillaries in a whole mouse brain with one-micron voxel resolution,” Neuroimage 87, 199–208 (2014).
[Crossref] [PubMed]

H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013).
[Crossref] [PubMed]

B. Zhang, A. Li, Z. Yang, J. Wu, Q. Luo, and H. Gong, “Modified Golgi-Cox method for micrometer scale sectioning of the whole mouse brain,” J. Neurosci. Methods 197(1), 1–5 (2011).
[Crossref] [PubMed]

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

Wu, Z.

N. Renier, Z. Wu, D. J. Simon, J. Yang, P. Ariel, and M. Tessier-Lavigne, “iDISCO: a simple, rapid method to immunolabel large tissue samples for volume imaging,” Cell 159(4), 896–910 (2014).
[Crossref] [PubMed]

Wyszynski, M.

A. Burette, L. Khatri, M. Wyszynski, M. Sheng, E. B. Ziff, and R. J. Weinberg, “Differential cellular and subcellular localization of ampa receptor-binding protein and glutamate receptor-interacting protein,” J. Neurosci. 21(2), 495–503 (2001).
[PubMed]

Xiong, B.

H. Gong, D. Xu, J. Yuan, X. Li, C. Guo, J. Peng, Y. Li, L. A. Schwarz, A. Li, B. Hu, B. Xiong, Q. Sun, Y. Zhang, J. Liu, Q. Zhong, T. Xu, S. Zeng, and Q. Luo, “High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level,” Nat. Commun. 7, 12142 (2016).
[Crossref] [PubMed]

J. Wu, Y. He, Z. Yang, C. Guo, Q. Luo, W. Zhou, S. Chen, A. Li, B. Xiong, T. Jiang, and H. Gong, “3D BrainCV: simultaneous visualization and analysis of cells and capillaries in a whole mouse brain with one-micron voxel resolution,” Neuroimage 87, 199–208 (2014).
[Crossref] [PubMed]

Xiong, H.

Y. Gang, H. Zhou, Y. Jia, L. Liu, X. Liu, G. Rao, L. Li, X. Wang, X. Lv, H. Xiong, Z. Yang, Q. Luo, H. Gong, and S. Zeng, “Embedding and chemical reactivation of green fluorescent protein in the whole mouse brain for optical micro-imaging,” Front. Neurosci. 11, 121 (2017).
[Crossref] [PubMed]

H. Xiong, Z. Zhou, M. Zhu, X. Lv, A. Li, S. Li, L. Li, T. Yang, S. Wang, Z. Yang, T. Xu, Q. Luo, H. Gong, and S. Zeng, “Chemical reactivation of quenched fluorescent protein molecules enables resin-embedded fluorescence microimaging,” Nat. Commun. 5, 3992 (2014).
[Crossref] [PubMed]

Xu, D.

H. Gong, D. Xu, J. Yuan, X. Li, C. Guo, J. Peng, Y. Li, L. A. Schwarz, A. Li, B. Hu, B. Xiong, Q. Sun, Y. Zhang, J. Liu, Q. Zhong, T. Xu, S. Zeng, and Q. Luo, “High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level,” Nat. Commun. 7, 12142 (2016).
[Crossref] [PubMed]

Xu, T.

H. Gong, D. Xu, J. Yuan, X. Li, C. Guo, J. Peng, Y. Li, L. A. Schwarz, A. Li, B. Hu, B. Xiong, Q. Sun, Y. Zhang, J. Liu, Q. Zhong, T. Xu, S. Zeng, and Q. Luo, “High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level,” Nat. Commun. 7, 12142 (2016).
[Crossref] [PubMed]

H. Xiong, Z. Zhou, M. Zhu, X. Lv, A. Li, S. Li, L. Li, T. Yang, S. Wang, Z. Yang, T. Xu, Q. Luo, H. Gong, and S. Zeng, “Chemical reactivation of quenched fluorescent protein molecules enables resin-embedded fluorescence microimaging,” Nat. Commun. 5, 3992 (2014).
[Crossref] [PubMed]

H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013).
[Crossref] [PubMed]

Yamaguchi, S.

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
[Crossref] [PubMed]

Yan, C.

H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013).
[Crossref] [PubMed]

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

Yang, B.

B. Yang, J. B. Treweek, R. P. Kulkarni, B. E. Deverman, C. K. Chen, E. Lubeck, S. Shah, L. Cai, and V. Gradinaru, “Single-cell phenotyping within transparent intact tissue through whole-body clearing,” Cell 158(4), 945–958 (2014).
[Crossref] [PubMed]

Yang, J.

N. Renier, Z. Wu, D. J. Simon, J. Yang, P. Ariel, and M. Tessier-Lavigne, “iDISCO: a simple, rapid method to immunolabel large tissue samples for volume imaging,” Cell 159(4), 896–910 (2014).
[Crossref] [PubMed]

Yang, T.

T. Yang, T. Zheng, Z. Shang, X. Wang, X. Lv, J. Yuan, and S. Zeng, “Rapid imaging of large tissues using high-resolution stage-scanning microscopy,” Biomed. Opt. Express 6(5), 1867–1875 (2015).
[Crossref] [PubMed]

H. Xiong, Z. Zhou, M. Zhu, X. Lv, A. Li, S. Li, L. Li, T. Yang, S. Wang, Z. Yang, T. Xu, Q. Luo, H. Gong, and S. Zeng, “Chemical reactivation of quenched fluorescent protein molecules enables resin-embedded fluorescence microimaging,” Nat. Commun. 5, 3992 (2014).
[Crossref] [PubMed]

Yang, Z.

Y. Gang, H. Zhou, Y. Jia, L. Liu, X. Liu, G. Rao, L. Li, X. Wang, X. Lv, H. Xiong, Z. Yang, Q. Luo, H. Gong, and S. Zeng, “Embedding and chemical reactivation of green fluorescent protein in the whole mouse brain for optical micro-imaging,” Front. Neurosci. 11, 121 (2017).
[Crossref] [PubMed]

H. Xiong, Z. Zhou, M. Zhu, X. Lv, A. Li, S. Li, L. Li, T. Yang, S. Wang, Z. Yang, T. Xu, Q. Luo, H. Gong, and S. Zeng, “Chemical reactivation of quenched fluorescent protein molecules enables resin-embedded fluorescence microimaging,” Nat. Commun. 5, 3992 (2014).
[Crossref] [PubMed]

J. Wu, Y. He, Z. Yang, C. Guo, Q. Luo, W. Zhou, S. Chen, A. Li, B. Xiong, T. Jiang, and H. Gong, “3D BrainCV: simultaneous visualization and analysis of cells and capillaries in a whole mouse brain with one-micron voxel resolution,” Neuroimage 87, 199–208 (2014).
[Crossref] [PubMed]

Z. Yang, B. Hu, Y. Zhang, Q. Luo, and H. Gong, “Development of a plastic embedding method for large-volume and fluorescent-protein-expressing tissues,” PLoS One 8(4), e60877 (2013).
[Crossref] [PubMed]

H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013).
[Crossref] [PubMed]

T. Zheng, Z. Yang, A. Li, X. Lv, Z. Zhou, X. Wang, X. Qi, S. Li, Q. Luo, H. Gong, and S. Zeng, “Visualization of brain circuits using two-photon fluorescence micro-optical sectioning tomography,” Opt. Express 21(8), 9839–9850 (2013).
[Crossref] [PubMed]

T. Quan, T. Zheng, Z. Yang, W. Ding, S. Li, J. Li, H. Zhou, Q. Luo, H. Gong, and S. Zeng, “NeuroGPS: automated localization of neurons for brain circuits using L1 minimization model,” Sci. Rep. 3(1), 1414 (2013).
[Crossref] [PubMed]

B. Zhang, A. Li, Z. Yang, J. Wu, Q. Luo, and H. Gong, “Modified Golgi-Cox method for micrometer scale sectioning of the whole mouse brain,” J. Neurosci. Methods 197(1), 1–5 (2011).
[Crossref] [PubMed]

Yokota, H.

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
[Crossref] [PubMed]

Yokoyama, C.

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
[Crossref] [PubMed]

Yu, H.

Y. Sun, H. Yu, D. Zheng, Q. Cao, Y. Wang, D. Harris, and Y. Wang, “Sudan black B reduces autofluorescence in murine renal tissue,” Arch. Pathol. Lab. Med. 135(10), 1335–1342 (2011).
[Crossref] [PubMed]

Yu, Z.

M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V. V. Hodirnau, M. P. Scheffer, A. Seybert, S. Malkusch, E. M. Schuman, M. Heilemann, and A. S. Frangakis, “Correlative light- and electron microscopy with chemical tags,” J. Struct. Biol. 186(2), 205–213 (2014).
[Crossref] [PubMed]

Yuan, J.

H. Gong, D. Xu, J. Yuan, X. Li, C. Guo, J. Peng, Y. Li, L. A. Schwarz, A. Li, B. Hu, B. Xiong, Q. Sun, Y. Zhang, J. Liu, Q. Zhong, T. Xu, S. Zeng, and Q. Luo, “High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level,” Nat. Commun. 7, 12142 (2016).
[Crossref] [PubMed]

T. Yang, T. Zheng, Z. Shang, X. Wang, X. Lv, J. Yuan, and S. Zeng, “Rapid imaging of large tissues using high-resolution stage-scanning microscopy,” Biomed. Opt. Express 6(5), 1867–1875 (2015).
[Crossref] [PubMed]

Zalocusky, K. A.

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
[Crossref] [PubMed]

Zeng, S.

Y. Gang, H. Zhou, Y. Jia, L. Liu, X. Liu, G. Rao, L. Li, X. Wang, X. Lv, H. Xiong, Z. Yang, Q. Luo, H. Gong, and S. Zeng, “Embedding and chemical reactivation of green fluorescent protein in the whole mouse brain for optical micro-imaging,” Front. Neurosci. 11, 121 (2017).
[Crossref] [PubMed]

S. Li, H. Zhou, T. Quan, J. Li, Y. Li, A. Li, Q. Luo, H. Gong, and S. Zeng, “SparseTracer: the reconstruction of discontinuous neuronal morphology in noisy images,” Neuroinformatics 15(2), 133–149 (2017).
[Crossref] [PubMed]

T. Quan, H. Zhou, J. Li, S. Li, A. Li, Y. Li, X. Lv, Q. Luo, H. Gong, and S. Zeng, “NeuroGPS-Tree: automatic reconstruction of large-scale neuronal populations with dense neurites,” Nat. Methods 13(1), 51–54 (2016).
[PubMed]

H. Gong, D. Xu, J. Yuan, X. Li, C. Guo, J. Peng, Y. Li, L. A. Schwarz, A. Li, B. Hu, B. Xiong, Q. Sun, Y. Zhang, J. Liu, Q. Zhong, T. Xu, S. Zeng, and Q. Luo, “High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level,” Nat. Commun. 7, 12142 (2016).
[Crossref] [PubMed]

T. Yang, T. Zheng, Z. Shang, X. Wang, X. Lv, J. Yuan, and S. Zeng, “Rapid imaging of large tissues using high-resolution stage-scanning microscopy,” Biomed. Opt. Express 6(5), 1867–1875 (2015).
[Crossref] [PubMed]

J. Li, T. Quan, S. Li, H. Zhou, Q. Luo, H. Gong, and S. Zeng, “Reconstruction of micron resolution mouse brain surface from large-scale imaging dataset using resampling-based variational model,” Sci. Rep. 5(1), 12782 (2015).
[Crossref] [PubMed]

H. Xiong, Z. Zhou, M. Zhu, X. Lv, A. Li, S. Li, L. Li, T. Yang, S. Wang, Z. Yang, T. Xu, Q. Luo, H. Gong, and S. Zeng, “Chemical reactivation of quenched fluorescent protein molecules enables resin-embedded fluorescence microimaging,” Nat. Commun. 5, 3992 (2014).
[Crossref] [PubMed]

H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013).
[Crossref] [PubMed]

T. Zheng, Z. Yang, A. Li, X. Lv, Z. Zhou, X. Wang, X. Qi, S. Li, Q. Luo, H. Gong, and S. Zeng, “Visualization of brain circuits using two-photon fluorescence micro-optical sectioning tomography,” Opt. Express 21(8), 9839–9850 (2013).
[Crossref] [PubMed]

T. Quan, T. Zheng, Z. Yang, W. Ding, S. Li, J. Li, H. Zhou, Q. Luo, H. Gong, and S. Zeng, “NeuroGPS: automated localization of neurons for brain circuits using L1 minimization model,” Sci. Rep. 3(1), 1414 (2013).
[Crossref] [PubMed]

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

Zhang, B.

B. Zhang, A. Li, Z. Yang, J. Wu, Q. Luo, and H. Gong, “Modified Golgi-Cox method for micrometer scale sectioning of the whole mouse brain,” J. Neurosci. Methods 197(1), 1–5 (2011).
[Crossref] [PubMed]

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

Zhang, Y.

H. Gong, D. Xu, J. Yuan, X. Li, C. Guo, J. Peng, Y. Li, L. A. Schwarz, A. Li, B. Hu, B. Xiong, Q. Sun, Y. Zhang, J. Liu, Q. Zhong, T. Xu, S. Zeng, and Q. Luo, “High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level,” Nat. Commun. 7, 12142 (2016).
[Crossref] [PubMed]

Z. Yang, B. Hu, Y. Zhang, Q. Luo, and H. Gong, “Development of a plastic embedding method for large-volume and fluorescent-protein-expressing tissues,” PLoS One 8(4), e60877 (2013).
[Crossref] [PubMed]

Zheng, D.

Y. Sun, H. Yu, D. Zheng, Q. Cao, Y. Wang, D. Harris, and Y. Wang, “Sudan black B reduces autofluorescence in murine renal tissue,” Arch. Pathol. Lab. Med. 135(10), 1335–1342 (2011).
[Crossref] [PubMed]

Zheng, T.

Zhong, Q.

H. Gong, D. Xu, J. Yuan, X. Li, C. Guo, J. Peng, Y. Li, L. A. Schwarz, A. Li, B. Hu, B. Xiong, Q. Sun, Y. Zhang, J. Liu, Q. Zhong, T. Xu, S. Zeng, and Q. Luo, “High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level,” Nat. Commun. 7, 12142 (2016).
[Crossref] [PubMed]

Zhou, H.

Y. Gang, H. Zhou, Y. Jia, L. Liu, X. Liu, G. Rao, L. Li, X. Wang, X. Lv, H. Xiong, Z. Yang, Q. Luo, H. Gong, and S. Zeng, “Embedding and chemical reactivation of green fluorescent protein in the whole mouse brain for optical micro-imaging,” Front. Neurosci. 11, 121 (2017).
[Crossref] [PubMed]

S. Li, H. Zhou, T. Quan, J. Li, Y. Li, A. Li, Q. Luo, H. Gong, and S. Zeng, “SparseTracer: the reconstruction of discontinuous neuronal morphology in noisy images,” Neuroinformatics 15(2), 133–149 (2017).
[Crossref] [PubMed]

T. Quan, H. Zhou, J. Li, S. Li, A. Li, Y. Li, X. Lv, Q. Luo, H. Gong, and S. Zeng, “NeuroGPS-Tree: automatic reconstruction of large-scale neuronal populations with dense neurites,” Nat. Methods 13(1), 51–54 (2016).
[PubMed]

J. Li, T. Quan, S. Li, H. Zhou, Q. Luo, H. Gong, and S. Zeng, “Reconstruction of micron resolution mouse brain surface from large-scale imaging dataset using resampling-based variational model,” Sci. Rep. 5(1), 12782 (2015).
[Crossref] [PubMed]

T. Quan, T. Zheng, Z. Yang, W. Ding, S. Li, J. Li, H. Zhou, Q. Luo, H. Gong, and S. Zeng, “NeuroGPS: automated localization of neurons for brain circuits using L1 minimization model,” Sci. Rep. 3(1), 1414 (2013).
[Crossref] [PubMed]

Zhou, W.

J. Wu, Y. He, Z. Yang, C. Guo, Q. Luo, W. Zhou, S. Chen, A. Li, B. Xiong, T. Jiang, and H. Gong, “3D BrainCV: simultaneous visualization and analysis of cells and capillaries in a whole mouse brain with one-micron voxel resolution,” Neuroimage 87, 199–208 (2014).
[Crossref] [PubMed]

Zhou, Z.

H. Xiong, Z. Zhou, M. Zhu, X. Lv, A. Li, S. Li, L. Li, T. Yang, S. Wang, Z. Yang, T. Xu, Q. Luo, H. Gong, and S. Zeng, “Chemical reactivation of quenched fluorescent protein molecules enables resin-embedded fluorescence microimaging,” Nat. Commun. 5, 3992 (2014).
[Crossref] [PubMed]

T. Zheng, Z. Yang, A. Li, X. Lv, Z. Zhou, X. Wang, X. Qi, S. Li, Q. Luo, H. Gong, and S. Zeng, “Visualization of brain circuits using two-photon fluorescence micro-optical sectioning tomography,” Opt. Express 21(8), 9839–9850 (2013).
[Crossref] [PubMed]

Zhu, M.

H. Xiong, Z. Zhou, M. Zhu, X. Lv, A. Li, S. Li, L. Li, T. Yang, S. Wang, Z. Yang, T. Xu, Q. Luo, H. Gong, and S. Zeng, “Chemical reactivation of quenched fluorescent protein molecules enables resin-embedded fluorescence microimaging,” Nat. Commun. 5, 3992 (2014).
[Crossref] [PubMed]

Zhuang, X.

D. Kim, T. J. Deerinck, Y. M. Sigal, H. P. Babcock, M. H. Ellisman, and X. Zhuang, “Correlative stochastic optical reconstruction microscopy and electron microscopy,” PLoS One 10(4), e0124581 (2015).
[Crossref] [PubMed]

Ziff, E. B.

A. Burette, L. Khatri, M. Wyszynski, M. Sheng, E. B. Ziff, and R. J. Weinberg, “Differential cellular and subcellular localization of ampa receptor-binding protein and glutamate receptor-interacting protein,” J. Neurosci. 21(2), 495–503 (2001).
[PubMed]

Anat. Embryol. (Berl.) (1)

W. J. Weninger, S. H. Geyer, T. J. Mohun, D. Rasskin-Gutman, T. Matsui, I. Ribeiro, L. F. Costa, J. C. Izpisúa-Belmonte, and G. B. Müller, “High-resolution episcopic microscopy: a rapid technique for high detailed 3D analysis of gene activity in the context of tissue architecture and morphology,” Anat. Embryol. (Berl.) 211(3), 213–221 (2006).
[Crossref] [PubMed]

Annu. Rev. Neurosci. (1)

B. A. Wilt, L. D. Burns, E. T. Wei Ho, K. K. Ghosh, E. A. Mukamel, and M. J. Schnitzer, “Advances in light microscopy for neuroscience,” Annu. Rev. Neurosci. 32(1), 435–506 (2009).
[Crossref] [PubMed]

Arch. Pathol. Lab. Med. (1)

Y. Sun, H. Yu, D. Zheng, Q. Cao, Y. Wang, D. Harris, and Y. Wang, “Sudan black B reduces autofluorescence in murine renal tissue,” Arch. Pathol. Lab. Med. 135(10), 1335–1342 (2011).
[Crossref] [PubMed]

Biomed. Opt. Express (1)

Cell (4)

N. Renier, Z. Wu, D. J. Simon, J. Yang, P. Ariel, and M. Tessier-Lavigne, “iDISCO: a simple, rapid method to immunolabel large tissue samples for volume imaging,” Cell 159(4), 896–910 (2014).
[Crossref] [PubMed]

B. Yang, J. B. Treweek, R. P. Kulkarni, B. E. Deverman, C. K. Chen, E. Lubeck, S. Shah, L. Cai, and V. Gradinaru, “Single-cell phenotyping within transparent intact tissue through whole-body clearing,” Cell 158(4), 945–958 (2014).
[Crossref] [PubMed]

E. Murray, J. H. 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, M. P. Frosch, V. J. Wedeen, H. S. Seung, and K. Chung, “Simple, scalable proteomic imaging for high-dimensional profiling of intact systems,” Cell 163(6), 1500–1514 (2015).
[Crossref] [PubMed]

E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, “Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis,” Cell 157(3), 726–739 (2014).
[Crossref] [PubMed]

Front. Neurosci. (1)

Y. Gang, H. Zhou, Y. Jia, L. Liu, X. Liu, G. Rao, L. Li, X. Wang, X. Lv, H. Xiong, Z. Yang, Q. Luo, H. Gong, and S. Zeng, “Embedding and chemical reactivation of green fluorescent protein in the whole mouse brain for optical micro-imaging,” Front. Neurosci. 11, 121 (2017).
[Crossref] [PubMed]

Histochem. J. (1)

G. R. Newman and J. A. Hobot, “Resins for combined light and electron microscopy: a half century of development,” Histochem. J. 31(8), 495–505 (1999).
[Crossref] [PubMed]

J. Exp. Med. (1)

A. H. Coons and M. H. Kaplan, “Localization of antigen in tissue cells; improvements in a method for the detection of antigen by means of fluorescent antibody,” J. Exp. Med. 91(1), 1–13 (1949).
[Crossref] [PubMed]

J. Immunol. (1)

A. H. Coons, H. J. Creech, R. N. Jones, and E. Berliner, “The demonstration of pneumococcal antigen in tissues by the use of fluorescent antibody,” J. Immunol. 45(3), 159–170 (1942).

J. Innov. Opt. Health Sci. (2)

S. Karma, J. Homan, C. Stoianovici, and B. Choi, “Enhanced fluorescence imaging with DMSO-mediated optical clearing,” J. Innov. Opt. Health Sci. 3(3), 153–158 (2010).
[Crossref]

L. Silvestri, A. L. Allegra Mascaro, J. Lotti, L. Sacconi, and F. S. Pavone, “Advanced optical techniques to explore brain structure and function,” J. Innov. Opt. Health Sci. 6(1), 1230002 (2013).
[Crossref]

J. Microsc. (1)

S. S. Biel, K. Kawaschinski, K. P. Wittern, U. Hintze, and R. Wepf, “From tissue to cellular ultrastructure: closing the gap between micro- and nanostructural imaging,” J. Microsc. 212(1), 91–99 (2003).
[Crossref] [PubMed]

J. Neurosci. (2)

A. Burette, L. Khatri, M. Wyszynski, M. Sheng, E. B. Ziff, and R. J. Weinberg, “Differential cellular and subcellular localization of ampa receptor-binding protein and glutamate receptor-interacting protein,” J. Neurosci. 21(2), 495–503 (2001).
[PubMed]

F. Collman, J. Buchanan, K. D. Phend, K. D. Micheva, R. J. Weinberg, and S. J. Smith, “Mapping synapses by conjugate light-electron array tomography,” J. Neurosci. 35(14), 5792–5807 (2015).
[Crossref] [PubMed]

J. Neurosci. Methods (1)

B. Zhang, A. Li, Z. Yang, J. Wu, Q. Luo, and H. Gong, “Modified Golgi-Cox method for micrometer scale sectioning of the whole mouse brain,” J. Neurosci. Methods 197(1), 1–5 (2011).
[Crossref] [PubMed]

J. Struct. Biol. (2)

M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V. V. Hodirnau, M. P. Scheffer, A. Seybert, S. Malkusch, E. M. Schuman, M. Heilemann, and A. S. Frangakis, “Correlative light- and electron microscopy with chemical tags,” J. Struct. Biol. 186(2), 205–213 (2014).
[Crossref] [PubMed]

M. A. Karreman, A. V. Agronskaia, E. G. van Donselaar, K. Vocking, F. Fereidouni, B. M. Humbel, C. T. Verrips, A. J. Verkleij, and H. C. Gerritsen, “Optimizing immuno-labeling for correlative fluorescence and electron microscopy on a single specimen,” J. Struct. Biol. 180(2), 382–386 (2012).
[Crossref] [PubMed]

Microsc. Microanal. (1)

S. Wessel, S. Pagel, M. Ritter, H. Hohenberg, and R. Wepf, “Topographic Measurements of Real Structures in reflection Confocal Laser Scanning Microscope (CLSM),” Microsc. Microanal. 9(S03), 162–163 (2003).

Nat. Commun. (2)

H. Gong, D. Xu, J. Yuan, X. Li, C. Guo, J. Peng, Y. Li, L. A. Schwarz, A. Li, B. Hu, B. Xiong, Q. Sun, Y. Zhang, J. Liu, Q. Zhong, T. Xu, S. Zeng, and Q. Luo, “High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level,” Nat. Commun. 7, 12142 (2016).
[Crossref] [PubMed]

H. Xiong, Z. Zhou, M. Zhu, X. Lv, A. Li, S. Li, L. Li, T. Yang, S. Wang, Z. Yang, T. Xu, Q. Luo, H. Gong, and S. Zeng, “Chemical reactivation of quenched fluorescent protein molecules enables resin-embedded fluorescence microimaging,” Nat. Commun. 5, 3992 (2014).
[Crossref] [PubMed]

Nat. Methods (2)

T. Quan, H. Zhou, J. Li, S. Li, A. Li, Y. Li, X. Lv, Q. Luo, H. Gong, and S. Zeng, “NeuroGPS-Tree: automatic reconstruction of large-scale neuronal populations with dense neurites,” Nat. Methods 13(1), 51–54 (2016).
[PubMed]

T. Alanentalo, A. Asayesh, H. Morrison, C. E. Lorén, D. Holmberg, J. Sharpe, and U. Ahlgren, “Tomographic molecular imaging and 3D quantification within adult mouse organs,” Nat. Methods 4(1), 31–33 (2007).
[Crossref] [PubMed]

Nat. Neurosci. (1)

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
[Crossref] [PubMed]

Nature (1)

K. Chung, J. Wallace, S. Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth, “Structural and molecular interrogation of intact biological systems,” Nature 497(7449), 332–337 (2013).
[Crossref] [PubMed]

Neuroimage (2)

H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013).
[Crossref] [PubMed]

J. Wu, Y. He, Z. Yang, C. Guo, Q. Luo, W. Zhou, S. Chen, A. Li, B. Xiong, T. Jiang, and H. Gong, “3D BrainCV: simultaneous visualization and analysis of cells and capillaries in a whole mouse brain with one-micron voxel resolution,” Neuroimage 87, 199–208 (2014).
[Crossref] [PubMed]

Neuroinformatics (1)

S. Li, H. Zhou, T. Quan, J. Li, Y. Li, A. Li, Q. Luo, H. Gong, and S. Zeng, “SparseTracer: the reconstruction of discontinuous neuronal morphology in noisy images,” Neuroinformatics 15(2), 133–149 (2017).
[Crossref] [PubMed]

Opt. Express (1)

PLoS One (2)

Z. Yang, B. Hu, Y. Zhang, Q. Luo, and H. Gong, “Development of a plastic embedding method for large-volume and fluorescent-protein-expressing tissues,” PLoS One 8(4), e60877 (2013).
[Crossref] [PubMed]

D. Kim, T. J. Deerinck, Y. M. Sigal, H. P. Babcock, M. H. Ellisman, and X. Zhuang, “Correlative stochastic optical reconstruction microscopy and electron microscopy,” PLoS One 10(4), e0124581 (2015).
[Crossref] [PubMed]

Sci. Rep. (2)

J. Li, T. Quan, S. Li, H. Zhou, Q. Luo, H. Gong, and S. Zeng, “Reconstruction of micron resolution mouse brain surface from large-scale imaging dataset using resampling-based variational model,” Sci. Rep. 5(1), 12782 (2015).
[Crossref] [PubMed]

T. Quan, T. Zheng, Z. Yang, W. Ding, S. Li, J. Li, H. Zhou, Q. Luo, H. Gong, and S. Zeng, “NeuroGPS: automated localization of neurons for brain circuits using L1 minimization model,” Sci. Rep. 3(1), 1414 (2013).
[Crossref] [PubMed]

Science (3)

S. B. Newman, E. Borysko, and M. Swerdlow, “New sectioning techniques for light and electron microscopy,” Science 110(2846), 66–68 (1949).
[Crossref] [PubMed]

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

Vet. Pathol. (1)

J. A. Ramos-Vara, “Technical aspects of immunohistochemistry,” Vet. Pathol. 42(4), 405–426 (2005).
[Crossref] [PubMed]

Cited By

OSA participates in Crossref's Cited-By Linking service. Citing articles from OSA journals and other participating publishers are listed here.

Alert me when this article is cited.


Figures (8)

Fig. 1
Fig. 1 Immunofluorescence-labeled brain slices before and after resin embedding. (a) Images of labeled brain slices before and after GMA, Lowicryl HM20 or LR White resin embedding, respectively. All slices were immunolabeled by primary antibody (anti-TH), and were labeled with the various secondary antibodies conjugated with four fluorescent dyes: CF488, CF568, CY3, or CY5, respectively. All images were taken at a 0.42 × 0.42 × 1 μm3 voxel size on an LSM780 confocal microscope (ZEISS). (b) Fluorescent intensity change of immunostained brain slices after being embedding with different resins. We calculated the fluorescent intensity changes from labeled neuronal somas. The fluorescent intensities were compared before and after resin embedding using ImageJ software. The values in the bar graph are given as the means ± SD (n = 25 neurons from three slices for each independent sample). (c) Small shifts occurred in the absorption spectra of the dyes (CF488, CF568, CY3, and CY5) in Lowicryl HM20 resin polymer, compared to those in PBS buffer. Scale bar in (a): 50 μm.

Download Full Size | PPT Slide | PDF

Fig. 2
Fig. 2 Preservation of immunofluorescence labeled fine details of neurite in resin-embedded brain tissue. (a) Fluorescence image of neurons labeled by PRV-GFP virus; slices were imaged after immunofluorescent labeling (b), and after resin embedding (c). (d) Fluorescent intensities of pixels crossed by red, purple, and green lines (shown in a, b, c, respectively) are plotted in the corresponding colors. (e) Morphology of neurons labeled by RV-DsRed virus before immunostaining, after immunofluorescent labeling (f), and after resin embedding (g). (h) Fluorescent intensities of pixels crossed by the red, purple, and green dashed lines (shown in e, f, and g, respectively) are plotted in the corresponding color. Images in panels (a-c) were recorded at a 0.42 × 0.42 × 1.00 μm3 voxel size using a confocal microscope (LSM780, ZEISS) with a 20 × 1.0 NA water objective. Images in panels (e-g) were recorded at a 0.21 × 0.21 × 1.00 μm3 voxel size using a confocal microscope (LSM780, ZEISS) with a 40 × 1.0 NA oil objective. All the images represent maximum intensity z-projections of 20-μm-thickness. Scale bar: (a-g) 50 μm.

Download Full Size | PPT Slide | PDF

Fig. 3
Fig. 3 Resin embedding is compatible with various antibodies and fluorescent tracers staining in brain tissue. (a-i) Images of immune- and fluorescent tracer-labeled neurons in mouse brain tissue after Lowicryl HM20 resin embedding. (a) Immunolabeling of TdTomato-labeled mouse cortex from ChAT-cre; Rosa26lsl-tdTomato transgenic mice. (b) TH-immunolabeled thalamic neurons in C57 mouse brain tissue. (c) Immunolabeling of GFP-expressing hippocampal neurons from a Thy1-GFP-M transgenic mouse. (d-h) Mouse brain slices were immunolabeled by FoxP2 (d), cFos (e), parvalbumin (f), cholera toxin beta (g), and PSD-95 (h), respectively. Images in panel a-h were acquired on an LSM780 confocal microscope (ZEISS). (i) 3D volume image of immnofluorescent signals (Alexa 488) labeled by parvalbumin in mouse cortex, images were acquired by a two-photon microscope (LSM780). Scale bar: (a-g) 50 μm; (h) 10 μm.

Download Full Size | PPT Slide | PDF

Fig. 4
Fig. 4 Fluorescent images of Lectin-DyLight 594 labeled vasculature in the brain tissue after Lowicryl HM20 resin embedding. (a) Maximum intensity projections of a 20-μm-thick coronal slice. (b-d) Corresponding magnification of regions indicated in (a). (e-g) High magnification images of the boxed regions in (b-d), respectively. All images were acquired using 20 × (NA = 1.0), at a 0.42 × 0.42 × 1.00 μm3 voxel size on a confocal microscope (LSM780, ZEISS). Scale bars: (a) 1 mm; (b-d) 100 μm; (e-g) 30 μm.

Download Full Size | PPT Slide | PDF

Fig. 5
Fig. 5 Imaging large volume immunolabeled mouse brain tissue after Lowicryl HM20 resin embedding. (a) 3D presentation of the TH immunolabeled mouse brain block. Enlargements of the fine structures of TH-positive axonal fibers in the cortex (b) and TH-positive soma located in the thalamus (c). Images were acquired by successive high-resolution stage-scanning microscopy at a 0.16 × 0.16 × 1.00 μm3 voxel size. (a) 6200 × 5000 × 1200 μm3; (b) 480 × 480 × 380 μm3; (c) 480 × 480 × 510 μm3.

Download Full Size | PPT Slide | PDF

Fig. 6
Fig. 6 Effects of SBB on background fluorescence in the resin embedded brain tissue. Images obtained from immunostained brain tissue that were embedded in resin (HM20, GMA and LR white) with (g-l) and without 0.2% SBB (control, a-f), respectively. Mouse brain tissue was immunostained with anti-tyrosine hydroxylase primary antibody and CF488 or CY3-conjugated secondary antibodies. All images were recorded at 0.17 × 0.17 μm/pixel on the same wide field microscope (Nikon Ni-E) at room temperature. Scale bar: (a-l): 50 μm.

Download Full Size | PPT Slide | PDF

Fig. 7
Fig. 7 Schematic diagram for three-dimensional fluorescent imaging. The resin-embedded biological sample was mounted on a precision motion stage that moves between the stage-scanning microscopy and the microtome. Strip imaging methods combined with line illumination were applied for rapid surface imaging. After the surface layer of specimen was imaged, the recorded layer (1-μm thick) was removed by a fixed diamond knife. The sectioning-imaging cycles was repeated for collecting three-dimensional imaging data sets.

Download Full Size | PPT Slide | PDF

Fig. 8
Fig. 8 Comparison of signal and background fluorescence of the images obtained using successive high-resolution stage-scanning block-face imaging. (a) Maximal intensity projections of the 100-mm thickness z-stacks images without preprocessing. Image stacks were selected from the same data set in Fig. 5. The mean signal intensity was measured from the red dashed circle area. The mean value of the background was measured from a blue dashed line drawn across the background area close to soma. The fluorescent signal intensity was calculated by subtracting the mean value of background from the mean value of the soma. (b) The normalized fluorescent intensities of signal value were compared with background values. 36 somas were measured from different images of the same data set. This result shows that the signal-to-background ratio is 15.1 ± 5.5. (c) Fluorescent intensities of pixels crossed by the blue, green and red lines were plotted in curves with the corresponding color in (a). The signal-to-background ratio values are given as the means ± SD.

Download Full Size | PPT Slide | PDF

Tables (4)

Tables Icon

Table 1 Primary antibodies tested on mouse brain tissue.

View Table | View all tables in this article
Tables Icon

Table 2 Secondary antibodies tested on mouse brain tissue.

View Table | View all tables in this article
Tables Icon

Table 3 Fluorescent tracers and dyes tested on mouse brain tissue.

View Table | View all tables in this article
Tables Icon

Table 4 The cutting performance of the polymerized tissue block.

View Table | View all tables in this article

Metrics