Abstract

3D STORM is one of the leading methods for super-resolution imaging, with resolution down to 10 nm in the lateral direction, and 30–50 nm in the axial direction. However, there is one important requirement to perform this type of imaging: making dye molecules blink. This usually relies on the utilization of complex buffers, containing different chemicals and sensitive enzymatic systems, limiting the reproducibility of the method. We report here that the commercial mounting medium Vectashield can be used for STORM of Alexa-647, and yields images comparable or superior to those obtained with more complex buffers, especially for 3D imaging. We expect that this advance will promote the versatile utilization of 3D STORM by removing one of its entry barriers, as well as provide a more reproducible way to compare optical setups and data processing algorithms.

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2012 (5)

S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods9, 195–200 (2012).
[CrossRef]

P. Gönczy, “Towards a molecular architecture of centriole assembly,” Nat. Rev. Mol. Cell Biol.13, 425–435 (2012).
[CrossRef] [PubMed]

S. Lawo, M. Hasegan, G. D. Gupta, and L. Pelletier, “Subdiffraction imaging of centrosomes reveals higher-order organizational features of pericentriolar material,” Nat. Cell. Biol.14, 1148–1158 (2012).
[CrossRef] [PubMed]

I. H. Stein, S. Capone, J. H. Smit, F. Baumann, T. Cordes, and P. Tinnefeld, “Linking single-molecule blinking to chromophore structure and redox potentials,” ChemPhysChem13, 931–937 (2012).
[CrossRef]

A. Lampe, V. J. Haucke, S. Sigrist, M. Heileman, and J. Schmoranzer, “Multi-colour direct STORM with red emitting carbocyanines,” Biol. Cell104, 229–237 (2012).
[CrossRef]

2011 (4)

G. Dempsey, J. Vaughan, K. Chen, M. Bates, and X. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat. Methods8, 1027–1036 (2011).
[CrossRef] [PubMed]

T. Cordes, A. Maiser, C. Steinhauer, L. Schermelleh, and P. Tinnefeld, “Mechanisms and advancement of antifading agents for fluorescence microscopy and single-molecule spectroscopy,” Phys. Chem. Chem. Phys.13, 6699–6709 (2011).
[CrossRef] [PubMed]

S. J. Holden, S. Uphoff, and A.N. Kapanidis, “DAOSTORM: an algorithm for high-density super-resolution microscopy,” Nat. Methods8, 279–280 (2011).
[CrossRef] [PubMed]

S. Van De Linde, A. Löschberger, T. Klein, M. Heidbreder, S. Wolter, M. Heilemann, and M. Sauer, “Direct stochastic optical reconstruction microscopy with standard fluorescent probes,” Nat. Protoc.6, 991–1009 (2011).
[CrossRef] [PubMed]

2010 (1)

X. Shi, J. Lim, and T. Ha, “Acidification of the oxygen scavenging system in single-molecule fluorescence studies: in situ sensing with a ratiometric dual-emission probe,” Anal. Chem.82, 6132–6138 (2010).
[CrossRef] [PubMed]

2009 (4)

J. Vogelsang, T. Cordes, and P. Tinnefeld, “Single-molecule photophysics of oxazines on DNA and its application in a FRET switch,” Photochem. Photobiol. Sci.8, 486–496 (2009).
[CrossRef] [PubMed]

T. Dertinger, R. Colyera, G. Iyer, S. Weiss, and J. Enderlein, “Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI),” Proc. Natl. Acad. Sci. U.S.A.106, 22287–22292 (2009).
[CrossRef] [PubMed]

G. T. Dempsey, M. Bates, W. E. Kowtoniuk, D. R. Liu, R. Y. Tsien, and X. Zhuang, “Photoswitching mechanism of cyanine dyes,” J. Am. Chem. Soc.131, 18192–18193 (2009).
[CrossRef] [PubMed]

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A.106, 3125–3130 (2009).
[CrossRef] [PubMed]

2008 (6)

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods5, 527–529 (2008).
[CrossRef] [PubMed]

C. Steinhauer, C. Forthmann, J. Vogelsang, and P. Tinnefeld, “Superresolution microscopy on the basis of engineered dark states,” J. Am. Chem. Soc.130, 16840–16841 (2008).
[CrossRef] [PubMed]

M. Heilemann, S. van de Linde, M. Schuttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes,” Angew. Chem. Int. Ed.47, 6172–6176 (2008).
[CrossRef]

L. Schermelleh, P. M. Carlton, S. Haase, L. Shao, L. Winoto, P. Kner, B. Burke, M. C. Cardoso, D. A. Agard, M. G. L. Gustafsson, H. Leonhardt, and J. W. Sedat, “Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy,” Science320, 1332–1336 (2008).
[CrossRef] [PubMed]

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science319, 810–813 (2008).
[CrossRef] [PubMed]

B. Huang, S. A. Jones, B. Brandenburg, and X. Zhuang, “Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution,” Nat. Methods5, 1047–1052 (2008).
[CrossRef] [PubMed]

2007 (2)

J. Widengren, A. Chmyrov, C. Eggeling, P. Löfdahl, and C. A. M. Seidel, “Strategies to improve photostabilities in ultrasensitive fluorescence spectroscopy,” J. Phys. Chem. A111, 429–444 (2007).
[CrossRef] [PubMed]

J. Fölling, V. Belov, R. Medda, A. Schönle, A. Egner, C. Eggeling, M. Bossi, and S. W. Hell, “Photochromic rhodamines provide nanoscopy with optical sectioning,” Angew. Chem. Int. Ed.46, 6266–6270 (2007).
[CrossRef]

2006 (4)

T. Staudt, M. C. Lang, R. Medda, J. Engelhardt, and S. W. Hell, “‘2,2’-Thiodiethanol: A new water soluble mounting medium for high resolution optical microscopy” Microsc. Res. Tech.70, 1–9 (2006).
[CrossRef]

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science313, 1642–1645 (2006).
[CrossRef] [PubMed]

S. T. Hess, T. P. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J.91, 4258–4272 (2006).
[CrossRef] [PubMed]

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods3, 793–796 (2006).
[CrossRef] [PubMed]

2005 (2)

M. Heilemann, E. Margeat, R. Kasper, M. Sauer, and P. Tinnefeld, “Carbocyanine dyes as efficient reversible single-molecule optical switch,” J. Am. Chem. Soc.127, 3801–3806 (2005).
[CrossRef] [PubMed]

M. Bates, T. R. Blosser, and X. Zhuang, “Short-range spectroscopic ruler based on a single-molecule optical switch,” Phys. Rev. Lett.94, 108101 (2005).
[CrossRef] [PubMed]

2002 (1)

R. E. Thompson, D. R. Larson, and W. W. Webb, “Precise nanometer localization analysis for individual fluorescent probes,” Biophys. J.82, 2775–2783 (2002).
[CrossRef] [PubMed]

1985 (1)

K. Valnes and P. Brandtzaeg, “Retardation of immunofluorescence fading during microscopy,” J. Histochem. Cytochem.33, 755–761 (1985).
[CrossRef] [PubMed]

Agard, D. A.

L. Schermelleh, P. M. Carlton, S. Haase, L. Shao, L. Winoto, P. Kner, B. Burke, M. C. Cardoso, D. A. Agard, M. G. L. Gustafsson, H. Leonhardt, and J. W. Sedat, “Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy,” Science320, 1332–1336 (2008).
[CrossRef] [PubMed]

Alushin, G.

E. Nogales and G. Alushin, “4.6 Tubulin and microtubule structure: mechanistic insights into dynamic instability and its biological relevance,” in Comprehensive Biophysics, E. H. Egelman, ed. (Elsevier, 2012), pp. 72–92.
[CrossRef]

Bates, M.

G. Dempsey, J. Vaughan, K. Chen, M. Bates, and X. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat. Methods8, 1027–1036 (2011).
[CrossRef] [PubMed]

G. T. Dempsey, M. Bates, W. E. Kowtoniuk, D. R. Liu, R. Y. Tsien, and X. Zhuang, “Photoswitching mechanism of cyanine dyes,” J. Am. Chem. Soc.131, 18192–18193 (2009).
[CrossRef] [PubMed]

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science319, 810–813 (2008).
[CrossRef] [PubMed]

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods3, 793–796 (2006).
[CrossRef] [PubMed]

M. Bates, T. R. Blosser, and X. Zhuang, “Short-range spectroscopic ruler based on a single-molecule optical switch,” Phys. Rev. Lett.94, 108101 (2005).
[CrossRef] [PubMed]

Baumann, F.

I. H. Stein, S. Capone, J. H. Smit, F. Baumann, T. Cordes, and P. Tinnefeld, “Linking single-molecule blinking to chromophore structure and redox potentials,” ChemPhysChem13, 931–937 (2012).
[CrossRef]

Belov, V.

J. Fölling, V. Belov, R. Medda, A. Schönle, A. Egner, C. Eggeling, M. Bossi, and S. W. Hell, “Photochromic rhodamines provide nanoscopy with optical sectioning,” Angew. Chem. Int. Ed.46, 6266–6270 (2007).
[CrossRef]

Bennett, B. T.

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods5, 527–529 (2008).
[CrossRef] [PubMed]

Betzig, E.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science313, 1642–1645 (2006).
[CrossRef] [PubMed]

Bewersdorf, J.

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods5, 527–529 (2008).
[CrossRef] [PubMed]

Blosser, T. R.

M. Bates, T. R. Blosser, and X. Zhuang, “Short-range spectroscopic ruler based on a single-molecule optical switch,” Phys. Rev. Lett.94, 108101 (2005).
[CrossRef] [PubMed]

Bonifacino, J. S.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science313, 1642–1645 (2006).
[CrossRef] [PubMed]

Bossi, M.

J. Fölling, V. Belov, R. Medda, A. Schönle, A. Egner, C. Eggeling, M. Bossi, and S. W. Hell, “Photochromic rhodamines provide nanoscopy with optical sectioning,” Angew. Chem. Int. Ed.46, 6266–6270 (2007).
[CrossRef]

Brandenburg, B.

B. Huang, S. A. Jones, B. Brandenburg, and X. Zhuang, “Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution,” Nat. Methods5, 1047–1052 (2008).
[CrossRef] [PubMed]

Brandtzaeg, P.

K. Valnes and P. Brandtzaeg, “Retardation of immunofluorescence fading during microscopy,” J. Histochem. Cytochem.33, 755–761 (1985).
[CrossRef] [PubMed]

Burke, B.

L. Schermelleh, P. M. Carlton, S. Haase, L. Shao, L. Winoto, P. Kner, B. Burke, M. C. Cardoso, D. A. Agard, M. G. L. Gustafsson, H. Leonhardt, and J. W. Sedat, “Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy,” Science320, 1332–1336 (2008).
[CrossRef] [PubMed]

Burnette, D. T.

S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods9, 195–200 (2012).
[CrossRef]

Capone, S.

I. H. Stein, S. Capone, J. H. Smit, F. Baumann, T. Cordes, and P. Tinnefeld, “Linking single-molecule blinking to chromophore structure and redox potentials,” ChemPhysChem13, 931–937 (2012).
[CrossRef]

Cardoso, M. C.

L. Schermelleh, P. M. Carlton, S. Haase, L. Shao, L. Winoto, P. Kner, B. Burke, M. C. Cardoso, D. A. Agard, M. G. L. Gustafsson, H. Leonhardt, and J. W. Sedat, “Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy,” Science320, 1332–1336 (2008).
[CrossRef] [PubMed]

Carlton, P. M.

L. Schermelleh, P. M. Carlton, S. Haase, L. Shao, L. Winoto, P. Kner, B. Burke, M. C. Cardoso, D. A. Agard, M. G. L. Gustafsson, H. Leonhardt, and J. W. Sedat, “Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy,” Science320, 1332–1336 (2008).
[CrossRef] [PubMed]

Chen, K.

G. Dempsey, J. Vaughan, K. Chen, M. Bates, and X. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat. Methods8, 1027–1036 (2011).
[CrossRef] [PubMed]

Chmyrov, A.

J. Widengren, A. Chmyrov, C. Eggeling, P. Löfdahl, and C. A. M. Seidel, “Strategies to improve photostabilities in ultrasensitive fluorescence spectroscopy,” J. Phys. Chem. A111, 429–444 (2007).
[CrossRef] [PubMed]

Colyera, R.

T. Dertinger, R. Colyera, G. Iyer, S. Weiss, and J. Enderlein, “Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI),” Proc. Natl. Acad. Sci. U.S.A.106, 22287–22292 (2009).
[CrossRef] [PubMed]

Cordes, T.

I. H. Stein, S. Capone, J. H. Smit, F. Baumann, T. Cordes, and P. Tinnefeld, “Linking single-molecule blinking to chromophore structure and redox potentials,” ChemPhysChem13, 931–937 (2012).
[CrossRef]

T. Cordes, A. Maiser, C. Steinhauer, L. Schermelleh, and P. Tinnefeld, “Mechanisms and advancement of antifading agents for fluorescence microscopy and single-molecule spectroscopy,” Phys. Chem. Chem. Phys.13, 6699–6709 (2011).
[CrossRef] [PubMed]

J. Vogelsang, T. Cordes, and P. Tinnefeld, “Single-molecule photophysics of oxazines on DNA and its application in a FRET switch,” Photochem. Photobiol. Sci.8, 486–496 (2009).
[CrossRef] [PubMed]

Cox, S.

S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods9, 195–200 (2012).
[CrossRef]

Davidson, M. W.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A.106, 3125–3130 (2009).
[CrossRef] [PubMed]

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science313, 1642–1645 (2006).
[CrossRef] [PubMed]

Dempsey, G.

G. Dempsey, J. Vaughan, K. Chen, M. Bates, and X. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat. Methods8, 1027–1036 (2011).
[CrossRef] [PubMed]

Dempsey, G. T.

G. T. Dempsey, M. Bates, W. E. Kowtoniuk, D. R. Liu, R. Y. Tsien, and X. Zhuang, “Photoswitching mechanism of cyanine dyes,” J. Am. Chem. Soc.131, 18192–18193 (2009).
[CrossRef] [PubMed]

Dertinger, T.

T. Dertinger, R. Colyera, G. Iyer, S. Weiss, and J. Enderlein, “Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI),” Proc. Natl. Acad. Sci. U.S.A.106, 22287–22292 (2009).
[CrossRef] [PubMed]

Eggeling, C.

J. Widengren, A. Chmyrov, C. Eggeling, P. Löfdahl, and C. A. M. Seidel, “Strategies to improve photostabilities in ultrasensitive fluorescence spectroscopy,” J. Phys. Chem. A111, 429–444 (2007).
[CrossRef] [PubMed]

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T. Staudt, M. C. Lang, R. Medda, J. Engelhardt, and S. W. Hell, “‘2,2’-Thiodiethanol: A new water soluble mounting medium for high resolution optical microscopy” Microsc. Res. Tech.70, 1–9 (2006).
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G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A.106, 3125–3130 (2009).
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J. Fölling, V. Belov, R. Medda, A. Schönle, A. Egner, C. Eggeling, M. Bossi, and S. W. Hell, “Photochromic rhodamines provide nanoscopy with optical sectioning,” Angew. Chem. Int. Ed.46, 6266–6270 (2007).
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G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A.106, 3125–3130 (2009).
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S. T. Hess, T. P. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J.91, 4258–4272 (2006).
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S. Lawo, M. Hasegan, G. D. Gupta, and L. Pelletier, “Subdiffraction imaging of centrosomes reveals higher-order organizational features of pericentriolar material,” Nat. Cell. Biol.14, 1148–1158 (2012).
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L. Schermelleh, P. M. Carlton, S. Haase, L. Shao, L. Winoto, P. Kner, B. Burke, M. C. Cardoso, D. A. Agard, M. G. L. Gustafsson, H. Leonhardt, and J. W. Sedat, “Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy,” Science320, 1332–1336 (2008).
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X. Shi, J. Lim, and T. Ha, “Acidification of the oxygen scavenging system in single-molecule fluorescence studies: in situ sensing with a ratiometric dual-emission probe,” Anal. Chem.82, 6132–6138 (2010).
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L. Schermelleh, P. M. Carlton, S. Haase, L. Shao, L. Winoto, P. Kner, B. Burke, M. C. Cardoso, D. A. Agard, M. G. L. Gustafsson, H. Leonhardt, and J. W. Sedat, “Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy,” Science320, 1332–1336 (2008).
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A. Lampe, V. J. Haucke, S. Sigrist, M. Heileman, and J. Schmoranzer, “Multi-colour direct STORM with red emitting carbocyanines,” Biol. Cell104, 229–237 (2012).
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J. Fölling, V. Belov, R. Medda, A. Schönle, A. Egner, C. Eggeling, M. Bossi, and S. W. Hell, “Photochromic rhodamines provide nanoscopy with optical sectioning,” Angew. Chem. Int. Ed.46, 6266–6270 (2007).
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G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A.106, 3125–3130 (2009).
[CrossRef] [PubMed]

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science313, 1642–1645 (2006).
[CrossRef] [PubMed]

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M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods5, 527–529 (2008).
[CrossRef] [PubMed]

S. T. Hess, T. P. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J.91, 4258–4272 (2006).
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S. J. Holden, S. Uphoff, and A.N. Kapanidis, “DAOSTORM: an algorithm for high-density super-resolution microscopy,” Nat. Methods8, 279–280 (2011).
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B. Huang, S. A. Jones, B. Brandenburg, and X. Zhuang, “Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution,” Nat. Methods5, 1047–1052 (2008).
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T. Dertinger, R. Colyera, G. Iyer, S. Weiss, and J. Enderlein, “Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI),” Proc. Natl. Acad. Sci. U.S.A.106, 22287–22292 (2009).
[CrossRef] [PubMed]

Jones, G. E.

S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods9, 195–200 (2012).
[CrossRef]

Jones, S. A.

B. Huang, S. A. Jones, B. Brandenburg, and X. Zhuang, “Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution,” Nat. Methods5, 1047–1052 (2008).
[CrossRef] [PubMed]

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S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods9, 195–200 (2012).
[CrossRef]

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M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods5, 527–529 (2008).
[CrossRef] [PubMed]

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G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A.106, 3125–3130 (2009).
[CrossRef] [PubMed]

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S. J. Holden, S. Uphoff, and A.N. Kapanidis, “DAOSTORM: an algorithm for high-density super-resolution microscopy,” Nat. Methods8, 279–280 (2011).
[CrossRef] [PubMed]

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M. Heilemann, S. van de Linde, M. Schuttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes,” Angew. Chem. Int. Ed.47, 6172–6176 (2008).
[CrossRef]

M. Heilemann, E. Margeat, R. Kasper, M. Sauer, and P. Tinnefeld, “Carbocyanine dyes as efficient reversible single-molecule optical switch,” J. Am. Chem. Soc.127, 3801–3806 (2005).
[CrossRef] [PubMed]

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S. Van De Linde, A. Löschberger, T. Klein, M. Heidbreder, S. Wolter, M. Heilemann, and M. Sauer, “Direct stochastic optical reconstruction microscopy with standard fluorescent probes,” Nat. Protoc.6, 991–1009 (2011).
[CrossRef] [PubMed]

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L. Schermelleh, P. M. Carlton, S. Haase, L. Shao, L. Winoto, P. Kner, B. Burke, M. C. Cardoso, D. A. Agard, M. G. L. Gustafsson, H. Leonhardt, and J. W. Sedat, “Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy,” Science320, 1332–1336 (2008).
[CrossRef] [PubMed]

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G. T. Dempsey, M. Bates, W. E. Kowtoniuk, D. R. Liu, R. Y. Tsien, and X. Zhuang, “Photoswitching mechanism of cyanine dyes,” J. Am. Chem. Soc.131, 18192–18193 (2009).
[CrossRef] [PubMed]

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A. Lampe, V. J. Haucke, S. Sigrist, M. Heileman, and J. Schmoranzer, “Multi-colour direct STORM with red emitting carbocyanines,” Biol. Cell104, 229–237 (2012).
[CrossRef]

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T. Staudt, M. C. Lang, R. Medda, J. Engelhardt, and S. W. Hell, “‘2,2’-Thiodiethanol: A new water soluble mounting medium for high resolution optical microscopy” Microsc. Res. Tech.70, 1–9 (2006).
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S. Lawo, M. Hasegan, G. D. Gupta, and L. Pelletier, “Subdiffraction imaging of centrosomes reveals higher-order organizational features of pericentriolar material,” Nat. Cell. Biol.14, 1148–1158 (2012).
[CrossRef] [PubMed]

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L. Schermelleh, P. M. Carlton, S. Haase, L. Shao, L. Winoto, P. Kner, B. Burke, M. C. Cardoso, D. A. Agard, M. G. L. Gustafsson, H. Leonhardt, and J. W. Sedat, “Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy,” Science320, 1332–1336 (2008).
[CrossRef] [PubMed]

Lessard, M. D.

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods5, 527–529 (2008).
[CrossRef] [PubMed]

Lim, J.

X. Shi, J. Lim, and T. Ha, “Acidification of the oxygen scavenging system in single-molecule fluorescence studies: in situ sensing with a ratiometric dual-emission probe,” Anal. Chem.82, 6132–6138 (2010).
[CrossRef] [PubMed]

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E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science313, 1642–1645 (2006).
[CrossRef] [PubMed]

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S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods9, 195–200 (2012).
[CrossRef]

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A.106, 3125–3130 (2009).
[CrossRef] [PubMed]

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science313, 1642–1645 (2006).
[CrossRef] [PubMed]

Liu, D. R.

G. T. Dempsey, M. Bates, W. E. Kowtoniuk, D. R. Liu, R. Y. Tsien, and X. Zhuang, “Photoswitching mechanism of cyanine dyes,” J. Am. Chem. Soc.131, 18192–18193 (2009).
[CrossRef] [PubMed]

Löfdahl, P.

J. Widengren, A. Chmyrov, C. Eggeling, P. Löfdahl, and C. A. M. Seidel, “Strategies to improve photostabilities in ultrasensitive fluorescence spectroscopy,” J. Phys. Chem. A111, 429–444 (2007).
[CrossRef] [PubMed]

Löschberger, A.

S. Van De Linde, A. Löschberger, T. Klein, M. Heidbreder, S. Wolter, M. Heilemann, and M. Sauer, “Direct stochastic optical reconstruction microscopy with standard fluorescent probes,” Nat. Protoc.6, 991–1009 (2011).
[CrossRef] [PubMed]

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T. Cordes, A. Maiser, C. Steinhauer, L. Schermelleh, and P. Tinnefeld, “Mechanisms and advancement of antifading agents for fluorescence microscopy and single-molecule spectroscopy,” Phys. Chem. Chem. Phys.13, 6699–6709 (2011).
[CrossRef] [PubMed]

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G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A.106, 3125–3130 (2009).
[CrossRef] [PubMed]

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M. Heilemann, E. Margeat, R. Kasper, M. Sauer, and P. Tinnefeld, “Carbocyanine dyes as efficient reversible single-molecule optical switch,” J. Am. Chem. Soc.127, 3801–3806 (2005).
[CrossRef] [PubMed]

Mason, M. D.

S. T. Hess, T. P. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J.91, 4258–4272 (2006).
[CrossRef] [PubMed]

Medda, R.

J. Fölling, V. Belov, R. Medda, A. Schönle, A. Egner, C. Eggeling, M. Bossi, and S. W. Hell, “Photochromic rhodamines provide nanoscopy with optical sectioning,” Angew. Chem. Int. Ed.46, 6266–6270 (2007).
[CrossRef]

T. Staudt, M. C. Lang, R. Medda, J. Engelhardt, and S. W. Hell, “‘2,2’-Thiodiethanol: A new water soluble mounting medium for high resolution optical microscopy” Microsc. Res. Tech.70, 1–9 (2006).
[CrossRef]

Mlodzianoski, M. J.

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods5, 527–529 (2008).
[CrossRef] [PubMed]

Monypenny, J.

S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods9, 195–200 (2012).
[CrossRef]

Mukherjee, A.

M. Heilemann, S. van de Linde, M. Schuttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes,” Angew. Chem. Int. Ed.47, 6172–6176 (2008).
[CrossRef]

Nagpure, B. S.

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods5, 527–529 (2008).
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E. Nogales and G. Alushin, “4.6 Tubulin and microtubule structure: mechanistic insights into dynamic instability and its biological relevance,” in Comprehensive Biophysics, E. H. Egelman, ed. (Elsevier, 2012), pp. 72–92.
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Olenych, S.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science313, 1642–1645 (2006).
[CrossRef] [PubMed]

Patterson, G. H.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science313, 1642–1645 (2006).
[CrossRef] [PubMed]

Pelletier, L.

S. Lawo, M. Hasegan, G. D. Gupta, and L. Pelletier, “Subdiffraction imaging of centrosomes reveals higher-order organizational features of pericentriolar material,” Nat. Cell. Biol.14, 1148–1158 (2012).
[CrossRef] [PubMed]

Rosten, E.

S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods9, 195–200 (2012).
[CrossRef]

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M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods3, 793–796 (2006).
[CrossRef] [PubMed]

Sauer, M.

S. Van De Linde, A. Löschberger, T. Klein, M. Heidbreder, S. Wolter, M. Heilemann, and M. Sauer, “Direct stochastic optical reconstruction microscopy with standard fluorescent probes,” Nat. Protoc.6, 991–1009 (2011).
[CrossRef] [PubMed]

M. Heilemann, S. van de Linde, M. Schuttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes,” Angew. Chem. Int. Ed.47, 6172–6176 (2008).
[CrossRef]

M. Heilemann, E. Margeat, R. Kasper, M. Sauer, and P. Tinnefeld, “Carbocyanine dyes as efficient reversible single-molecule optical switch,” J. Am. Chem. Soc.127, 3801–3806 (2005).
[CrossRef] [PubMed]

Schermelleh, L.

T. Cordes, A. Maiser, C. Steinhauer, L. Schermelleh, and P. Tinnefeld, “Mechanisms and advancement of antifading agents for fluorescence microscopy and single-molecule spectroscopy,” Phys. Chem. Chem. Phys.13, 6699–6709 (2011).
[CrossRef] [PubMed]

L. Schermelleh, P. M. Carlton, S. Haase, L. Shao, L. Winoto, P. Kner, B. Burke, M. C. Cardoso, D. A. Agard, M. G. L. Gustafsson, H. Leonhardt, and J. W. Sedat, “Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy,” Science320, 1332–1336 (2008).
[CrossRef] [PubMed]

Schmoranzer, J.

A. Lampe, V. J. Haucke, S. Sigrist, M. Heileman, and J. Schmoranzer, “Multi-colour direct STORM with red emitting carbocyanines,” Biol. Cell104, 229–237 (2012).
[CrossRef]

Schönle, A.

J. Fölling, V. Belov, R. Medda, A. Schönle, A. Egner, C. Eggeling, M. Bossi, and S. W. Hell, “Photochromic rhodamines provide nanoscopy with optical sectioning,” Angew. Chem. Int. Ed.46, 6266–6270 (2007).
[CrossRef]

Schuttpelz, M.

M. Heilemann, S. van de Linde, M. Schuttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes,” Angew. Chem. Int. Ed.47, 6172–6176 (2008).
[CrossRef]

Sedat, J. W.

L. Schermelleh, P. M. Carlton, S. Haase, L. Shao, L. Winoto, P. Kner, B. Burke, M. C. Cardoso, D. A. Agard, M. G. L. Gustafsson, H. Leonhardt, and J. W. Sedat, “Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy,” Science320, 1332–1336 (2008).
[CrossRef] [PubMed]

Seefeldt, B.

M. Heilemann, S. van de Linde, M. Schuttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes,” Angew. Chem. Int. Ed.47, 6172–6176 (2008).
[CrossRef]

Seidel, C. A. M.

J. Widengren, A. Chmyrov, C. Eggeling, P. Löfdahl, and C. A. M. Seidel, “Strategies to improve photostabilities in ultrasensitive fluorescence spectroscopy,” J. Phys. Chem. A111, 429–444 (2007).
[CrossRef] [PubMed]

Shao, L.

L. Schermelleh, P. M. Carlton, S. Haase, L. Shao, L. Winoto, P. Kner, B. Burke, M. C. Cardoso, D. A. Agard, M. G. L. Gustafsson, H. Leonhardt, and J. W. Sedat, “Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy,” Science320, 1332–1336 (2008).
[CrossRef] [PubMed]

Shi, X.

X. Shi, J. Lim, and T. Ha, “Acidification of the oxygen scavenging system in single-molecule fluorescence studies: in situ sensing with a ratiometric dual-emission probe,” Anal. Chem.82, 6132–6138 (2010).
[CrossRef] [PubMed]

Shtengel, G.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A.106, 3125–3130 (2009).
[CrossRef] [PubMed]

Sigrist, S.

A. Lampe, V. J. Haucke, S. Sigrist, M. Heileman, and J. Schmoranzer, “Multi-colour direct STORM with red emitting carbocyanines,” Biol. Cell104, 229–237 (2012).
[CrossRef]

Smit, J. H.

I. H. Stein, S. Capone, J. H. Smit, F. Baumann, T. Cordes, and P. Tinnefeld, “Linking single-molecule blinking to chromophore structure and redox potentials,” ChemPhysChem13, 931–937 (2012).
[CrossRef]

Sougrat, R.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A.106, 3125–3130 (2009).
[CrossRef] [PubMed]

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science313, 1642–1645 (2006).
[CrossRef] [PubMed]

Staudt, T.

T. Staudt, M. C. Lang, R. Medda, J. Engelhardt, and S. W. Hell, “‘2,2’-Thiodiethanol: A new water soluble mounting medium for high resolution optical microscopy” Microsc. Res. Tech.70, 1–9 (2006).
[CrossRef]

Stein, I. H.

I. H. Stein, S. Capone, J. H. Smit, F. Baumann, T. Cordes, and P. Tinnefeld, “Linking single-molecule blinking to chromophore structure and redox potentials,” ChemPhysChem13, 931–937 (2012).
[CrossRef]

Steinhauer, C.

T. Cordes, A. Maiser, C. Steinhauer, L. Schermelleh, and P. Tinnefeld, “Mechanisms and advancement of antifading agents for fluorescence microscopy and single-molecule spectroscopy,” Phys. Chem. Chem. Phys.13, 6699–6709 (2011).
[CrossRef] [PubMed]

C. Steinhauer, C. Forthmann, J. Vogelsang, and P. Tinnefeld, “Superresolution microscopy on the basis of engineered dark states,” J. Am. Chem. Soc.130, 16840–16841 (2008).
[CrossRef] [PubMed]

Thompson, R. E.

R. E. Thompson, D. R. Larson, and W. W. Webb, “Precise nanometer localization analysis for individual fluorescent probes,” Biophys. J.82, 2775–2783 (2002).
[CrossRef] [PubMed]

Tinnefeld, P.

I. H. Stein, S. Capone, J. H. Smit, F. Baumann, T. Cordes, and P. Tinnefeld, “Linking single-molecule blinking to chromophore structure and redox potentials,” ChemPhysChem13, 931–937 (2012).
[CrossRef]

T. Cordes, A. Maiser, C. Steinhauer, L. Schermelleh, and P. Tinnefeld, “Mechanisms and advancement of antifading agents for fluorescence microscopy and single-molecule spectroscopy,” Phys. Chem. Chem. Phys.13, 6699–6709 (2011).
[CrossRef] [PubMed]

J. Vogelsang, T. Cordes, and P. Tinnefeld, “Single-molecule photophysics of oxazines on DNA and its application in a FRET switch,” Photochem. Photobiol. Sci.8, 486–496 (2009).
[CrossRef] [PubMed]

M. Heilemann, S. van de Linde, M. Schuttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes,” Angew. Chem. Int. Ed.47, 6172–6176 (2008).
[CrossRef]

C. Steinhauer, C. Forthmann, J. Vogelsang, and P. Tinnefeld, “Superresolution microscopy on the basis of engineered dark states,” J. Am. Chem. Soc.130, 16840–16841 (2008).
[CrossRef] [PubMed]

M. Heilemann, E. Margeat, R. Kasper, M. Sauer, and P. Tinnefeld, “Carbocyanine dyes as efficient reversible single-molecule optical switch,” J. Am. Chem. Soc.127, 3801–3806 (2005).
[CrossRef] [PubMed]

Tsien, R. Y.

G. T. Dempsey, M. Bates, W. E. Kowtoniuk, D. R. Liu, R. Y. Tsien, and X. Zhuang, “Photoswitching mechanism of cyanine dyes,” J. Am. Chem. Soc.131, 18192–18193 (2009).
[CrossRef] [PubMed]

Uphoff, S.

S. J. Holden, S. Uphoff, and A.N. Kapanidis, “DAOSTORM: an algorithm for high-density super-resolution microscopy,” Nat. Methods8, 279–280 (2011).
[CrossRef] [PubMed]

Valnes, K.

K. Valnes and P. Brandtzaeg, “Retardation of immunofluorescence fading during microscopy,” J. Histochem. Cytochem.33, 755–761 (1985).
[CrossRef] [PubMed]

Van De Linde, S.

S. Van De Linde, A. Löschberger, T. Klein, M. Heidbreder, S. Wolter, M. Heilemann, and M. Sauer, “Direct stochastic optical reconstruction microscopy with standard fluorescent probes,” Nat. Protoc.6, 991–1009 (2011).
[CrossRef] [PubMed]

M. Heilemann, S. van de Linde, M. Schuttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes,” Angew. Chem. Int. Ed.47, 6172–6176 (2008).
[CrossRef]

Vaughan, J.

G. Dempsey, J. Vaughan, K. Chen, M. Bates, and X. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat. Methods8, 1027–1036 (2011).
[CrossRef] [PubMed]

Vogelsang, J.

J. Vogelsang, T. Cordes, and P. Tinnefeld, “Single-molecule photophysics of oxazines on DNA and its application in a FRET switch,” Photochem. Photobiol. Sci.8, 486–496 (2009).
[CrossRef] [PubMed]

C. Steinhauer, C. Forthmann, J. Vogelsang, and P. Tinnefeld, “Superresolution microscopy on the basis of engineered dark states,” J. Am. Chem. Soc.130, 16840–16841 (2008).
[CrossRef] [PubMed]

Wang, W.

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science319, 810–813 (2008).
[CrossRef] [PubMed]

Waterman, C. M.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A.106, 3125–3130 (2009).
[CrossRef] [PubMed]

Webb, W. W.

R. E. Thompson, D. R. Larson, and W. W. Webb, “Precise nanometer localization analysis for individual fluorescent probes,” Biophys. J.82, 2775–2783 (2002).
[CrossRef] [PubMed]

Weiss, S.

T. Dertinger, R. Colyera, G. Iyer, S. Weiss, and J. Enderlein, “Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI),” Proc. Natl. Acad. Sci. U.S.A.106, 22287–22292 (2009).
[CrossRef] [PubMed]

Widengren, J.

J. Widengren, A. Chmyrov, C. Eggeling, P. Löfdahl, and C. A. M. Seidel, “Strategies to improve photostabilities in ultrasensitive fluorescence spectroscopy,” J. Phys. Chem. A111, 429–444 (2007).
[CrossRef] [PubMed]

Winoto, L.

L. Schermelleh, P. M. Carlton, S. Haase, L. Shao, L. Winoto, P. Kner, B. Burke, M. C. Cardoso, D. A. Agard, M. G. L. Gustafsson, H. Leonhardt, and J. W. Sedat, “Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy,” Science320, 1332–1336 (2008).
[CrossRef] [PubMed]

Wolter, S.

S. Van De Linde, A. Löschberger, T. Klein, M. Heidbreder, S. Wolter, M. Heilemann, and M. Sauer, “Direct stochastic optical reconstruction microscopy with standard fluorescent probes,” Nat. Protoc.6, 991–1009 (2011).
[CrossRef] [PubMed]

Zhuang, X.

G. Dempsey, J. Vaughan, K. Chen, M. Bates, and X. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat. Methods8, 1027–1036 (2011).
[CrossRef] [PubMed]

G. T. Dempsey, M. Bates, W. E. Kowtoniuk, D. R. Liu, R. Y. Tsien, and X. Zhuang, “Photoswitching mechanism of cyanine dyes,” J. Am. Chem. Soc.131, 18192–18193 (2009).
[CrossRef] [PubMed]

B. Huang, S. A. Jones, B. Brandenburg, and X. Zhuang, “Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution,” Nat. Methods5, 1047–1052 (2008).
[CrossRef] [PubMed]

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science319, 810–813 (2008).
[CrossRef] [PubMed]

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods3, 793–796 (2006).
[CrossRef] [PubMed]

M. Bates, T. R. Blosser, and X. Zhuang, “Short-range spectroscopic ruler based on a single-molecule optical switch,” Phys. Rev. Lett.94, 108101 (2005).
[CrossRef] [PubMed]

Anal. Chem. (1)

X. Shi, J. Lim, and T. Ha, “Acidification of the oxygen scavenging system in single-molecule fluorescence studies: in situ sensing with a ratiometric dual-emission probe,” Anal. Chem.82, 6132–6138 (2010).
[CrossRef] [PubMed]

Angew. Chem. Int. Ed. (2)

M. Heilemann, S. van de Linde, M. Schuttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes,” Angew. Chem. Int. Ed.47, 6172–6176 (2008).
[CrossRef]

J. Fölling, V. Belov, R. Medda, A. Schönle, A. Egner, C. Eggeling, M. Bossi, and S. W. Hell, “Photochromic rhodamines provide nanoscopy with optical sectioning,” Angew. Chem. Int. Ed.46, 6266–6270 (2007).
[CrossRef]

Biol. Cell (1)

A. Lampe, V. J. Haucke, S. Sigrist, M. Heileman, and J. Schmoranzer, “Multi-colour direct STORM with red emitting carbocyanines,” Biol. Cell104, 229–237 (2012).
[CrossRef]

Biophys. J. (2)

R. E. Thompson, D. R. Larson, and W. W. Webb, “Precise nanometer localization analysis for individual fluorescent probes,” Biophys. J.82, 2775–2783 (2002).
[CrossRef] [PubMed]

S. T. Hess, T. P. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J.91, 4258–4272 (2006).
[CrossRef] [PubMed]

ChemPhysChem (1)

I. H. Stein, S. Capone, J. H. Smit, F. Baumann, T. Cordes, and P. Tinnefeld, “Linking single-molecule blinking to chromophore structure and redox potentials,” ChemPhysChem13, 931–937 (2012).
[CrossRef]

J. Am. Chem. Soc. (3)

M. Heilemann, E. Margeat, R. Kasper, M. Sauer, and P. Tinnefeld, “Carbocyanine dyes as efficient reversible single-molecule optical switch,” J. Am. Chem. Soc.127, 3801–3806 (2005).
[CrossRef] [PubMed]

G. T. Dempsey, M. Bates, W. E. Kowtoniuk, D. R. Liu, R. Y. Tsien, and X. Zhuang, “Photoswitching mechanism of cyanine dyes,” J. Am. Chem. Soc.131, 18192–18193 (2009).
[CrossRef] [PubMed]

C. Steinhauer, C. Forthmann, J. Vogelsang, and P. Tinnefeld, “Superresolution microscopy on the basis of engineered dark states,” J. Am. Chem. Soc.130, 16840–16841 (2008).
[CrossRef] [PubMed]

J. Histochem. Cytochem. (1)

K. Valnes and P. Brandtzaeg, “Retardation of immunofluorescence fading during microscopy,” J. Histochem. Cytochem.33, 755–761 (1985).
[CrossRef] [PubMed]

J. Phys. Chem. A (1)

J. Widengren, A. Chmyrov, C. Eggeling, P. Löfdahl, and C. A. M. Seidel, “Strategies to improve photostabilities in ultrasensitive fluorescence spectroscopy,” J. Phys. Chem. A111, 429–444 (2007).
[CrossRef] [PubMed]

Microsc. Res. Tech. (1)

T. Staudt, M. C. Lang, R. Medda, J. Engelhardt, and S. W. Hell, “‘2,2’-Thiodiethanol: A new water soluble mounting medium for high resolution optical microscopy” Microsc. Res. Tech.70, 1–9 (2006).
[CrossRef]

Nat. Cell. Biol. (1)

S. Lawo, M. Hasegan, G. D. Gupta, and L. Pelletier, “Subdiffraction imaging of centrosomes reveals higher-order organizational features of pericentriolar material,” Nat. Cell. Biol.14, 1148–1158 (2012).
[CrossRef] [PubMed]

Nat. Methods (6)

G. Dempsey, J. Vaughan, K. Chen, M. Bates, and X. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat. Methods8, 1027–1036 (2011).
[CrossRef] [PubMed]

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods5, 527–529 (2008).
[CrossRef] [PubMed]

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods3, 793–796 (2006).
[CrossRef] [PubMed]

B. Huang, S. A. Jones, B. Brandenburg, and X. Zhuang, “Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution,” Nat. Methods5, 1047–1052 (2008).
[CrossRef] [PubMed]

S. J. Holden, S. Uphoff, and A.N. Kapanidis, “DAOSTORM: an algorithm for high-density super-resolution microscopy,” Nat. Methods8, 279–280 (2011).
[CrossRef] [PubMed]

S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods9, 195–200 (2012).
[CrossRef]

Nat. Protoc. (1)

S. Van De Linde, A. Löschberger, T. Klein, M. Heidbreder, S. Wolter, M. Heilemann, and M. Sauer, “Direct stochastic optical reconstruction microscopy with standard fluorescent probes,” Nat. Protoc.6, 991–1009 (2011).
[CrossRef] [PubMed]

Nat. Rev. Mol. Cell Biol. (1)

P. Gönczy, “Towards a molecular architecture of centriole assembly,” Nat. Rev. Mol. Cell Biol.13, 425–435 (2012).
[CrossRef] [PubMed]

Photochem. Photobiol. Sci. (1)

J. Vogelsang, T. Cordes, and P. Tinnefeld, “Single-molecule photophysics of oxazines on DNA and its application in a FRET switch,” Photochem. Photobiol. Sci.8, 486–496 (2009).
[CrossRef] [PubMed]

Phys. Chem. Chem. Phys. (1)

T. Cordes, A. Maiser, C. Steinhauer, L. Schermelleh, and P. Tinnefeld, “Mechanisms and advancement of antifading agents for fluorescence microscopy and single-molecule spectroscopy,” Phys. Chem. Chem. Phys.13, 6699–6709 (2011).
[CrossRef] [PubMed]

Phys. Rev. Lett. (1)

M. Bates, T. R. Blosser, and X. Zhuang, “Short-range spectroscopic ruler based on a single-molecule optical switch,” Phys. Rev. Lett.94, 108101 (2005).
[CrossRef] [PubMed]

Proc. Natl. Acad. Sci. U.S.A. (2)

T. Dertinger, R. Colyera, G. Iyer, S. Weiss, and J. Enderlein, “Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI),” Proc. Natl. Acad. Sci. U.S.A.106, 22287–22292 (2009).
[CrossRef] [PubMed]

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A.106, 3125–3130 (2009).
[CrossRef] [PubMed]

Science (3)

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science313, 1642–1645 (2006).
[CrossRef] [PubMed]

L. Schermelleh, P. M. Carlton, S. Haase, L. Shao, L. Winoto, P. Kner, B. Burke, M. C. Cardoso, D. A. Agard, M. G. L. Gustafsson, H. Leonhardt, and J. W. Sedat, “Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy,” Science320, 1332–1336 (2008).
[CrossRef] [PubMed]

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science319, 810–813 (2008).
[CrossRef] [PubMed]

Other (1)

E. Nogales and G. Alushin, “4.6 Tubulin and microtubule structure: mechanistic insights into dynamic instability and its biological relevance,” in Comprehensive Biophysics, E. H. Egelman, ed. (Elsevier, 2012), pp. 72–92.
[CrossRef]

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Figures (9)

Fig. 1
Fig. 1

STORM imaging of microtubules (see section 2.2 for more details) in Vectashield. (A): Widefield image (B): Single frame, (C1): Reconstructed STORM image, with blow-up on the ROI in (C2). scale-bar = 5 μm for (A),(B),(C1) and 1 μm for C2.

Fig. 2
Fig. 2

Quantifying the quality of Vectashield as a STORM buffer for Alexa-647: (A) photon count distribution per frame (blue) and per molecule (red), obtained by grouping consecutive frame localizations and (B) standard deviation of multiple localizations (see section 2.3 for grouping details), with mean values displayed in the top right corner (C) Density of molecules as a function of number of recorded frames, averaged over three measurements. The error bar indicates the standard deviation. (D) STORM image of microtubule, on which the hollowness of the structure can be resolved, as quantified in the profile taken over the 200 nm yellow-boxed region with ≈ 35 nm between the two peaks, consistent with a 25 mm structure broadened by the antibodies.

Fig. 3
Fig. 3

(A) Absorption spectrum of Vectashield, as well as normalized emission spectra measured at 3 different wavelengths: 400 nm (B), 560 nm (C) and 630 nm (D) with normalization factor indicated in the top right corner.

Fig. 4
Fig. 4

STORM imaging of Alexa-647 stained microtubules in a Vectashield/TRIS-Glycerol mixture: (A) 50% Vectashield and (B) 25% Vectashield. The different panels represent: (1) STORM image reconstructed from 15.000 frames, scale-bar = 500 nm (2) photon count distribution per frame and per molecule, averaged over three data-sets, and (3) standard deviation of multiple localizations giving a measure of the frame localization precision.

Fig. 5
Fig. 5

Statistics on STORM imaging performed in 25% Vectashield - 75% TRIS-Glycerol in which were added 1% NPG (w/v) (A), 20 mM DABCO (B), and 10 mM Lipoic Acid (C). The different panels represent: (1) photon count distribution per frame and per molecule, averaged over three datasets, (2) standard deviation of multiple localizations giving a measure of the frame localization precision, and (3) Density of molecules as a function of number of recorded frames, averaged over three measurements, with error bars indicating the standard deviation.

Fig. 6
Fig. 6

3D STORM of Alexa-647-labeled microtubules in Vectashield: (A) Imaging performed in 25% Vectashield-75 % TRIS-Glycerol, scale-bar = 5 μm. (B1&2): axial profile taken from the two regions delimited in A (yellow for (B1), showing a single microtubule; red for (B2) showing two well-resolved microtubules crossing at a distance of ≈ 160 nm).

Fig. 7
Fig. 7

(A) Index matching with Vectashield: Optical index as a function of Vectashield concentration starting from PBS (red) or TDE (blue), and imaging performed at n = 1.5 (adapted to oil objectives) and n=1.4 (adapted to glycerol objectives) (B–D) STORM imaging of microtubules immunostained with Alexa-647 for the 25% Vectashield-75% TDE buffer and 50% Vectashield - 50% PBS buffer respectively, scale-bar = 500 nm (C–E): photon count distribution per frame and per molecule, averaged over three datasets for the 25% Vectashield-75% TDE buffer and 50% Vectashield - 50% PBS buffer respectively.

Fig. 8
Fig. 8

(A) STORM image of CEP-152 stained with Cy3 using a buffer 40% Vectashield + 1% NPG + 20 mM DABCO, which improves the quality of Cy3 blinking. Scale-bar = 500 nm (B) Radial intensity distribution measured from the yellow ROI defined in (A), and Lorentzian fit showing a peak at r = 143 nm.

Fig. 9
Fig. 9

STORM images obtained with the other working dyes (A) Alexa-555 in 20% Vectashield-80% TRIS-Glycerol (B) Cy-5 (C) CF-647 (D) Alexa-700, all in pure Vec-tashield. scale-bar = 5 μm.

Tables (1)

Tables Icon

Table 1 Screening of Other Dyes in Pure Vectashield (Except When Explicitly Stated) Performed by Imaging Antibody Stained-Microtubules and Assessing the Quality of the Images Obtained*

Equations (2)

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w x ( z ) = w 0 * 1 + ( ( x c ) / d ) 2 + A ( ( x c ) / d ) 3 + B ( ( x c ) / d ) 4
M ( z ) = ( w x m w x ( z ) ) 2 + ( w y m w y ( z ) ) 2

Metrics