Abstract

Three-dimensional (3D) high-resolution imaging can help us better understand the brain, and CUBIC is a powerful technique to render the brain transparent, thus benefiting 3D imaging. In this study, we combined CUBIC with immunofluorescence staining (IFS) and successfully acquired 3D high-resolution images of cerebral vessels, astrocytes, dopaminergic neurons and pericytes, providing us abundant information about the change in spatial frequency content for cellular scale features. Additionally, we found that a longer duration of antibody incubation produced deeper staining. Our study indicates the broad application prospects of IFS-based CUBIC for studying specific cerebral structures and diseases related to alterations of these structures.

© 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

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References

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    [Crossref] [PubMed]
  2. D. S. Richardson and J. W. Lichtman, “Clarifying Tissue Clearing,” Cell 162(2), 246–257 (2015).
    [Crossref] [PubMed]
  3. 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]
  4. E. A. Susaki, K. Tainaka, D. Perrin, H. Yukinaga, A. Kuno, and H. R. Ueda, “Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging,” Nat. Protoc. 10(11), 1709–1727 (2015).
    [Crossref] [PubMed]
  5. S. I. Kubota, K. Takahashi, J. Nishida, Y. Morishita, S. Ehata, K. Tainaka, K. Miyazono, and H. R. Ueda, “Whole-Body Profiling of Cancer Metastasis with Single-Cell Resolution,” Cell Reports 20(1), 236–250 (2017).
    [Crossref] [PubMed]
  6. P. Matryba, L. Bozycki, M. Pawłowska, L. Kaczmarek, and M. Stefaniuk, “Optimized perfusion-based CUBIC protocol for the efficient whole-body clearing and imaging of rat organs,” J. Biophotonics 11(5), e201700248 (2018).
    [Crossref] [PubMed]
  7. I. Nehrhoff, D. Bocancea, J. Vaquero, J. J. Vaquero, J. Ripoll, M. Desco, and M. V. Gómez-Gaviro, “3D imaging in CUBIC-cleared mouse heart tissue: going deeper,” Biomed. Opt. Express 7(9), 3716–3720 (2016).
    [Crossref] [PubMed]
  8. S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
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  9. M. V. Gómez-Gaviro, E. Balaban, D. Bocancea, M. T. Lorrio, M. Pompeiano, M. Desco, J. Ripoll, and J. J. Vaquero, “Optimized CUBIC protocol for three-dimensional imaging of chicken embryos at single-cell resolution,” Development 144(11), 2092–2097 (2017).
    [Crossref] [PubMed]
  10. H. Liang, H. Wang, S. Wang, R. Francis, G. Paxinos, and X. Huang, “3D imaging of PSD-95 in the mouse brain using the advanced CUBIC method,” Mol. Brain 11(1), 50 (2018).
    [Crossref] [PubMed]
  11. Z. Zhao, A. R. Nelson, C. Betsholtz, and B. V. Zlokovic, “Establishment and Dysfunction of the Blood-Brain Barrier,” Cell 163(5), 1064–1078 (2015).
    [Crossref] [PubMed]
  12. J. Seo, M. Choe, and S. Y. Kim, “Clearing and Labeling Techniques for Large-Scale Biological Tissues,” Mol. Cells 39(6), 439–446 (2016).
    [Crossref] [PubMed]
  13. M. Frétaud, L. Rivière, É. Job, S. Gay, J. J. Lareyre, J. S. Joly, P. Affaticati, and V. Thermes, “High-resolution 3D imaging of whole organ after clearing: taking a new look at the zebrafish testis,” Sci. Rep. 7(1), 43012 (2017).
    [Crossref] [PubMed]
  14. M. Orlich and F. Kiefer, “A qualitative comparison of ten tissue clearing techniques,” Histol. Histopathol. 33(2), 181–199 (2018).
    [PubMed]
  15. E. Lee, J. Choi, Y. Jo, J. Y. Kim, Y. J. Jang, H. M. Lee, S. Y. Kim, H. J. Lee, K. Cho, N. Jung, E. M. Hur, S. J. Jeong, C. Moon, Y. Choe, I. J. Rhyu, H. Kim, and W. Sun, “ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging,” Sci. Rep. 6(1), 18631 (2016).
    [Crossref] [PubMed]
  16. B. Lloyd-Lewis, F. M. Davis, O. B. Harris, J. R. Hitchcock, F. C. Lourenco, M. Pasche, and C. J. Watson, “Imaging the mammary gland and mammary tumours in 3D: optical tissue clearing and immunofluorescence methods,” Breast Cancer Res. 18(1), 127 (2016).
    [Crossref] [PubMed]
  17. F. M. Davis, B. Lloyd-Lewis, O. B. Harris, S. Kozar, D. J. Winton, L. Muresan, and C. J. Watson, “Single-cell lineage tracing in the mammary gland reveals stochastic clonal dispersion of stem/progenitor cell progeny,” Nat. Commun. 7(1), 13053 (2016).
    [Crossref] [PubMed]
  18. S. Y. Kim, J. H. Cho, E. Murray, N. Bakh, H. Choi, K. Ohn, L. Ruelas, A. Hubbert, M. McCue, S. L. Vassallo, P. J. Keller, and K. Chung, “Stochastic electrotransport selectively enhances the transport of highly electromobile molecules,” Proc. Natl. Acad. Sci. U.S.A. 112(46), E6274–E6283 (2015).
    [Crossref] [PubMed]
  19. 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]
  20. 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]

2018 (3)

M. Orlich and F. Kiefer, “A qualitative comparison of ten tissue clearing techniques,” Histol. Histopathol. 33(2), 181–199 (2018).
[PubMed]

H. Liang, H. Wang, S. Wang, R. Francis, G. Paxinos, and X. Huang, “3D imaging of PSD-95 in the mouse brain using the advanced CUBIC method,” Mol. Brain 11(1), 50 (2018).
[Crossref] [PubMed]

P. Matryba, L. Bozycki, M. Pawłowska, L. Kaczmarek, and M. Stefaniuk, “Optimized perfusion-based CUBIC protocol for the efficient whole-body clearing and imaging of rat organs,” J. Biophotonics 11(5), e201700248 (2018).
[Crossref] [PubMed]

2017 (4)

S. I. Kubota, K. Takahashi, J. Nishida, Y. Morishita, S. Ehata, K. Tainaka, K. Miyazono, and H. R. Ueda, “Whole-Body Profiling of Cancer Metastasis with Single-Cell Resolution,” Cell Reports 20(1), 236–250 (2017).
[Crossref] [PubMed]

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

M. V. Gómez-Gaviro, E. Balaban, D. Bocancea, M. T. Lorrio, M. Pompeiano, M. Desco, J. Ripoll, and J. J. Vaquero, “Optimized CUBIC protocol for three-dimensional imaging of chicken embryos at single-cell resolution,” Development 144(11), 2092–2097 (2017).
[Crossref] [PubMed]

M. Frétaud, L. Rivière, É. Job, S. Gay, J. J. Lareyre, J. S. Joly, P. Affaticati, and V. Thermes, “High-resolution 3D imaging of whole organ after clearing: taking a new look at the zebrafish testis,” Sci. Rep. 7(1), 43012 (2017).
[Crossref] [PubMed]

2016 (5)

J. Seo, M. Choe, and S. Y. Kim, “Clearing and Labeling Techniques for Large-Scale Biological Tissues,” Mol. Cells 39(6), 439–446 (2016).
[Crossref] [PubMed]

E. Lee, J. Choi, Y. Jo, J. Y. Kim, Y. J. Jang, H. M. Lee, S. Y. Kim, H. J. Lee, K. Cho, N. Jung, E. M. Hur, S. J. Jeong, C. Moon, Y. Choe, I. J. Rhyu, H. Kim, and W. Sun, “ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging,” Sci. Rep. 6(1), 18631 (2016).
[Crossref] [PubMed]

B. Lloyd-Lewis, F. M. Davis, O. B. Harris, J. R. Hitchcock, F. C. Lourenco, M. Pasche, and C. J. Watson, “Imaging the mammary gland and mammary tumours in 3D: optical tissue clearing and immunofluorescence methods,” Breast Cancer Res. 18(1), 127 (2016).
[Crossref] [PubMed]

F. M. Davis, B. Lloyd-Lewis, O. B. Harris, S. Kozar, D. J. Winton, L. Muresan, and C. J. Watson, “Single-cell lineage tracing in the mammary gland reveals stochastic clonal dispersion of stem/progenitor cell progeny,” Nat. Commun. 7(1), 13053 (2016).
[Crossref] [PubMed]

I. Nehrhoff, D. Bocancea, J. Vaquero, J. J. Vaquero, J. Ripoll, M. Desco, and M. V. Gómez-Gaviro, “3D imaging in CUBIC-cleared mouse heart tissue: going deeper,” Biomed. Opt. Express 7(9), 3716–3720 (2016).
[Crossref] [PubMed]

2015 (5)

E. A. Susaki, K. Tainaka, D. Perrin, H. Yukinaga, A. Kuno, and H. R. Ueda, “Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging,” Nat. Protoc. 10(11), 1709–1727 (2015).
[Crossref] [PubMed]

S. Y. Kim, J. H. Cho, E. Murray, N. Bakh, H. Choi, K. Ohn, L. Ruelas, A. Hubbert, M. McCue, S. L. Vassallo, P. J. Keller, and K. Chung, “Stochastic electrotransport selectively enhances the transport of highly electromobile molecules,” Proc. Natl. Acad. Sci. U.S.A. 112(46), E6274–E6283 (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]

D. S. Richardson and J. W. Lichtman, “Clarifying Tissue Clearing,” Cell 162(2), 246–257 (2015).
[Crossref] [PubMed]

Z. Zhao, A. R. Nelson, C. Betsholtz, and B. V. Zlokovic, “Establishment and Dysfunction of the Blood-Brain Barrier,” Cell 163(5), 1064–1078 (2015).
[Crossref] [PubMed]

2014 (1)

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]

2013 (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]

2011 (1)

K. J. Friston, “Functional and effective connectivity: a review,” Brain Connect. 1(1), 13–36 (2011).
[Crossref] [PubMed]

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]

Affaticati, P.

M. Frétaud, L. Rivière, É. Job, S. Gay, J. J. Lareyre, J. S. Joly, P. Affaticati, and V. Thermes, “High-resolution 3D imaging of whole organ after clearing: taking a new look at the zebrafish testis,” Sci. Rep. 7(1), 43012 (2017).
[Crossref] [PubMed]

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]

Bakh, N.

S. Y. Kim, J. H. Cho, E. Murray, N. Bakh, H. Choi, K. Ohn, L. Ruelas, A. Hubbert, M. McCue, S. L. Vassallo, P. J. Keller, and K. Chung, “Stochastic electrotransport selectively enhances the transport of highly electromobile molecules,” Proc. Natl. Acad. Sci. U.S.A. 112(46), E6274–E6283 (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]

Balaban, E.

M. V. Gómez-Gaviro, E. Balaban, D. Bocancea, M. T. Lorrio, M. Pompeiano, M. Desco, J. Ripoll, and J. J. Vaquero, “Optimized CUBIC protocol for three-dimensional imaging of chicken embryos at single-cell resolution,” Development 144(11), 2092–2097 (2017).
[Crossref] [PubMed]

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]

Betsholtz, C.

Z. Zhao, A. R. Nelson, C. Betsholtz, and B. V. Zlokovic, “Establishment and Dysfunction of the Blood-Brain Barrier,” Cell 163(5), 1064–1078 (2015).
[Crossref] [PubMed]

Bocancea, D.

M. V. Gómez-Gaviro, E. Balaban, D. Bocancea, M. T. Lorrio, M. Pompeiano, M. Desco, J. Ripoll, and J. J. Vaquero, “Optimized CUBIC protocol for three-dimensional imaging of chicken embryos at single-cell resolution,” Development 144(11), 2092–2097 (2017).
[Crossref] [PubMed]

I. Nehrhoff, D. Bocancea, J. Vaquero, J. J. Vaquero, J. Ripoll, M. Desco, and M. V. Gómez-Gaviro, “3D imaging in CUBIC-cleared mouse heart tissue: going deeper,” Biomed. Opt. Express 7(9), 3716–3720 (2016).
[Crossref] [PubMed]

Bozycki, L.

P. Matryba, L. Bozycki, M. Pawłowska, L. Kaczmarek, and M. Stefaniuk, “Optimized perfusion-based CUBIC protocol for the efficient whole-body clearing and imaging of rat organs,” J. Biophotonics 11(5), e201700248 (2018).
[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]

S. Y. Kim, J. H. Cho, E. Murray, N. Bakh, H. Choi, K. Ohn, L. Ruelas, A. Hubbert, M. McCue, S. L. Vassallo, P. J. Keller, and K. Chung, “Stochastic electrotransport selectively enhances the transport of highly electromobile molecules,” Proc. Natl. Acad. Sci. U.S.A. 112(46), E6274–E6283 (2015).
[Crossref] [PubMed]

Cho, K.

E. Lee, J. Choi, Y. Jo, J. Y. Kim, Y. J. Jang, H. M. Lee, S. Y. Kim, H. J. Lee, K. Cho, N. Jung, E. M. Hur, S. J. Jeong, C. Moon, Y. Choe, I. J. Rhyu, H. Kim, and W. Sun, “ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging,” Sci. Rep. 6(1), 18631 (2016).
[Crossref] [PubMed]

Choe, M.

J. Seo, M. Choe, and S. Y. Kim, “Clearing and Labeling Techniques for Large-Scale Biological Tissues,” Mol. Cells 39(6), 439–446 (2016).
[Crossref] [PubMed]

Choe, Y.

E. Lee, J. Choi, Y. Jo, J. Y. Kim, Y. J. Jang, H. M. Lee, S. Y. Kim, H. J. Lee, K. Cho, N. Jung, E. M. Hur, S. J. Jeong, C. Moon, Y. Choe, I. J. Rhyu, H. Kim, and W. Sun, “ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging,” Sci. Rep. 6(1), 18631 (2016).
[Crossref] [PubMed]

Choi, H.

S. Y. Kim, J. H. Cho, E. Murray, N. Bakh, H. Choi, K. Ohn, L. Ruelas, A. Hubbert, M. McCue, S. L. Vassallo, P. J. Keller, and K. Chung, “Stochastic electrotransport selectively enhances the transport of highly electromobile molecules,” Proc. Natl. Acad. Sci. U.S.A. 112(46), E6274–E6283 (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]

Choi, J.

E. Lee, J. Choi, Y. Jo, J. Y. Kim, Y. J. Jang, H. M. Lee, S. Y. Kim, H. J. Lee, K. Cho, N. Jung, E. M. Hur, S. J. Jeong, C. Moon, Y. Choe, I. J. Rhyu, H. Kim, and W. Sun, “ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging,” Sci. Rep. 6(1), 18631 (2016).
[Crossref] [PubMed]

Chung, K.

S. Y. Kim, J. H. Cho, E. Murray, N. Bakh, H. Choi, K. Ohn, L. Ruelas, A. Hubbert, M. McCue, S. L. Vassallo, P. J. Keller, and K. Chung, “Stochastic electrotransport selectively enhances the transport of highly electromobile molecules,” Proc. Natl. Acad. Sci. U.S.A. 112(46), E6274–E6283 (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]

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]

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]

Davis, F. M.

F. M. Davis, B. Lloyd-Lewis, O. B. Harris, S. Kozar, D. J. Winton, L. Muresan, and C. J. Watson, “Single-cell lineage tracing in the mammary gland reveals stochastic clonal dispersion of stem/progenitor cell progeny,” Nat. Commun. 7(1), 13053 (2016).
[Crossref] [PubMed]

B. Lloyd-Lewis, F. M. Davis, O. B. Harris, J. R. Hitchcock, F. C. Lourenco, M. Pasche, and C. J. Watson, “Imaging the mammary gland and mammary tumours in 3D: optical tissue clearing and immunofluorescence methods,” Breast Cancer Res. 18(1), 127 (2016).
[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]

Desco, M.

M. V. Gómez-Gaviro, E. Balaban, D. Bocancea, M. T. Lorrio, M. Pompeiano, M. Desco, J. Ripoll, and J. J. Vaquero, “Optimized CUBIC protocol for three-dimensional imaging of chicken embryos at single-cell resolution,” Development 144(11), 2092–2097 (2017).
[Crossref] [PubMed]

I. Nehrhoff, D. Bocancea, J. Vaquero, J. J. Vaquero, J. Ripoll, M. Desco, and M. V. Gómez-Gaviro, “3D imaging in CUBIC-cleared mouse heart tissue: going deeper,” Biomed. Opt. Express 7(9), 3716–3720 (2016).
[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]

Ehata, S.

S. I. Kubota, K. Takahashi, J. Nishida, Y. Morishita, S. Ehata, K. Tainaka, K. Miyazono, and H. R. Ueda, “Whole-Body Profiling of Cancer Metastasis with Single-Cell Resolution,” Cell Reports 20(1), 236–250 (2017).
[Crossref] [PubMed]

Francis, R.

H. Liang, H. Wang, S. Wang, R. Francis, G. Paxinos, and X. Huang, “3D imaging of PSD-95 in the mouse brain using the advanced CUBIC method,” Mol. Brain 11(1), 50 (2018).
[Crossref] [PubMed]

Frétaud, M.

M. Frétaud, L. Rivière, É. Job, S. Gay, J. J. Lareyre, J. S. Joly, P. Affaticati, and V. Thermes, “High-resolution 3D imaging of whole organ after clearing: taking a new look at the zebrafish testis,” Sci. Rep. 7(1), 43012 (2017).
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Friston, K. J.

K. J. Friston, “Functional and effective connectivity: a review,” Brain Connect. 1(1), 13–36 (2011).
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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]

Gay, S.

M. Frétaud, L. Rivière, É. Job, S. Gay, J. J. Lareyre, J. S. Joly, P. Affaticati, and V. Thermes, “High-resolution 3D imaging of whole organ after clearing: taking a new look at the zebrafish testis,” Sci. Rep. 7(1), 43012 (2017).
[Crossref] [PubMed]

Gómez-Gaviro, M. V.

M. V. Gómez-Gaviro, E. Balaban, D. Bocancea, M. T. Lorrio, M. Pompeiano, M. Desco, J. Ripoll, and J. J. Vaquero, “Optimized CUBIC protocol for three-dimensional imaging of chicken embryos at single-cell resolution,” Development 144(11), 2092–2097 (2017).
[Crossref] [PubMed]

I. Nehrhoff, D. Bocancea, J. Vaquero, J. J. Vaquero, J. Ripoll, M. Desco, and M. V. Gómez-Gaviro, “3D imaging in CUBIC-cleared mouse heart tissue: going deeper,” Biomed. Opt. Express 7(9), 3716–3720 (2016).
[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.

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]

Harris, O. B.

F. M. Davis, B. Lloyd-Lewis, O. B. Harris, S. Kozar, D. J. Winton, L. Muresan, and C. J. Watson, “Single-cell lineage tracing in the mammary gland reveals stochastic clonal dispersion of stem/progenitor cell progeny,” Nat. Commun. 7(1), 13053 (2016).
[Crossref] [PubMed]

B. Lloyd-Lewis, F. M. Davis, O. B. Harris, J. R. Hitchcock, F. C. Lourenco, M. Pasche, and C. J. Watson, “Imaging the mammary gland and mammary tumours in 3D: optical tissue clearing and immunofluorescence methods,” Breast Cancer Res. 18(1), 127 (2016).
[Crossref] [PubMed]

Hitchcock, J. R.

B. Lloyd-Lewis, F. M. Davis, O. B. Harris, J. R. Hitchcock, F. C. Lourenco, M. Pasche, and C. J. Watson, “Imaging the mammary gland and mammary tumours in 3D: optical tissue clearing and immunofluorescence methods,” Breast Cancer Res. 18(1), 127 (2016).
[Crossref] [PubMed]

Hori, Y.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

Huang, X.

H. Liang, H. Wang, S. Wang, R. Francis, G. Paxinos, and X. Huang, “3D imaging of PSD-95 in the mouse brain using the advanced CUBIC method,” Mol. Brain 11(1), 50 (2018).
[Crossref] [PubMed]

Hubbert, A.

S. Y. Kim, J. H. Cho, E. Murray, N. Bakh, H. Choi, K. Ohn, L. Ruelas, A. Hubbert, M. McCue, S. L. Vassallo, P. J. Keller, and K. Chung, “Stochastic electrotransport selectively enhances the transport of highly electromobile molecules,” Proc. Natl. Acad. Sci. U.S.A. 112(46), E6274–E6283 (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]

Hur, E. M.

E. Lee, J. Choi, Y. Jo, J. Y. Kim, Y. J. Jang, H. M. Lee, S. Y. Kim, H. J. Lee, K. Cho, N. Jung, E. M. Hur, S. J. Jeong, C. Moon, Y. Choe, I. J. Rhyu, H. Kim, and W. Sun, “ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging,” Sci. Rep. 6(1), 18631 (2016).
[Crossref] [PubMed]

Iijima, S.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

Ikeda, J. I.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

Jang, Y. J.

E. Lee, J. Choi, Y. Jo, J. Y. Kim, Y. J. Jang, H. M. Lee, S. Y. Kim, H. J. Lee, K. Cho, N. Jung, E. M. Hur, S. J. Jeong, C. Moon, Y. Choe, I. J. Rhyu, H. Kim, and W. Sun, “ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging,” Sci. Rep. 6(1), 18631 (2016).
[Crossref] [PubMed]

Jeong, S. J.

E. Lee, J. Choi, Y. Jo, J. Y. Kim, Y. J. Jang, H. M. Lee, S. Y. Kim, H. J. Lee, K. Cho, N. Jung, E. M. Hur, S. J. Jeong, C. Moon, Y. Choe, I. J. Rhyu, H. Kim, and W. Sun, “ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging,” Sci. Rep. 6(1), 18631 (2016).
[Crossref] [PubMed]

Jo, Y.

E. Lee, J. Choi, Y. Jo, J. Y. Kim, Y. J. Jang, H. M. Lee, S. Y. Kim, H. J. Lee, K. Cho, N. Jung, E. M. Hur, S. J. Jeong, C. Moon, Y. Choe, I. J. Rhyu, H. Kim, and W. Sun, “ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging,” Sci. Rep. 6(1), 18631 (2016).
[Crossref] [PubMed]

Job, É.

M. Frétaud, L. Rivière, É. Job, S. Gay, J. J. Lareyre, J. S. Joly, P. Affaticati, and V. Thermes, “High-resolution 3D imaging of whole organ after clearing: taking a new look at the zebrafish testis,” Sci. Rep. 7(1), 43012 (2017).
[Crossref] [PubMed]

Joly, J. S.

M. Frétaud, L. Rivière, É. Job, S. Gay, J. J. Lareyre, J. S. Joly, P. Affaticati, and V. Thermes, “High-resolution 3D imaging of whole organ after clearing: taking a new look at the zebrafish testis,” Sci. Rep. 7(1), 43012 (2017).
[Crossref] [PubMed]

Jung, N.

E. Lee, J. Choi, Y. Jo, J. Y. Kim, Y. J. Jang, H. M. Lee, S. Y. Kim, H. J. Lee, K. Cho, N. Jung, E. M. Hur, S. J. Jeong, C. Moon, Y. Choe, I. J. Rhyu, H. Kim, and W. Sun, “ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging,” Sci. Rep. 6(1), 18631 (2016).
[Crossref] [PubMed]

Kaczmarek, L.

P. Matryba, L. Bozycki, M. Pawłowska, L. Kaczmarek, and M. Stefaniuk, “Optimized perfusion-based CUBIC protocol for the efficient whole-body clearing and imaging of rat organs,” J. Biophotonics 11(5), e201700248 (2018).
[Crossref] [PubMed]

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]

Keller, P. J.

S. Y. Kim, J. H. Cho, E. Murray, N. Bakh, H. Choi, K. Ohn, L. Ruelas, A. Hubbert, M. McCue, S. L. Vassallo, P. J. Keller, and K. Chung, “Stochastic electrotransport selectively enhances the transport of highly electromobile molecules,” Proc. Natl. Acad. Sci. U.S.A. 112(46), E6274–E6283 (2015).
[Crossref] [PubMed]

Kiefer, F.

M. Orlich and F. Kiefer, “A qualitative comparison of ten tissue clearing techniques,” Histol. Histopathol. 33(2), 181–199 (2018).
[PubMed]

Kim, H.

E. Lee, J. Choi, Y. Jo, J. Y. Kim, Y. J. Jang, H. M. Lee, S. Y. Kim, H. J. Lee, K. Cho, N. Jung, E. M. Hur, S. J. Jeong, C. Moon, Y. Choe, I. J. Rhyu, H. Kim, and W. Sun, “ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging,” Sci. Rep. 6(1), 18631 (2016).
[Crossref] [PubMed]

Kim, J. Y.

E. Lee, J. Choi, Y. Jo, J. Y. Kim, Y. J. Jang, H. M. Lee, S. Y. Kim, H. J. Lee, K. Cho, N. Jung, E. M. Hur, S. J. Jeong, C. Moon, Y. Choe, I. J. Rhyu, H. Kim, and W. Sun, “ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging,” Sci. Rep. 6(1), 18631 (2016).
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Kim, S. Y.

J. Seo, M. Choe, and S. Y. Kim, “Clearing and Labeling Techniques for Large-Scale Biological Tissues,” Mol. Cells 39(6), 439–446 (2016).
[Crossref] [PubMed]

E. Lee, J. Choi, Y. Jo, J. Y. Kim, Y. J. Jang, H. M. Lee, S. Y. Kim, H. J. Lee, K. Cho, N. Jung, E. M. Hur, S. J. Jeong, C. Moon, Y. Choe, I. J. Rhyu, H. Kim, and W. Sun, “ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging,” Sci. Rep. 6(1), 18631 (2016).
[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]

S. Y. Kim, J. H. Cho, E. Murray, N. Bakh, H. Choi, K. Ohn, L. Ruelas, A. Hubbert, M. McCue, S. L. Vassallo, P. J. Keller, and K. Chung, “Stochastic electrotransport selectively enhances the transport of highly electromobile molecules,” Proc. Natl. Acad. Sci. U.S.A. 112(46), E6274–E6283 (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]

Kozar, S.

F. M. Davis, B. Lloyd-Lewis, O. B. Harris, S. Kozar, D. J. Winton, L. Muresan, and C. J. Watson, “Single-cell lineage tracing in the mammary gland reveals stochastic clonal dispersion of stem/progenitor cell progeny,” Nat. Commun. 7(1), 13053 (2016).
[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]

Kubota, S. I.

S. I. Kubota, K. Takahashi, J. Nishida, Y. Morishita, S. Ehata, K. Tainaka, K. Miyazono, and H. R. Ueda, “Whole-Body Profiling of Cancer Metastasis with Single-Cell Resolution,” Cell Reports 20(1), 236–250 (2017).
[Crossref] [PubMed]

Kumanogoh, A.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

Kuno, A.

E. A. Susaki, K. Tainaka, D. Perrin, H. Yukinaga, A. Kuno, and H. R. Ueda, “Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging,” Nat. Protoc. 10(11), 1709–1727 (2015).
[Crossref] [PubMed]

Kurashige, M.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

Lareyre, J. J.

M. Frétaud, L. Rivière, É. Job, S. Gay, J. J. Lareyre, J. S. Joly, P. Affaticati, and V. Thermes, “High-resolution 3D imaging of whole organ after clearing: taking a new look at the zebrafish testis,” Sci. Rep. 7(1), 43012 (2017).
[Crossref] [PubMed]

Lee, E.

E. Lee, J. Choi, Y. Jo, J. Y. Kim, Y. J. Jang, H. M. Lee, S. Y. Kim, H. J. Lee, K. Cho, N. Jung, E. M. Hur, S. J. Jeong, C. Moon, Y. Choe, I. J. Rhyu, H. Kim, and W. Sun, “ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging,” Sci. Rep. 6(1), 18631 (2016).
[Crossref] [PubMed]

Lee, H. J.

E. Lee, J. Choi, Y. Jo, J. Y. Kim, Y. J. Jang, H. M. Lee, S. Y. Kim, H. J. Lee, K. Cho, N. Jung, E. M. Hur, S. J. Jeong, C. Moon, Y. Choe, I. J. Rhyu, H. Kim, and W. Sun, “ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging,” Sci. Rep. 6(1), 18631 (2016).
[Crossref] [PubMed]

Lee, H. M.

E. Lee, J. Choi, Y. Jo, J. Y. Kim, Y. J. Jang, H. M. Lee, S. Y. Kim, H. J. Lee, K. Cho, N. Jung, E. M. Hur, S. J. Jeong, C. Moon, Y. Choe, I. J. Rhyu, H. Kim, and W. Sun, “ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging,” Sci. Rep. 6(1), 18631 (2016).
[Crossref] [PubMed]

Liang, H.

H. Liang, H. Wang, S. Wang, R. Francis, G. Paxinos, and X. Huang, “3D imaging of PSD-95 in the mouse brain using the advanced CUBIC method,” Mol. Brain 11(1), 50 (2018).
[Crossref] [PubMed]

Lichtman, J. W.

D. S. Richardson and J. W. Lichtman, “Clarifying Tissue Clearing,” Cell 162(2), 246–257 (2015).
[Crossref] [PubMed]

Lloyd-Lewis, B.

F. M. Davis, B. Lloyd-Lewis, O. B. Harris, S. Kozar, D. J. Winton, L. Muresan, and C. J. Watson, “Single-cell lineage tracing in the mammary gland reveals stochastic clonal dispersion of stem/progenitor cell progeny,” Nat. Commun. 7(1), 13053 (2016).
[Crossref] [PubMed]

B. Lloyd-Lewis, F. M. Davis, O. B. Harris, J. R. Hitchcock, F. C. Lourenco, M. Pasche, and C. J. Watson, “Imaging the mammary gland and mammary tumours in 3D: optical tissue clearing and immunofluorescence methods,” Breast Cancer Res. 18(1), 127 (2016).
[Crossref] [PubMed]

Lorrio, M. T.

M. V. Gómez-Gaviro, E. Balaban, D. Bocancea, M. T. Lorrio, M. Pompeiano, M. Desco, J. Ripoll, and J. J. Vaquero, “Optimized CUBIC protocol for three-dimensional imaging of chicken embryos at single-cell resolution,” Development 144(11), 2092–2097 (2017).
[Crossref] [PubMed]

Lourenco, F. C.

B. Lloyd-Lewis, F. M. Davis, O. B. Harris, J. R. Hitchcock, F. C. Lourenco, M. Pasche, and C. J. Watson, “Imaging the mammary gland and mammary tumours in 3D: optical tissue clearing and immunofluorescence methods,” Breast Cancer Res. 18(1), 127 (2016).
[Crossref] [PubMed]

Matryba, P.

P. Matryba, L. Bozycki, M. Pawłowska, L. Kaczmarek, and M. Stefaniuk, “Optimized perfusion-based CUBIC protocol for the efficient whole-body clearing and imaging of rat organs,” J. Biophotonics 11(5), e201700248 (2018).
[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.

S. Y. Kim, J. H. Cho, E. Murray, N. Bakh, H. Choi, K. Ohn, L. Ruelas, A. Hubbert, M. McCue, S. L. Vassallo, P. J. Keller, and K. Chung, “Stochastic electrotransport selectively enhances the transport of highly electromobile molecules,” Proc. Natl. Acad. Sci. U.S.A. 112(46), E6274–E6283 (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]

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]

Miyazono, K.

S. I. Kubota, K. Takahashi, J. Nishida, Y. Morishita, S. Ehata, K. Tainaka, K. Miyazono, and H. R. Ueda, “Whole-Body Profiling of Cancer Metastasis with Single-Cell Resolution,” Cell Reports 20(1), 236–250 (2017).
[Crossref] [PubMed]

Moon, C.

E. Lee, J. Choi, Y. Jo, J. Y. Kim, Y. J. Jang, H. M. Lee, S. Y. Kim, H. J. Lee, K. Cho, N. Jung, E. M. Hur, S. J. Jeong, C. Moon, Y. Choe, I. J. Rhyu, H. Kim, and W. Sun, “ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging,” Sci. Rep. 6(1), 18631 (2016).
[Crossref] [PubMed]

Morii, E.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

Morishita, Y.

S. I. Kubota, K. Takahashi, J. Nishida, Y. Morishita, S. Ehata, K. Tainaka, K. Miyazono, and H. R. Ueda, “Whole-Body Profiling of Cancer Metastasis with Single-Cell Resolution,” Cell Reports 20(1), 236–250 (2017).
[Crossref] [PubMed]

Muresan, L.

F. M. Davis, B. Lloyd-Lewis, O. B. Harris, S. Kozar, D. J. Winton, L. Muresan, and C. J. Watson, “Single-cell lineage tracing in the mammary gland reveals stochastic clonal dispersion of stem/progenitor cell progeny,” Nat. Commun. 7(1), 13053 (2016).
[Crossref] [PubMed]

Murray, E.

S. Y. Kim, J. H. Cho, E. Murray, N. Bakh, H. Choi, K. Ohn, L. Ruelas, A. Hubbert, M. McCue, S. L. Vassallo, P. J. Keller, and K. Chung, “Stochastic electrotransport selectively enhances the transport of highly electromobile molecules,” Proc. Natl. Acad. Sci. U.S.A. 112(46), E6274–E6283 (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]

Nakahara, Y.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

Nehrhoff, I.

Nelson, A. R.

Z. Zhao, A. R. Nelson, C. Betsholtz, and B. V. Zlokovic, “Establishment and Dysfunction of the Blood-Brain Barrier,” Cell 163(5), 1064–1078 (2015).
[Crossref] [PubMed]

Nishida, J.

S. I. Kubota, K. Takahashi, J. Nishida, Y. Morishita, S. Ehata, K. Tainaka, K. Miyazono, and H. R. Ueda, “Whole-Body Profiling of Cancer Metastasis with Single-Cell Resolution,” Cell Reports 20(1), 236–250 (2017).
[Crossref] [PubMed]

Nojima, S.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

Ohn, K.

S. Y. Kim, J. H. Cho, E. Murray, N. Bakh, H. Choi, K. Ohn, L. Ruelas, A. Hubbert, M. McCue, S. L. Vassallo, P. J. Keller, and K. Chung, “Stochastic electrotransport selectively enhances the transport of highly electromobile molecules,” Proc. Natl. Acad. Sci. U.S.A. 112(46), E6274–E6283 (2015).
[Crossref] [PubMed]

Ohshima, K.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[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]

Orlich, M.

M. Orlich and F. Kiefer, “A qualitative comparison of ten tissue clearing techniques,” Histol. Histopathol. 33(2), 181–199 (2018).
[PubMed]

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]

Pasche, M.

B. Lloyd-Lewis, F. M. Davis, O. B. Harris, J. R. Hitchcock, F. C. Lourenco, M. Pasche, and C. J. Watson, “Imaging the mammary gland and mammary tumours in 3D: optical tissue clearing and immunofluorescence methods,” Breast Cancer Res. 18(1), 127 (2016).
[Crossref] [PubMed]

Pawlowska, M.

P. Matryba, L. Bozycki, M. Pawłowska, L. Kaczmarek, and M. Stefaniuk, “Optimized perfusion-based CUBIC protocol for the efficient whole-body clearing and imaging of rat organs,” J. Biophotonics 11(5), e201700248 (2018).
[Crossref] [PubMed]

Paxinos, G.

H. Liang, H. Wang, S. Wang, R. Francis, G. Paxinos, and X. Huang, “3D imaging of PSD-95 in the mouse brain using the advanced CUBIC method,” Mol. Brain 11(1), 50 (2018).
[Crossref] [PubMed]

Perrin, D.

E. A. Susaki, K. Tainaka, D. Perrin, H. Yukinaga, A. Kuno, and H. R. Ueda, “Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging,” Nat. Protoc. 10(11), 1709–1727 (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]

Pompeiano, M.

M. V. Gómez-Gaviro, E. Balaban, D. Bocancea, M. T. Lorrio, M. Pompeiano, M. Desco, J. Ripoll, and J. J. Vaquero, “Optimized CUBIC protocol for three-dimensional imaging of chicken embryos at single-cell resolution,” Development 144(11), 2092–2097 (2017).
[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]

Rhyu, I. J.

E. Lee, J. Choi, Y. Jo, J. Y. Kim, Y. J. Jang, H. M. Lee, S. Y. Kim, H. J. Lee, K. Cho, N. Jung, E. M. Hur, S. J. Jeong, C. Moon, Y. Choe, I. J. Rhyu, H. Kim, and W. Sun, “ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging,” Sci. Rep. 6(1), 18631 (2016).
[Crossref] [PubMed]

Richardson, D. S.

D. S. Richardson and J. W. Lichtman, “Clarifying Tissue Clearing,” Cell 162(2), 246–257 (2015).
[Crossref] [PubMed]

Ripoll, J.

M. V. Gómez-Gaviro, E. Balaban, D. Bocancea, M. T. Lorrio, M. Pompeiano, M. Desco, J. Ripoll, and J. J. Vaquero, “Optimized CUBIC protocol for three-dimensional imaging of chicken embryos at single-cell resolution,” Development 144(11), 2092–2097 (2017).
[Crossref] [PubMed]

I. Nehrhoff, D. Bocancea, J. Vaquero, J. J. Vaquero, J. Ripoll, M. Desco, and M. V. Gómez-Gaviro, “3D imaging in CUBIC-cleared mouse heart tissue: going deeper,” Biomed. Opt. Express 7(9), 3716–3720 (2016).
[Crossref] [PubMed]

Rivière, L.

M. Frétaud, L. Rivière, É. Job, S. Gay, J. J. Lareyre, J. S. Joly, P. Affaticati, and V. Thermes, “High-resolution 3D imaging of whole organ after clearing: taking a new look at the zebrafish testis,” Sci. Rep. 7(1), 43012 (2017).
[Crossref] [PubMed]

Ruelas, L.

S. Y. Kim, J. H. Cho, E. Murray, N. Bakh, H. Choi, K. Ohn, L. Ruelas, A. Hubbert, M. McCue, S. L. Vassallo, P. J. Keller, and K. Chung, “Stochastic electrotransport selectively enhances the transport of highly electromobile molecules,” Proc. Natl. Acad. Sci. U.S.A. 112(46), E6274–E6283 (2015).
[Crossref] [PubMed]

Seo, J.

J. Seo, M. Choe, and S. Y. Kim, “Clearing and Labeling Techniques for Large-Scale Biological Tissues,” Mol. Cells 39(6), 439–446 (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]

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]

Stefaniuk, M.

P. Matryba, L. Bozycki, M. Pawłowska, L. Kaczmarek, and M. Stefaniuk, “Optimized perfusion-based CUBIC protocol for the efficient whole-body clearing and imaging of rat organs,” J. Biophotonics 11(5), e201700248 (2018).
[Crossref] [PubMed]

Sun, W.

E. Lee, J. Choi, Y. Jo, J. Y. Kim, Y. J. Jang, H. M. Lee, S. Y. Kim, H. J. Lee, K. Cho, N. Jung, E. M. Hur, S. J. Jeong, C. Moon, Y. Choe, I. J. Rhyu, H. Kim, and W. Sun, “ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging,” Sci. Rep. 6(1), 18631 (2016).
[Crossref] [PubMed]

Susaki, E. A.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

E. A. Susaki, K. Tainaka, D. Perrin, H. Yukinaga, A. Kuno, and H. R. Ueda, “Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging,” Nat. Protoc. 10(11), 1709–1727 (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]

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]

Tahara, S.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

Tainaka, K.

S. I. Kubota, K. Takahashi, J. Nishida, Y. Morishita, S. Ehata, K. Tainaka, K. Miyazono, and H. R. Ueda, “Whole-Body Profiling of Cancer Metastasis with Single-Cell Resolution,” Cell Reports 20(1), 236–250 (2017).
[Crossref] [PubMed]

E. A. Susaki, K. Tainaka, D. Perrin, H. Yukinaga, A. Kuno, and H. R. Ueda, “Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging,” Nat. Protoc. 10(11), 1709–1727 (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]

Takachi, K.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

Takahashi, K.

S. I. Kubota, K. Takahashi, J. Nishida, Y. Morishita, S. Ehata, K. Tainaka, K. Miyazono, and H. R. Ueda, “Whole-Body Profiling of Cancer Metastasis with Single-Cell Resolution,” Cell Reports 20(1), 236–250 (2017).
[Crossref] [PubMed]

Takemoto, H.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[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]

Thermes, V.

M. Frétaud, L. Rivière, É. Job, S. Gay, J. J. Lareyre, J. S. Joly, P. Affaticati, and V. Thermes, “High-resolution 3D imaging of whole organ after clearing: taking a new look at the zebrafish testis,” Sci. Rep. 7(1), 43012 (2017).
[Crossref] [PubMed]

Tsujimura, N.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

Ueda, H. R.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

S. I. Kubota, K. Takahashi, J. Nishida, Y. Morishita, S. Ehata, K. Tainaka, K. Miyazono, and H. R. Ueda, “Whole-Body Profiling of Cancer Metastasis with Single-Cell Resolution,” Cell Reports 20(1), 236–250 (2017).
[Crossref] [PubMed]

E. A. Susaki, K. Tainaka, D. Perrin, H. Yukinaga, A. Kuno, and H. R. Ueda, “Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging,” Nat. Protoc. 10(11), 1709–1727 (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]

Vaquero, J.

Vaquero, J. J.

M. V. Gómez-Gaviro, E. Balaban, D. Bocancea, M. T. Lorrio, M. Pompeiano, M. Desco, J. Ripoll, and J. J. Vaquero, “Optimized CUBIC protocol for three-dimensional imaging of chicken embryos at single-cell resolution,” Development 144(11), 2092–2097 (2017).
[Crossref] [PubMed]

I. Nehrhoff, D. Bocancea, J. Vaquero, J. J. Vaquero, J. Ripoll, M. Desco, and M. V. Gómez-Gaviro, “3D imaging in CUBIC-cleared mouse heart tissue: going deeper,” Biomed. Opt. Express 7(9), 3716–3720 (2016).
[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]

Vassallo, S. L.

S. Y. Kim, J. H. Cho, E. Murray, N. Bakh, H. Choi, K. Ohn, L. Ruelas, A. Hubbert, M. McCue, S. L. Vassallo, P. J. Keller, and K. Chung, “Stochastic electrotransport selectively enhances the transport of highly electromobile molecules,” Proc. Natl. Acad. Sci. U.S.A. 112(46), E6274–E6283 (2015).
[Crossref] [PubMed]

Wada, N.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[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, H.

H. Liang, H. Wang, S. Wang, R. Francis, G. Paxinos, and X. Huang, “3D imaging of PSD-95 in the mouse brain using the advanced CUBIC method,” Mol. Brain 11(1), 50 (2018).
[Crossref] [PubMed]

Wang, S.

H. Liang, H. Wang, S. Wang, R. Francis, G. Paxinos, and X. Huang, “3D imaging of PSD-95 in the mouse brain using the advanced CUBIC method,” Mol. Brain 11(1), 50 (2018).
[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]

Watson, C. J.

F. M. Davis, B. Lloyd-Lewis, O. B. Harris, S. Kozar, D. J. Winton, L. Muresan, and C. J. Watson, “Single-cell lineage tracing in the mammary gland reveals stochastic clonal dispersion of stem/progenitor cell progeny,” Nat. Commun. 7(1), 13053 (2016).
[Crossref] [PubMed]

B. Lloyd-Lewis, F. M. Davis, O. B. Harris, J. R. Hitchcock, F. C. Lourenco, M. Pasche, and C. J. Watson, “Imaging the mammary gland and mammary tumours in 3D: optical tissue clearing and immunofluorescence methods,” Breast Cancer Res. 18(1), 127 (2016).
[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]

Winton, D. J.

F. M. Davis, B. Lloyd-Lewis, O. B. Harris, S. Kozar, D. J. Winton, L. Muresan, and C. J. Watson, “Single-cell lineage tracing in the mammary gland reveals stochastic clonal dispersion of stem/progenitor cell progeny,” Nat. Commun. 7(1), 13053 (2016).
[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]

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]

Yoshida, K.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

Yukinaga, H.

E. A. Susaki, K. Tainaka, D. Perrin, H. Yukinaga, A. Kuno, and H. R. Ueda, “Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging,” Nat. Protoc. 10(11), 1709–1727 (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]

Zhao, Z.

Z. Zhao, A. R. Nelson, C. Betsholtz, and B. V. Zlokovic, “Establishment and Dysfunction of the Blood-Brain Barrier,” Cell 163(5), 1064–1078 (2015).
[Crossref] [PubMed]

Zlokovic, B. V.

Z. Zhao, A. R. Nelson, C. Betsholtz, and B. V. Zlokovic, “Establishment and Dysfunction of the Blood-Brain Barrier,” Cell 163(5), 1064–1078 (2015).
[Crossref] [PubMed]

Biomed. Opt. Express (1)

Brain Connect. (1)

K. J. Friston, “Functional and effective connectivity: a review,” Brain Connect. 1(1), 13–36 (2011).
[Crossref] [PubMed]

Breast Cancer Res. (1)

B. Lloyd-Lewis, F. M. Davis, O. B. Harris, J. R. Hitchcock, F. C. Lourenco, M. Pasche, and C. J. Watson, “Imaging the mammary gland and mammary tumours in 3D: optical tissue clearing and immunofluorescence methods,” Breast Cancer Res. 18(1), 127 (2016).
[Crossref] [PubMed]

Cell (4)

Z. Zhao, A. R. Nelson, C. Betsholtz, and B. V. Zlokovic, “Establishment and Dysfunction of the Blood-Brain Barrier,” Cell 163(5), 1064–1078 (2015).
[Crossref] [PubMed]

D. S. Richardson and J. W. Lichtman, “Clarifying Tissue Clearing,” Cell 162(2), 246–257 (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]

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]

Cell Reports (1)

S. I. Kubota, K. Takahashi, J. Nishida, Y. Morishita, S. Ehata, K. Tainaka, K. Miyazono, and H. R. Ueda, “Whole-Body Profiling of Cancer Metastasis with Single-Cell Resolution,” Cell Reports 20(1), 236–250 (2017).
[Crossref] [PubMed]

Development (1)

M. V. Gómez-Gaviro, E. Balaban, D. Bocancea, M. T. Lorrio, M. Pompeiano, M. Desco, J. Ripoll, and J. J. Vaquero, “Optimized CUBIC protocol for three-dimensional imaging of chicken embryos at single-cell resolution,” Development 144(11), 2092–2097 (2017).
[Crossref] [PubMed]

Histol. Histopathol. (1)

M. Orlich and F. Kiefer, “A qualitative comparison of ten tissue clearing techniques,” Histol. Histopathol. 33(2), 181–199 (2018).
[PubMed]

J. Biophotonics (1)

P. Matryba, L. Bozycki, M. Pawłowska, L. Kaczmarek, and M. Stefaniuk, “Optimized perfusion-based CUBIC protocol for the efficient whole-body clearing and imaging of rat organs,” J. Biophotonics 11(5), e201700248 (2018).
[Crossref] [PubMed]

Mol. Brain (1)

H. Liang, H. Wang, S. Wang, R. Francis, G. Paxinos, and X. Huang, “3D imaging of PSD-95 in the mouse brain using the advanced CUBIC method,” Mol. Brain 11(1), 50 (2018).
[Crossref] [PubMed]

Mol. Cells (1)

J. Seo, M. Choe, and S. Y. Kim, “Clearing and Labeling Techniques for Large-Scale Biological Tissues,” Mol. Cells 39(6), 439–446 (2016).
[Crossref] [PubMed]

Nat. Commun. (1)

F. M. Davis, B. Lloyd-Lewis, O. B. Harris, S. Kozar, D. J. Winton, L. Muresan, and C. J. Watson, “Single-cell lineage tracing in the mammary gland reveals stochastic clonal dispersion of stem/progenitor cell progeny,” Nat. Commun. 7(1), 13053 (2016).
[Crossref] [PubMed]

Nat. Protoc. (1)

E. A. Susaki, K. Tainaka, D. Perrin, H. Yukinaga, A. Kuno, and H. R. Ueda, “Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging,” Nat. Protoc. 10(11), 1709–1727 (2015).
[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]

Proc. Natl. Acad. Sci. U.S.A. (1)

S. Y. Kim, J. H. Cho, E. Murray, N. Bakh, H. Choi, K. Ohn, L. Ruelas, A. Hubbert, M. McCue, S. L. Vassallo, P. J. Keller, and K. Chung, “Stochastic electrotransport selectively enhances the transport of highly electromobile molecules,” Proc. Natl. Acad. Sci. U.S.A. 112(46), E6274–E6283 (2015).
[Crossref] [PubMed]

Sci. Rep. (3)

E. Lee, J. Choi, Y. Jo, J. Y. Kim, Y. J. Jang, H. M. Lee, S. Y. Kim, H. J. Lee, K. Cho, N. Jung, E. M. Hur, S. J. Jeong, C. Moon, Y. Choe, I. J. Rhyu, H. Kim, and W. Sun, “ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging,” Sci. Rep. 6(1), 18631 (2016).
[Crossref] [PubMed]

M. Frétaud, L. Rivière, É. Job, S. Gay, J. J. Lareyre, J. S. Joly, P. Affaticati, and V. Thermes, “High-resolution 3D imaging of whole organ after clearing: taking a new look at the zebrafish testis,” Sci. Rep. 7(1), 43012 (2017).
[Crossref] [PubMed]

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

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Figures (3)

Fig. 1
Fig. 1 CUBIC significantly increased the transparency of the brain and the imaging depth. A: The pipeline of the modified CUBIC protocol; B: Macro images of the whole brain and thick brain blocks before and after clearing; C: The sample was placed in a glass-bottom dish and imaged with inverted confocal microscopy; The maximum imaging depths of cerebral vessels were 106.5 μm in uncleared brain blocks (D) and 1.2 mm in cleared brain blocks (E) (imaged with a Plan Apo VC 10x/0.45 DIC L objective).
Fig. 2
Fig. 2 IFS conducted on cleared samples. A, B, C and D demonstrate the GFAP (imaged with a Plan Apo VC 20X/0.75 DIC N2 objective, zoom2), TH (imaged with a Plan Apo VC 20X/0.75 DIC N2 objective, zoom1), desmin (imaged with a Plan Apo VC 20X/0.75 DIC N2 objective, zoom2.469) and PDGFRβ (imaged with a Plan Apo VC 20X/0.75 DIC N2 objective, zoom1) staining; A’, B’, C’ and D’ demonstrate images after 3D rendering with Imaris. E demonstrates the result of double staining with GFAP and TH, and E’ demonstrates the image after 3D rendering with Imaris.
Fig. 3
Fig. 3 A longer duration of antibody incubation produced deeper staining. A and B demonstrate IFS with GFAP for an incubation duration of 24 h (z = 322 μm) and 3 d (z = 640 μm), respectively. C and D demonstrate IFS with PDGFRβ for an incubation duration of 24 h (z = 451 μm) and 3 d (z = 670 μm), respectively (imaged with a Plan Apo VC 10x/0.45 DIC L objective). E illustrates the relationship between staining depth and antibody incubation time. ** indicates p<0.005. *** indicates p<0.0001. F illustrates the reduction of fluorescence intensity with depth.

Tables (1)

Tables Icon

Table 1 Reagents for CUBIC

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