Abstract

Single-molecule imaging inside cells is a valuable tool to study subcellular structures, gene expression, and the dynamics of biomolecules. Here, we present highly inclined swept tile illumination microscopy. By sweeping a thin highly inclined and laminated optical sheet (HILO) with confocal slit detection, our method provides a twofold thinner illumination and greater than fortyfold larger imaging area than conventional HILO microscopy, enabling 3D single-molecule imaging with a high signal-to-background ratio. We demonstrate single-molecule mRNA imaging with a few probes or a single probe in cultured cells and mouse brain tissues, and video-rate live-cell imaging.

© 2018 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

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References

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  22. E. Lubeck and L. Cai, “Single-cell systems biology by super-resolution imaging and combinatorial labeling,” Nat. Methods 9, 743–748 (2012).
    [Crossref]
  23. P. J. Keller, A. D. Schmidt, J. Wittbrodt, and E. H. K. Stelzer, “Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy,” Science 322, 1065–1069 (2008).
    [Crossref]
  24. G. Lukinavicius, L. Reymond, E. D’Este, A. Masharina, F. Gottfert, H. Ta, A. Guther, M. Fournier, S. Rizzo, H. Waldmann, C. Blaukopf, C. Sommer, D. W. Gerlich, H. D. Arndt, S. W. Hell, and K. Johnsson, “Fluorogenic probes for live-cell imaging of the cytoskeleton,” Nat. Methods 11, 731–733 (2014).
    [Crossref]
  25. N. A. Hosny, M. Y. Song, J. T. Connelly, S. Ameer-Beg, M. M. Knight, and A. P. Wheeler, “Super-resolution imaging strategies for cell biologists using a spinning disk microscope,” PLoS ONE 8, e74604 (2013).
    [Crossref]
  26. M. B. Bouchard, V. Voleti, C. S. Mendes, C. Lacefield, W. B. Grueber, R. S. Mann, R. M. Bruno, and E. M. C. Hillman, “Swept confocally-aligned planar excitation (SCAPE) microscopy for high-speed volumetric imaging of behaving organisms,” Nat. Photonics 9, 113–119 (2015).
    [Crossref]
  27. J. Tang, Y. Sun, S. Pang, and K. Y. Han, “Spatially encoded fast single-molecule fluorescence spectroscopy with full field-of-view,” Sci. Rep. 7, 10945 (2017).
    [Crossref]

2018 (2)

A. K. Gustavsson, P. N. Petrov, M. Y. Lee, Y. Shechtman, and W. E. Moerner, “3D single-molecule super-resolution microscopy with a tilted light sheet,” Nat. Commun. 9, 123 (2018).
[Crossref]

M. A. Reyer, E. L. McLean, S. Chennakesavalu, and J. Y. Fei, “An automated image analysis method for segmenting fluorescent bacteria in three dimensions,” Biochemistry 57, 209–215 (2018).
[Crossref]

2017 (3)

G. M. Wadsworth, R. Y. Parikh, J. C. Choy, and H. D. Kim, “mRNA detection in budding yeast with single fluorophores,” Nucleic Acids Res. 45, e141 (2017).
[Crossref]

J. Tang, Y. Sun, S. Pang, and K. Y. Han, “Spatially encoded fast single-molecule fluorescence spectroscopy with full field-of-view,” Sci. Rep. 7, 10945 (2017).
[Crossref]

A. S. Hansen, I. Pustova, C. Cattoglio, R. Tjian, and X. Darzacq, “CTCF and cohesin regulate chromatin loop stability with distinct dynamics,” eLife 6, e25776 (2017).

2015 (2)

M. B. Bouchard, V. Voleti, C. S. Mendes, C. Lacefield, W. B. Grueber, R. S. Mann, R. M. Bruno, and E. M. C. Hillman, “Swept confocally-aligned planar excitation (SCAPE) microscopy for high-speed volumetric imaging of behaving organisms,” Nat. Photonics 9, 113–119 (2015).
[Crossref]

R. Galland, G. Grenci, A. Aravind, V. Viasnoff, V. Studer, and J.-B. Sibarita, “3D high- and super-resolution imaging using single-objective SPIM,” Nat. Methods 12, 641–644 (2015).
[Crossref]

2014 (4)

G. Lukinavicius, L. Reymond, E. D’Este, A. Masharina, F. Gottfert, H. Ta, A. Guther, M. Fournier, S. Rizzo, H. Waldmann, C. Blaukopf, C. Sommer, D. W. Gerlich, H. D. Arndt, S. W. Hell, and K. Johnsson, “Fluorogenic probes for live-cell imaging of the cytoskeleton,” Nat. Methods 11, 731–733 (2014).
[Crossref]

R. Jungmann, M. S. Avendano, J. B. Woehrstein, M. J. Dai, W. M. Shih, and P. Yin, “Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT,” Nat. Methods 11, 313–318 (2014).
[Crossref]

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Boehme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref]

M. E. Tanenbaum, L. A. Gilbert, L. S. Qi, J. S. Weissman, and R. D. Vale, “A protein-tagging system for signal amplification in gene expression and fluorescence imaging,” Cell 159, 635–646 (2014).
[Crossref]

2013 (4)

K. Xu, G. Zhong, and X. Zhuang, “Actin, spectrin, and associated proteins form a periodic cytoskeletal structure in axons,” Science 339, 452–456 (2013).
[Crossref]

N. A. Hosny, M. Y. Song, J. T. Connelly, S. Ameer-Beg, M. M. Knight, and A. P. Wheeler, “Super-resolution imaging strategies for cell biologists using a spinning disk microscope,” PLoS ONE 8, e74604 (2013).
[Crossref]

J. C. M. Gebhardt, D. M. Suter, R. Roy, Z. W. Zhao, A. R. Chapman, S. Basu, T. Maniatis, and X. S. Xie, “Single-molecule imaging of transcription factor binding to DNA in live mammalian cells,” Nat. Methods 10, 421–426 (2013).
[Crossref]

M. J. Levesque, P. Ginart, Y. C. Wei, and A. Raj, “Visualizing SNVs to quantify allele-specific expression in single cells,” Nat. Methods 10, 865–867 (2013).
[Crossref]

2012 (2)

E. Lubeck and L. Cai, “Single-cell systems biology by super-resolution imaging and combinatorial labeling,” Nat. Methods 9, 743–748 (2012).
[Crossref]

E. Baumgart and U. Kubitscheck, “Scanned light sheet microscopy with confocal slit detection,” Opt. Express 20, 21805–21814 (2012).
[Crossref]

2011 (1)

F. C. Zanacchi, Z. Lavagnino, M. P. Donnorso, A. Del Bue, L. Furia, M. Faretta, and A. Diaspro, “Live-cell 3D super-resolution imaging in thick biological samples,” Nat. Methods 8, 1047–1049 (2011).
[Crossref]

2010 (1)

R. Jungmann, C. Steinhauer, M. Scheible, A. Kuzyk, P. Tinnefeld, and F. C. Simmel, “Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami,” Nano Lett. 10, 4756–4761 (2010).
[Crossref]

2008 (4)

M. Tokunaga, N. Imamoto, and K. Sakata-Sogawa, “Highly inclined thin illumination enables clear single-molecule imaging in cells,” Nat. Methods 5, 159–161 (2008).
[Crossref]

C. A. Konopka and S. Y. Bednarek, “Variable-angle epifluorescence microscopy: a new way to look at protein dynamics in the plant cell cortex,” Plant J. 53, 186–196 (2008).
[Crossref]

A. Raj, P. van den Bogaard, S. A. Rifkin, A. van Oudenaarden, and S. Tyagi, “Imaging individual mRNA molecules using multiple singly labeled probes,” Nat. Methods 5, 877–879 (2008).
[Crossref]

P. J. Keller, A. D. Schmidt, J. Wittbrodt, and E. H. K. Stelzer, “Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy,” Science 322, 1065–1069 (2008).
[Crossref]

2007 (1)

B. X. Cui, C. B. Wu, L. Chen, A. Ramirez, E. L. Bearer, W. P. Li, W. C. Mobley, and S. Chu, “One at a time, live tracking of NGF axonal transport using quantum dots,” Proc. Natl. Acad. Sci. USA 104, 13666–13671 (2007).
[Crossref]

2004 (1)

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305, 1007–1009 (2004).
[Crossref]

2002 (1)

T. Ha, I. Rasnik, W. Cheng, H. P. Babcock, G. H. Gauss, T. M. Lohman, and S. Chu, “Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase,” Nature 419, 638–641 (2002).
[Crossref]

1995 (1)

T. Funatsu, Y. Harada, M. Tokunaga, K. Saito, and T. Yanagida, “Imaging of single fluorescent molecules and individual ATP turnovers by single myosin molecules in aqueous-solution,” Nature 374, 555–559 (1995).
[Crossref]

Ameer-Beg, S.

N. A. Hosny, M. Y. Song, J. T. Connelly, S. Ameer-Beg, M. M. Knight, and A. P. Wheeler, “Super-resolution imaging strategies for cell biologists using a spinning disk microscope,” PLoS ONE 8, e74604 (2013).
[Crossref]

Aravind, A.

R. Galland, G. Grenci, A. Aravind, V. Viasnoff, V. Studer, and J.-B. Sibarita, “3D high- and super-resolution imaging using single-objective SPIM,” Nat. Methods 12, 641–644 (2015).
[Crossref]

Arndt, H. D.

G. Lukinavicius, L. Reymond, E. D’Este, A. Masharina, F. Gottfert, H. Ta, A. Guther, M. Fournier, S. Rizzo, H. Waldmann, C. Blaukopf, C. Sommer, D. W. Gerlich, H. D. Arndt, S. W. Hell, and K. Johnsson, “Fluorogenic probes for live-cell imaging of the cytoskeleton,” Nat. Methods 11, 731–733 (2014).
[Crossref]

Avendano, M. S.

R. Jungmann, M. S. Avendano, J. B. Woehrstein, M. J. Dai, W. M. Shih, and P. Yin, “Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT,” Nat. Methods 11, 313–318 (2014).
[Crossref]

Babcock, H. P.

T. Ha, I. Rasnik, W. Cheng, H. P. Babcock, G. H. Gauss, T. M. Lohman, and S. Chu, “Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase,” Nature 419, 638–641 (2002).
[Crossref]

Basu, S.

J. C. M. Gebhardt, D. M. Suter, R. Roy, Z. W. Zhao, A. R. Chapman, S. Basu, T. Maniatis, and X. S. Xie, “Single-molecule imaging of transcription factor binding to DNA in live mammalian cells,” Nat. Methods 10, 421–426 (2013).
[Crossref]

Baumgart, E.

Bearer, E. L.

B. X. Cui, C. B. Wu, L. Chen, A. Ramirez, E. L. Bearer, W. P. Li, W. C. Mobley, and S. Chu, “One at a time, live tracking of NGF axonal transport using quantum dots,” Proc. Natl. Acad. Sci. USA 104, 13666–13671 (2007).
[Crossref]

Bednarek, S. Y.

C. A. Konopka and S. Y. Bednarek, “Variable-angle epifluorescence microscopy: a new way to look at protein dynamics in the plant cell cortex,” Plant J. 53, 186–196 (2008).
[Crossref]

Bembenek, J. N.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Boehme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref]

Betzig, E.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Boehme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref]

Blaukopf, C.

G. Lukinavicius, L. Reymond, E. D’Este, A. Masharina, F. Gottfert, H. Ta, A. Guther, M. Fournier, S. Rizzo, H. Waldmann, C. Blaukopf, C. Sommer, D. W. Gerlich, H. D. Arndt, S. W. Hell, and K. Johnsson, “Fluorogenic probes for live-cell imaging of the cytoskeleton,” Nat. Methods 11, 731–733 (2014).
[Crossref]

Boehme, R.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Boehme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref]

Bouchard, M. B.

M. B. Bouchard, V. Voleti, C. S. Mendes, C. Lacefield, W. B. Grueber, R. S. Mann, R. M. Bruno, and E. M. C. Hillman, “Swept confocally-aligned planar excitation (SCAPE) microscopy for high-speed volumetric imaging of behaving organisms,” Nat. Photonics 9, 113–119 (2015).
[Crossref]

Bruno, R. M.

M. B. Bouchard, V. Voleti, C. S. Mendes, C. Lacefield, W. B. Grueber, R. S. Mann, R. M. Bruno, and E. M. C. Hillman, “Swept confocally-aligned planar excitation (SCAPE) microscopy for high-speed volumetric imaging of behaving organisms,” Nat. Photonics 9, 113–119 (2015).
[Crossref]

Cai, L.

E. Lubeck and L. Cai, “Single-cell systems biology by super-resolution imaging and combinatorial labeling,” Nat. Methods 9, 743–748 (2012).
[Crossref]

Cattoglio, C.

A. S. Hansen, I. Pustova, C. Cattoglio, R. Tjian, and X. Darzacq, “CTCF and cohesin regulate chromatin loop stability with distinct dynamics,” eLife 6, e25776 (2017).

Chapman, A. R.

J. C. M. Gebhardt, D. M. Suter, R. Roy, Z. W. Zhao, A. R. Chapman, S. Basu, T. Maniatis, and X. S. Xie, “Single-molecule imaging of transcription factor binding to DNA in live mammalian cells,” Nat. Methods 10, 421–426 (2013).
[Crossref]

Chen, B.-C.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Boehme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref]

Chen, L.

B. X. Cui, C. B. Wu, L. Chen, A. Ramirez, E. L. Bearer, W. P. Li, W. C. Mobley, and S. Chu, “One at a time, live tracking of NGF axonal transport using quantum dots,” Proc. Natl. Acad. Sci. USA 104, 13666–13671 (2007).
[Crossref]

Cheng, W.

T. Ha, I. Rasnik, W. Cheng, H. P. Babcock, G. H. Gauss, T. M. Lohman, and S. Chu, “Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase,” Nature 419, 638–641 (2002).
[Crossref]

Chennakesavalu, S.

M. A. Reyer, E. L. McLean, S. Chennakesavalu, and J. Y. Fei, “An automated image analysis method for segmenting fluorescent bacteria in three dimensions,” Biochemistry 57, 209–215 (2018).
[Crossref]

Choy, J. C.

G. M. Wadsworth, R. Y. Parikh, J. C. Choy, and H. D. Kim, “mRNA detection in budding yeast with single fluorophores,” Nucleic Acids Res. 45, e141 (2017).
[Crossref]

Chu, S.

B. X. Cui, C. B. Wu, L. Chen, A. Ramirez, E. L. Bearer, W. P. Li, W. C. Mobley, and S. Chu, “One at a time, live tracking of NGF axonal transport using quantum dots,” Proc. Natl. Acad. Sci. USA 104, 13666–13671 (2007).
[Crossref]

T. Ha, I. Rasnik, W. Cheng, H. P. Babcock, G. H. Gauss, T. M. Lohman, and S. Chu, “Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase,” Nature 419, 638–641 (2002).
[Crossref]

Connelly, J. T.

N. A. Hosny, M. Y. Song, J. T. Connelly, S. Ameer-Beg, M. M. Knight, and A. P. Wheeler, “Super-resolution imaging strategies for cell biologists using a spinning disk microscope,” PLoS ONE 8, e74604 (2013).
[Crossref]

Cui, B. X.

B. X. Cui, C. B. Wu, L. Chen, A. Ramirez, E. L. Bearer, W. P. Li, W. C. Mobley, and S. Chu, “One at a time, live tracking of NGF axonal transport using quantum dots,” Proc. Natl. Acad. Sci. USA 104, 13666–13671 (2007).
[Crossref]

D’Este, E.

G. Lukinavicius, L. Reymond, E. D’Este, A. Masharina, F. Gottfert, H. Ta, A. Guther, M. Fournier, S. Rizzo, H. Waldmann, C. Blaukopf, C. Sommer, D. W. Gerlich, H. D. Arndt, S. W. Hell, and K. Johnsson, “Fluorogenic probes for live-cell imaging of the cytoskeleton,” Nat. Methods 11, 731–733 (2014).
[Crossref]

Dai, M. J.

R. Jungmann, M. S. Avendano, J. B. Woehrstein, M. J. Dai, W. M. Shih, and P. Yin, “Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT,” Nat. Methods 11, 313–318 (2014).
[Crossref]

Darzacq, X.

A. S. Hansen, I. Pustova, C. Cattoglio, R. Tjian, and X. Darzacq, “CTCF and cohesin regulate chromatin loop stability with distinct dynamics,” eLife 6, e25776 (2017).

Davidson, M. W.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Boehme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
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J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305, 1007–1009 (2004).
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F. C. Zanacchi, Z. Lavagnino, M. P. Donnorso, A. Del Bue, L. Furia, M. Faretta, and A. Diaspro, “Live-cell 3D super-resolution imaging in thick biological samples,” Nat. Methods 8, 1047–1049 (2011).
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F. C. Zanacchi, Z. Lavagnino, M. P. Donnorso, A. Del Bue, L. Furia, M. Faretta, and A. Diaspro, “Live-cell 3D super-resolution imaging in thick biological samples,” Nat. Methods 8, 1047–1049 (2011).
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F. C. Zanacchi, Z. Lavagnino, M. P. Donnorso, A. Del Bue, L. Furia, M. Faretta, and A. Diaspro, “Live-cell 3D super-resolution imaging in thick biological samples,” Nat. Methods 8, 1047–1049 (2011).
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B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Boehme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
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F. C. Zanacchi, Z. Lavagnino, M. P. Donnorso, A. Del Bue, L. Furia, M. Faretta, and A. Diaspro, “Live-cell 3D super-resolution imaging in thick biological samples,” Nat. Methods 8, 1047–1049 (2011).
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Fei, J. Y.

M. A. Reyer, E. L. McLean, S. Chennakesavalu, and J. Y. Fei, “An automated image analysis method for segmenting fluorescent bacteria in three dimensions,” Biochemistry 57, 209–215 (2018).
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G. Lukinavicius, L. Reymond, E. D’Este, A. Masharina, F. Gottfert, H. Ta, A. Guther, M. Fournier, S. Rizzo, H. Waldmann, C. Blaukopf, C. Sommer, D. W. Gerlich, H. D. Arndt, S. W. Hell, and K. Johnsson, “Fluorogenic probes for live-cell imaging of the cytoskeleton,” Nat. Methods 11, 731–733 (2014).
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B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Boehme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
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T. Funatsu, Y. Harada, M. Tokunaga, K. Saito, and T. Yanagida, “Imaging of single fluorescent molecules and individual ATP turnovers by single myosin molecules in aqueous-solution,” Nature 374, 555–559 (1995).
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Furia, L.

F. C. Zanacchi, Z. Lavagnino, M. P. Donnorso, A. Del Bue, L. Furia, M. Faretta, and A. Diaspro, “Live-cell 3D super-resolution imaging in thick biological samples,” Nat. Methods 8, 1047–1049 (2011).
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R. Galland, G. Grenci, A. Aravind, V. Viasnoff, V. Studer, and J.-B. Sibarita, “3D high- and super-resolution imaging using single-objective SPIM,” Nat. Methods 12, 641–644 (2015).
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T. Ha, I. Rasnik, W. Cheng, H. P. Babcock, G. H. Gauss, T. M. Lohman, and S. Chu, “Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase,” Nature 419, 638–641 (2002).
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J. C. M. Gebhardt, D. M. Suter, R. Roy, Z. W. Zhao, A. R. Chapman, S. Basu, T. Maniatis, and X. S. Xie, “Single-molecule imaging of transcription factor binding to DNA in live mammalian cells,” Nat. Methods 10, 421–426 (2013).
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G. Lukinavicius, L. Reymond, E. D’Este, A. Masharina, F. Gottfert, H. Ta, A. Guther, M. Fournier, S. Rizzo, H. Waldmann, C. Blaukopf, C. Sommer, D. W. Gerlich, H. D. Arndt, S. W. Hell, and K. Johnsson, “Fluorogenic probes for live-cell imaging of the cytoskeleton,” Nat. Methods 11, 731–733 (2014).
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M. E. Tanenbaum, L. A. Gilbert, L. S. Qi, J. S. Weissman, and R. D. Vale, “A protein-tagging system for signal amplification in gene expression and fluorescence imaging,” Cell 159, 635–646 (2014).
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M. J. Levesque, P. Ginart, Y. C. Wei, and A. Raj, “Visualizing SNVs to quantify allele-specific expression in single cells,” Nat. Methods 10, 865–867 (2013).
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G. Lukinavicius, L. Reymond, E. D’Este, A. Masharina, F. Gottfert, H. Ta, A. Guther, M. Fournier, S. Rizzo, H. Waldmann, C. Blaukopf, C. Sommer, D. W. Gerlich, H. D. Arndt, S. W. Hell, and K. Johnsson, “Fluorogenic probes for live-cell imaging of the cytoskeleton,” Nat. Methods 11, 731–733 (2014).
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R. Galland, G. Grenci, A. Aravind, V. Viasnoff, V. Studer, and J.-B. Sibarita, “3D high- and super-resolution imaging using single-objective SPIM,” Nat. Methods 12, 641–644 (2015).
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B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Boehme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
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Grueber, W. B.

M. B. Bouchard, V. Voleti, C. S. Mendes, C. Lacefield, W. B. Grueber, R. S. Mann, R. M. Bruno, and E. M. C. Hillman, “Swept confocally-aligned planar excitation (SCAPE) microscopy for high-speed volumetric imaging of behaving organisms,” Nat. Photonics 9, 113–119 (2015).
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Gustavsson, A. K.

A. K. Gustavsson, P. N. Petrov, M. Y. Lee, Y. Shechtman, and W. E. Moerner, “3D single-molecule super-resolution microscopy with a tilted light sheet,” Nat. Commun. 9, 123 (2018).
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G. Lukinavicius, L. Reymond, E. D’Este, A. Masharina, F. Gottfert, H. Ta, A. Guther, M. Fournier, S. Rizzo, H. Waldmann, C. Blaukopf, C. Sommer, D. W. Gerlich, H. D. Arndt, S. W. Hell, and K. Johnsson, “Fluorogenic probes for live-cell imaging of the cytoskeleton,” Nat. Methods 11, 731–733 (2014).
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Ha, T.

T. Ha, I. Rasnik, W. Cheng, H. P. Babcock, G. H. Gauss, T. M. Lohman, and S. Chu, “Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase,” Nature 419, 638–641 (2002).
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Hammer, J. A.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Boehme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
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A. S. Hansen, I. Pustova, C. Cattoglio, R. Tjian, and X. Darzacq, “CTCF and cohesin regulate chromatin loop stability with distinct dynamics,” eLife 6, e25776 (2017).

Harada, Y.

T. Funatsu, Y. Harada, M. Tokunaga, K. Saito, and T. Yanagida, “Imaging of single fluorescent molecules and individual ATP turnovers by single myosin molecules in aqueous-solution,” Nature 374, 555–559 (1995).
[Crossref]

Hell, S. W.

G. Lukinavicius, L. Reymond, E. D’Este, A. Masharina, F. Gottfert, H. Ta, A. Guther, M. Fournier, S. Rizzo, H. Waldmann, C. Blaukopf, C. Sommer, D. W. Gerlich, H. D. Arndt, S. W. Hell, and K. Johnsson, “Fluorogenic probes for live-cell imaging of the cytoskeleton,” Nat. Methods 11, 731–733 (2014).
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Hillman, E. M. C.

M. B. Bouchard, V. Voleti, C. S. Mendes, C. Lacefield, W. B. Grueber, R. S. Mann, R. M. Bruno, and E. M. C. Hillman, “Swept confocally-aligned planar excitation (SCAPE) microscopy for high-speed volumetric imaging of behaving organisms,” Nat. Photonics 9, 113–119 (2015).
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N. A. Hosny, M. Y. Song, J. T. Connelly, S. Ameer-Beg, M. M. Knight, and A. P. Wheeler, “Super-resolution imaging strategies for cell biologists using a spinning disk microscope,” PLoS ONE 8, e74604 (2013).
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J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305, 1007–1009 (2004).
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B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Boehme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
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Johnsson, K.

G. Lukinavicius, L. Reymond, E. D’Este, A. Masharina, F. Gottfert, H. Ta, A. Guther, M. Fournier, S. Rizzo, H. Waldmann, C. Blaukopf, C. Sommer, D. W. Gerlich, H. D. Arndt, S. W. Hell, and K. Johnsson, “Fluorogenic probes for live-cell imaging of the cytoskeleton,” Nat. Methods 11, 731–733 (2014).
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B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Boehme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
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G. M. Wadsworth, R. Y. Parikh, J. C. Choy, and H. D. Kim, “mRNA detection in budding yeast with single fluorophores,” Nucleic Acids Res. 45, e141 (2017).
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N. A. Hosny, M. Y. Song, J. T. Connelly, S. Ameer-Beg, M. M. Knight, and A. P. Wheeler, “Super-resolution imaging strategies for cell biologists using a spinning disk microscope,” PLoS ONE 8, e74604 (2013).
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C. A. Konopka and S. Y. Bednarek, “Variable-angle epifluorescence microscopy: a new way to look at protein dynamics in the plant cell cortex,” Plant J. 53, 186–196 (2008).
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Kuzyk, A.

R. Jungmann, C. Steinhauer, M. Scheible, A. Kuzyk, P. Tinnefeld, and F. C. Simmel, “Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami,” Nano Lett. 10, 4756–4761 (2010).
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Lacefield, C.

M. B. Bouchard, V. Voleti, C. S. Mendes, C. Lacefield, W. B. Grueber, R. S. Mann, R. M. Bruno, and E. M. C. Hillman, “Swept confocally-aligned planar excitation (SCAPE) microscopy for high-speed volumetric imaging of behaving organisms,” Nat. Photonics 9, 113–119 (2015).
[Crossref]

Lavagnino, Z.

F. C. Zanacchi, Z. Lavagnino, M. P. Donnorso, A. Del Bue, L. Furia, M. Faretta, and A. Diaspro, “Live-cell 3D super-resolution imaging in thick biological samples,” Nat. Methods 8, 1047–1049 (2011).
[Crossref]

Lee, M. Y.

A. K. Gustavsson, P. N. Petrov, M. Y. Lee, Y. Shechtman, and W. E. Moerner, “3D single-molecule super-resolution microscopy with a tilted light sheet,” Nat. Commun. 9, 123 (2018).
[Crossref]

Legant, W. R.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Boehme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
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M. J. Levesque, P. Ginart, Y. C. Wei, and A. Raj, “Visualizing SNVs to quantify allele-specific expression in single cells,” Nat. Methods 10, 865–867 (2013).
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B. X. Cui, C. B. Wu, L. Chen, A. Ramirez, E. L. Bearer, W. P. Li, W. C. Mobley, and S. Chu, “One at a time, live tracking of NGF axonal transport using quantum dots,” Proc. Natl. Acad. Sci. USA 104, 13666–13671 (2007).
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Lippincott-Schwartz, J.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Boehme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref]

Liu, Z.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Boehme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref]

Lohman, T. M.

T. Ha, I. Rasnik, W. Cheng, H. P. Babcock, G. H. Gauss, T. M. Lohman, and S. Chu, “Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase,” Nature 419, 638–641 (2002).
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G. Lukinavicius, L. Reymond, E. D’Este, A. Masharina, F. Gottfert, H. Ta, A. Guther, M. Fournier, S. Rizzo, H. Waldmann, C. Blaukopf, C. Sommer, D. W. Gerlich, H. D. Arndt, S. W. Hell, and K. Johnsson, “Fluorogenic probes for live-cell imaging of the cytoskeleton,” Nat. Methods 11, 731–733 (2014).
[Crossref]

Maniatis, T.

J. C. M. Gebhardt, D. M. Suter, R. Roy, Z. W. Zhao, A. R. Chapman, S. Basu, T. Maniatis, and X. S. Xie, “Single-molecule imaging of transcription factor binding to DNA in live mammalian cells,” Nat. Methods 10, 421–426 (2013).
[Crossref]

Mann, R. S.

M. B. Bouchard, V. Voleti, C. S. Mendes, C. Lacefield, W. B. Grueber, R. S. Mann, R. M. Bruno, and E. M. C. Hillman, “Swept confocally-aligned planar excitation (SCAPE) microscopy for high-speed volumetric imaging of behaving organisms,” Nat. Photonics 9, 113–119 (2015).
[Crossref]

Masharina, A.

G. Lukinavicius, L. Reymond, E. D’Este, A. Masharina, F. Gottfert, H. Ta, A. Guther, M. Fournier, S. Rizzo, H. Waldmann, C. Blaukopf, C. Sommer, D. W. Gerlich, H. D. Arndt, S. W. Hell, and K. Johnsson, “Fluorogenic probes for live-cell imaging of the cytoskeleton,” Nat. Methods 11, 731–733 (2014).
[Crossref]

McLean, E. L.

M. A. Reyer, E. L. McLean, S. Chennakesavalu, and J. Y. Fei, “An automated image analysis method for segmenting fluorescent bacteria in three dimensions,” Biochemistry 57, 209–215 (2018).
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Mendes, C. S.

M. B. Bouchard, V. Voleti, C. S. Mendes, C. Lacefield, W. B. Grueber, R. S. Mann, R. M. Bruno, and E. M. C. Hillman, “Swept confocally-aligned planar excitation (SCAPE) microscopy for high-speed volumetric imaging of behaving organisms,” Nat. Photonics 9, 113–119 (2015).
[Crossref]

Milkie, D. E.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Boehme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref]

Mimori-Kiyosue, Y.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Boehme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref]

Mitchell, D. M.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Boehme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref]

Mobley, W. C.

B. X. Cui, C. B. Wu, L. Chen, A. Ramirez, E. L. Bearer, W. P. Li, W. C. Mobley, and S. Chu, “One at a time, live tracking of NGF axonal transport using quantum dots,” Proc. Natl. Acad. Sci. USA 104, 13666–13671 (2007).
[Crossref]

Moerner, W. E.

A. K. Gustavsson, P. N. Petrov, M. Y. Lee, Y. Shechtman, and W. E. Moerner, “3D single-molecule super-resolution microscopy with a tilted light sheet,” Nat. Commun. 9, 123 (2018).
[Crossref]

Mullins, R. D.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Boehme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
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Pang, S.

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M. E. Tanenbaum, L. A. Gilbert, L. S. Qi, J. S. Weissman, and R. D. Vale, “A protein-tagging system for signal amplification in gene expression and fluorescence imaging,” Cell 159, 635–646 (2014).
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B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Boehme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
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M. E. Tanenbaum, L. A. Gilbert, L. S. Qi, J. S. Weissman, and R. D. Vale, “A protein-tagging system for signal amplification in gene expression and fluorescence imaging,” Cell 159, 635–646 (2014).
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J. Tang, Y. Sun, S. Pang, and K. Y. Han, “Spatially encoded fast single-molecule fluorescence spectroscopy with full field-of-view,” Sci. Rep. 7, 10945 (2017).
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R. Jungmann, C. Steinhauer, M. Scheible, A. Kuzyk, P. Tinnefeld, and F. C. Simmel, “Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami,” Nano Lett. 10, 4756–4761 (2010).
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A. S. Hansen, I. Pustova, C. Cattoglio, R. Tjian, and X. Darzacq, “CTCF and cohesin regulate chromatin loop stability with distinct dynamics,” eLife 6, e25776 (2017).

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M. Tokunaga, N. Imamoto, and K. Sakata-Sogawa, “Highly inclined thin illumination enables clear single-molecule imaging in cells,” Nat. Methods 5, 159–161 (2008).
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T. Funatsu, Y. Harada, M. Tokunaga, K. Saito, and T. Yanagida, “Imaging of single fluorescent molecules and individual ATP turnovers by single myosin molecules in aqueous-solution,” Nature 374, 555–559 (1995).
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B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Boehme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
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A. Raj, P. van den Bogaard, S. A. Rifkin, A. van Oudenaarden, and S. Tyagi, “Imaging individual mRNA molecules using multiple singly labeled probes,” Nat. Methods 5, 877–879 (2008).
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M. E. Tanenbaum, L. A. Gilbert, L. S. Qi, J. S. Weissman, and R. D. Vale, “A protein-tagging system for signal amplification in gene expression and fluorescence imaging,” Cell 159, 635–646 (2014).
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A. Raj, P. van den Bogaard, S. A. Rifkin, A. van Oudenaarden, and S. Tyagi, “Imaging individual mRNA molecules using multiple singly labeled probes,” Nat. Methods 5, 877–879 (2008).
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B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Boehme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
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Wei, Y. C.

M. J. Levesque, P. Ginart, Y. C. Wei, and A. Raj, “Visualizing SNVs to quantify allele-specific expression in single cells,” Nat. Methods 10, 865–867 (2013).
[Crossref]

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M. E. Tanenbaum, L. A. Gilbert, L. S. Qi, J. S. Weissman, and R. D. Vale, “A protein-tagging system for signal amplification in gene expression and fluorescence imaging,” Cell 159, 635–646 (2014).
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N. A. Hosny, M. Y. Song, J. T. Connelly, S. Ameer-Beg, M. M. Knight, and A. P. Wheeler, “Super-resolution imaging strategies for cell biologists using a spinning disk microscope,” PLoS ONE 8, e74604 (2013).
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P. J. Keller, A. D. Schmidt, J. Wittbrodt, and E. H. K. Stelzer, “Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy,” Science 322, 1065–1069 (2008).
[Crossref]

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305, 1007–1009 (2004).
[Crossref]

Woehrstein, J. B.

R. Jungmann, M. S. Avendano, J. B. Woehrstein, M. J. Dai, W. M. Shih, and P. Yin, “Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT,” Nat. Methods 11, 313–318 (2014).
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Wu, C. B.

B. X. Cui, C. B. Wu, L. Chen, A. Ramirez, E. L. Bearer, W. P. Li, W. C. Mobley, and S. Chu, “One at a time, live tracking of NGF axonal transport using quantum dots,” Proc. Natl. Acad. Sci. USA 104, 13666–13671 (2007).
[Crossref]

Wu, X. S.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Boehme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
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Xie, X. S.

J. C. M. Gebhardt, D. M. Suter, R. Roy, Z. W. Zhao, A. R. Chapman, S. Basu, T. Maniatis, and X. S. Xie, “Single-molecule imaging of transcription factor binding to DNA in live mammalian cells,” Nat. Methods 10, 421–426 (2013).
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Xu, K.

K. Xu, G. Zhong, and X. Zhuang, “Actin, spectrin, and associated proteins form a periodic cytoskeletal structure in axons,” Science 339, 452–456 (2013).
[Crossref]

Yanagida, T.

T. Funatsu, Y. Harada, M. Tokunaga, K. Saito, and T. Yanagida, “Imaging of single fluorescent molecules and individual ATP turnovers by single myosin molecules in aqueous-solution,” Nature 374, 555–559 (1995).
[Crossref]

Yin, P.

R. Jungmann, M. S. Avendano, J. B. Woehrstein, M. J. Dai, W. M. Shih, and P. Yin, “Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT,” Nat. Methods 11, 313–318 (2014).
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Zanacchi, F. C.

F. C. Zanacchi, Z. Lavagnino, M. P. Donnorso, A. Del Bue, L. Furia, M. Faretta, and A. Diaspro, “Live-cell 3D super-resolution imaging in thick biological samples,” Nat. Methods 8, 1047–1049 (2011).
[Crossref]

Zhao, Z. W.

J. C. M. Gebhardt, D. M. Suter, R. Roy, Z. W. Zhao, A. R. Chapman, S. Basu, T. Maniatis, and X. S. Xie, “Single-molecule imaging of transcription factor binding to DNA in live mammalian cells,” Nat. Methods 10, 421–426 (2013).
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Zhong, G.

K. Xu, G. Zhong, and X. Zhuang, “Actin, spectrin, and associated proteins form a periodic cytoskeletal structure in axons,” Science 339, 452–456 (2013).
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Zhuang, X.

K. Xu, G. Zhong, and X. Zhuang, “Actin, spectrin, and associated proteins form a periodic cytoskeletal structure in axons,” Science 339, 452–456 (2013).
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Biochemistry (1)

M. A. Reyer, E. L. McLean, S. Chennakesavalu, and J. Y. Fei, “An automated image analysis method for segmenting fluorescent bacteria in three dimensions,” Biochemistry 57, 209–215 (2018).
[Crossref]

Cell (1)

M. E. Tanenbaum, L. A. Gilbert, L. S. Qi, J. S. Weissman, and R. D. Vale, “A protein-tagging system for signal amplification in gene expression and fluorescence imaging,” Cell 159, 635–646 (2014).
[Crossref]

eLife (1)

A. S. Hansen, I. Pustova, C. Cattoglio, R. Tjian, and X. Darzacq, “CTCF and cohesin regulate chromatin loop stability with distinct dynamics,” eLife 6, e25776 (2017).

Nano Lett. (1)

R. Jungmann, C. Steinhauer, M. Scheible, A. Kuzyk, P. Tinnefeld, and F. C. Simmel, “Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami,” Nano Lett. 10, 4756–4761 (2010).
[Crossref]

Nat. Commun. (1)

A. K. Gustavsson, P. N. Petrov, M. Y. Lee, Y. Shechtman, and W. E. Moerner, “3D single-molecule super-resolution microscopy with a tilted light sheet,” Nat. Commun. 9, 123 (2018).
[Crossref]

Nat. Methods (9)

M. Tokunaga, N. Imamoto, and K. Sakata-Sogawa, “Highly inclined thin illumination enables clear single-molecule imaging in cells,” Nat. Methods 5, 159–161 (2008).
[Crossref]

A. Raj, P. van den Bogaard, S. A. Rifkin, A. van Oudenaarden, and S. Tyagi, “Imaging individual mRNA molecules using multiple singly labeled probes,” Nat. Methods 5, 877–879 (2008).
[Crossref]

R. Jungmann, M. S. Avendano, J. B. Woehrstein, M. J. Dai, W. M. Shih, and P. Yin, “Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT,” Nat. Methods 11, 313–318 (2014).
[Crossref]

F. C. Zanacchi, Z. Lavagnino, M. P. Donnorso, A. Del Bue, L. Furia, M. Faretta, and A. Diaspro, “Live-cell 3D super-resolution imaging in thick biological samples,” Nat. Methods 8, 1047–1049 (2011).
[Crossref]

J. C. M. Gebhardt, D. M. Suter, R. Roy, Z. W. Zhao, A. R. Chapman, S. Basu, T. Maniatis, and X. S. Xie, “Single-molecule imaging of transcription factor binding to DNA in live mammalian cells,” Nat. Methods 10, 421–426 (2013).
[Crossref]

R. Galland, G. Grenci, A. Aravind, V. Viasnoff, V. Studer, and J.-B. Sibarita, “3D high- and super-resolution imaging using single-objective SPIM,” Nat. Methods 12, 641–644 (2015).
[Crossref]

M. J. Levesque, P. Ginart, Y. C. Wei, and A. Raj, “Visualizing SNVs to quantify allele-specific expression in single cells,” Nat. Methods 10, 865–867 (2013).
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Figures (6)

Fig. 1.
Fig. 1. Highly inclined swept tile (HIST) microscopy. (a) Highly inclined illumination at glass and water interface. dz, beam thickness; R, illumination width; IP, imaging plane. (b) Schematic of HIST microscopy. A tile beam is swept across the FOV by a galvo mirror and the emitted fluorescence is detected by an sCMOS camera with confocal slit detection. CL1-2, cylindrical lens; GM, galvo mirror; M, mirror. (c–g) Illumination schemes (top, x z cross-section) and single-molecule fluorescence images of Atto647N labeled DNA embedded in a hydrogel (bottom, x y cross-section) by (c) epi, (d) large area HILO, (e) small area HILO, (f) tile, and (g) HIST illumination at excitation wavelength of 638 nm. The images were taken 5 μm above the surface, and the camera frame rate was 800    ms 1 . The average illumination intensity was 30    W / cm 2 . Inset, zoom-in single-molecule images. All images are raw data. Scale bar, 20 μm and 5 μm (inset).
Fig. 2.
Fig. 2. Performance of HIST microscopy for single-molecule imaging. (a) Line profiles of large-area HILO and HIST illumination taken from Figs. 1(d) and 1(g) along white dashed lines. (b) Relative SBR for each illumination method. More than 100 single-molecule spots were used for analysis.
Fig. 3.
Fig. 3. Characterization of HIST microscopy. (a) Fluorescence images of 20 nm beads in 3D hydrogel with a compression ratio of 8. Scale bar, 10 μm. (b) Standard deviation projection along the y direction of (a). (c) Beam thickness of a highly inclined illumination beam (tile) with 638 and 561 nm excitation lights when 8 × compression ratio used. The beam thickness was 3.7 ± 0.3 and 3.6 ± 0.2    μm , respectively. (d) SBR dependence on imaging depth using 20 nm beads in 3D hydrogel and r = 8 HIST illumination system.
Fig. 4.
Fig. 4. Single-molecule RNA FISH imaging on mammalian cells with different numbers of probes. (a) smFISH images of EEF2 on A549 cells with epi and HIST illumination with four probes. A maximum intensity projection was performed on 20 z stacks (5 μm thickness). The illumination power was 40    W / cm 2 and the integration time was 400 ms. DAPI stain is in blue. (b) Signal to background ratio for different numbers of FISH probes with epi and HIST illumination. More than 100 single-molecule spots were analyzed and the error bars denote standard deviation from the mean. (c) Images of EEF2 on A549 cells with epi and HIST illumination for different numbers of probes. (d) Zoom-in images of epi and HIST illumination with a single probe. All FISH probes were labeled with AF647. Scale bars, (a) 20 μm, (c) 10 μm, and (d) 5 μm.
Fig. 5.
Fig. 5. Single-molecule RNA FISH imaging on mouse brain tissues with 5 probes. (a) smFISH images of EEF2 with 5 FISH probes by epi and HIST illumination. The integration time was 800 ms. z-stack images were obtained from z = 4    μm to z = 7    μm and maximum projected (at coverslip, z = 0    μm ). (b) Magnified images of the boxed region in (a). White circles indicate identified mRNA spots. (c) Control experiment of mouse brain smFISH imaging with 0.5% RNase treatment. All FISH probes were labeled with AF647. Scale bars, 10 μm (a,c), 2 μm (b).
Fig. 6.
Fig. 6. Live-cell imaging. Images of actin in U2OS cells with (a) HIST and (b) HILO illumination. (c) Time-lapse imaging with HIST microscopy reveals a shrinkage of U2OS cells after treatment with trypsin-EDTA. The average power was 5    W / cm 2 and the integration time was 1/23 s. Scale bars, 20 μm.

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