Abstract

Spectroscopic single-molecule localization microscopy (sSMLM) captures the full emission spectra of individual molecules while simultaneously localizing their spatial locations at a precision greatly exceeding the optical diffraction limit. To achieve this, sSMLM uses a dispersive optical component to separate the emitted photons into dedicated spatial and spectral imaging channels for simultaneous acquisition. While adding a cylindrical lens in the spatial imaging channel enabled three-dimensional (3D) imaging in sSMLM, the inherent astigmatism leads to technical hurdles in spectral calibration and nonuniform lateral resolution at different depths. We found that implementing the biplane method based on the already established spatial and spectral imaging channels offers a much more attractive solution for 3D sSMLM. It allows for more efficient use of the limited photon budget and provides homogeneous lateral resolution compared with the astigmatism-based method using a cylindrical lens. Here we report 3D biplane sSMLM and demonstrate its multi-color 3D imaging capability by imaging microtubules and mitochondria in fixed COS-7 cells immunostained with Alexa Fluor 647 and CF 660C dyes, respectively. We showed a lateral localization precision of 20 nm at an average photon count of 550, a spectral precision of 4 nm at an average photon count of 1250, and an axial localization resolution of 50 nm.

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

Full Article  |  PDF Article

Corrections

Ki-Hee Song, Yang Zhang, Gaoxiang Wang, Cheng Sun, and Hao F. Zhang, "Three-dimensional biplane spectroscopic single-molecule localization microscopy: erratum," Optica 6, 1374-1374 (2019)
https://www.osapublishing.org/optica/abstract.cfm?uri=optica-6-10-1374

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References

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    [Crossref]
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    [Crossref]
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    [Crossref]
  23. S. R. P. Pavani, M. A. Thompson, J. S. Biteen, S. J. Lord, N. Liu, R. J. Twieg, R. Piestun, and W. E. Moerner, “Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function,” Proc. Natl. Acad. Sci. USA 106, 2995–2999 (2009).
    [Crossref]
  24. G. Grover, K. DeLuca, S. Quirin, J. DeLuca, and R. Piestun, “Super-resolution photon-efficient imaging by nanometric double-helix point spread function localization of emitters (SPINDLE),” Opt. Express 20, 26681–26695 (2012).
    [Crossref]
  25. S. Quirin, S. R. Pavani, and R. Piestun, “Optimal 3D single-molecule localization for superresolution microscopy with aberrations and engineered point spread functions,” Proc. Natl. Acad. Sci. USA 109, 675–679 (2012).
    [Crossref]
  26. S. Jia, J. C. Vaughan, and X. Zhuang, “Isotropic 3D super-resolution imaging with a self-bending point spread function,” Nat. Photonics 8, 302–306 (2014).
    [Crossref]
  27. A. Aristov, B. Lelandais, E. Rensen, and C. Zimmer, “ZOLA-3D allows flexible 3D localization microscopy over an adjustable axial range,” Nat. Commun. 9, 2409 (2018).
    [Crossref]
  28. M. J. Mlodzianoski, P. J. Cheng-Hathaway, S. M. Bemiller, T. J. McCray, S. Liu, D. A. Miller, B. T. Lamb, G. E. Landreth, and F. Huang, “Active PSF shaping and adaptive optics enable volumetric localization microscopy through brain sections,” Nat. Methods 15, 583–586(2018).
    [Crossref]
  29. C. Smith, M. Huisman, M. Siemons, D. Grünwald, and S. Stallinga, “Simultaneous measurement of emission color and 3D position of single molecules,” Opt. Express 24, 4996–5013 (2016).
    [Crossref]
  30. K. Song, B. Dong, C. Sun, and H. F. Zhang, “Theoretical analysis of spectral precision in spectroscopic single-molecule localization microscopy,” Rev. Sci. Instrum. 89, 123703 (2018).
    [Crossref]
  31. M. Ovesny, P. Krizek, J. Borkovec, Z. Svindrych, and G. M. Hagen, “ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging,” Bioinformatics 30, 2389–2390 (2014).
    [Crossref]
  32. G. T. Dempsey, J. C. Vaughan, K. H. Chen, M. Bates, and X. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat. Methods 8, 1027–1036 (2011).
    [Crossref]

2019 (1)

2018 (7)

A. Aristov, B. Lelandais, E. Rensen, and C. Zimmer, “ZOLA-3D allows flexible 3D localization microscopy over an adjustable axial range,” Nat. Commun. 9, 2409 (2018).
[Crossref]

M. J. Mlodzianoski, P. J. Cheng-Hathaway, S. M. Bemiller, T. J. McCray, S. Liu, D. A. Miller, B. T. Lamb, G. E. Landreth, and F. Huang, “Active PSF shaping and adaptive optics enable volumetric localization microscopy through brain sections,” Nat. Methods 15, 583–586(2018).
[Crossref]

K. Song, B. Dong, C. Sun, and H. F. Zhang, “Theoretical analysis of spectral precision in spectroscopic single-molecule localization microscopy,” Rev. Sci. Instrum. 89, 123703 (2018).
[Crossref]

J. L. Davis, B. Dong, C. Sun, and H. F. Zhang, “Method to identify and minimize artifacts induced by fluorescent impurities in single-molecule localization microscopy,” J. Biomed. Opt. 23, 1–14 (2018).
[Crossref]

L. Xiang, M. Wojcik, S. J. Kenny, R. Yan, S. Moon, W. Li, and K. Xu, “Optical characterization of surface adlayers and their compositional demixing at the nanoscale,” Nat. Commun. 9, 1435 (2018).
[Crossref]

T. Huang, C. Phelps, J. Wang, L. J. Lin, A. Bittel, Z. Scott, S. Jacques, S. L. Gibbs, J. W. Gray, and X. Nan, “Simultaneous multicolor single-molecule tracking with single-laser excitation via spectral imaging,” Biophys. J. 114, 301–310 (2018).
[Crossref]

Y. Zhang, K.-H. Song, S. Tang, L. Ravelo, J. Cusido, C. Sun, H. F. Zhang, and F. M. Raymo, “Far-red photoactivatable BODIPYs for the super-resolution imaging of live cells,” J. Am. Chem. Soc. 140, 12741–12745 (2018).
[Crossref]

2017 (3)

B. Dong, B. T. Soetikno, X. Chen, V. Backman, C. Sun, and H. F. Zhang, “Parallel three-dimensional tracking of quantum rods using polarization-sensitive spectroscopic photon localization microscopy,” ACS Photon. 4, 1747–1752 (2017).
[Crossref]

D. Kim, Z. Zhang, and K. Xu, “Spectrally resolved super-resolution microscopy unveils multipath reaction pathways of single spiropyran molecules,” J. Am. Chem. Soc. 139, 9447–9450 (2017).
[Crossref]

S. Moon, R. Yan, S. J. Kenny, Y. Shyu, L. Xiang, W. Li, and K. Xu, “Spectrally resolved, functional super-resolution microscopy reveals nanoscale compositional heterogeneity in live-cell membranes,” J. Am. Chem. Soc. 139, 10944–10947 (2017).
[Crossref]

2016 (4)

B. Dong, L. Almassalha, B. E. Urban, T. Q. Nguyen, S. Khuon, T. L. Chew, V. Backman, C. Sun, and H. F. Zhang, “Super-resolution spectroscopic microscopy via photon localization,” Nat. Commun. 7, 12290 (2016).
[Crossref]

M. J. Mlodzianoski, N. M. Curthoys, M. S. Gunewardene, S. Carter, and S. T. Hess, “Super-resolution imaging of molecular emission spectra and single molecule spectral fluctuations,” PLoS One 11, e0147506 (2016).
[Crossref]

M. N. Bongiovanni, J. Godet, M. H. Horrocks, L. Tosatto, A. R. Carr, D. C. Wirthensohn, R. T. Ranasinghe, J. E. Lee, A. Ponjavic, J. V. Fritz, C. M. Dobson, D. Klenerman, and S. F. Lee, “Multi-dimensional super-resolution imaging enables surface hydrophobicity mapping,” Nat. Commun. 7, 13544 (2016).
[Crossref]

C. Smith, M. Huisman, M. Siemons, D. Grünwald, and S. Stallinga, “Simultaneous measurement of emission color and 3D position of single molecules,” Opt. Express 24, 4996–5013 (2016).
[Crossref]

2015 (2)

C. M. Winterflood, E. Platonova, D. Albrecht, and H. Ewers, “Dual-color 3D superresolution microscopy by combined spectral-demixing and biplane imaging,” Biophys. J. 109, 3–6 (2015).
[Crossref]

Z. Zhang, S. J. Kenny, M. Hauser, W. Li, and K. Xu, “Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-resolution microscopy,” Nat. Methods 12, 935–938 (2015).
[Crossref]

2014 (3)

J. Broeken, B. Rieger, and S. Stallinga, “Simultaneous measurement of position and color of single fluorescent emitters using diffractive optics,” Opt. Lett. 39, 3352–3355 (2014).
[Crossref]

M. Ovesny, P. Krizek, J. Borkovec, Z. Svindrych, and G. M. Hagen, “ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging,” Bioinformatics 30, 2389–2390 (2014).
[Crossref]

S. Jia, J. C. Vaughan, and X. Zhuang, “Isotropic 3D super-resolution imaging with a self-bending point spread function,” Nat. Photonics 8, 302–306 (2014).
[Crossref]

2012 (3)

S. Quirin, S. R. Pavani, and R. Piestun, “Optimal 3D single-molecule localization for superresolution microscopy with aberrations and engineered point spread functions,” Proc. Natl. Acad. Sci. USA 109, 675–679 (2012).
[Crossref]

K. Xu, H. P. Babcock, and X. Zhuang, “Dual-objective STORM reveals three-dimensional filament organization in the actin cytoskeleton,” Nat. Methods 9, 185–188 (2012).
[Crossref]

G. Grover, K. DeLuca, S. Quirin, J. DeLuca, and R. Piestun, “Super-resolution photon-efficient imaging by nanometric double-helix point spread function localization of emitters (SPINDLE),” Opt. Express 20, 26681–26695 (2012).
[Crossref]

2011 (2)

G. T. Dempsey, J. C. Vaughan, K. H. Chen, M. Bates, and X. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat. Methods 8, 1027–1036 (2011).
[Crossref]

D. Aquino, A. Schonle, C. Geisler, C. V. Middendorff, C. A. Wurm, Y. Okamura, T. Lang, S. W. Hell, and A. Egner, “Two-color nanoscopy of three-dimensional volumes by 4Pi detection of stochastically switched fluorophores,” Nat. Methods 8, 353–359 (2011).
[Crossref]

2009 (3)

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. USA 106, 3125–3130 (2009).
[Crossref]

M. J. Mlodzianoski, M. F. Juette, G. L. Beane, and J. Bewersdorf, “Experimental characterization of 3D localization techniques for particle-tracking and super-resolution microscopy,” Opt. Express 17, 8264–8277 (2009).
[Crossref]

S. R. P. Pavani, M. A. Thompson, J. S. Biteen, S. J. Lord, N. Liu, R. J. Twieg, R. Piestun, and W. E. Moerner, “Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function,” Proc. Natl. Acad. Sci. USA 106, 2995–2999 (2009).
[Crossref]

2008 (4)

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional Super-resolution Imaging by Stochastic Optical Reconstruction Microscopy,” Science 319, 810–813 (2008).
[Crossref]

B. Huang, S. A. Jones, B. Brandenburg, and X. Zhuang, “Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution,” Nat. Methods 5, 1047–1052 (2008).
[Crossref]

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. Methods 5, 527–529 (2008).
[Crossref]

S. Ram, P. Prabhat, J. Chao, E. S. Ward, and R. J. Ober, “High accuracy 3D quantum dot tracking with multifocal plane microscopy for the study of fast intracellular dynamics in live cells,” Biophys. J 95, 6025–6043 (2008).
[Crossref]

Albrecht, D.

C. M. Winterflood, E. Platonova, D. Albrecht, and H. Ewers, “Dual-color 3D superresolution microscopy by combined spectral-demixing and biplane imaging,” Biophys. J. 109, 3–6 (2015).
[Crossref]

Almassalha, L.

B. Dong, L. Almassalha, B. E. Urban, T. Q. Nguyen, S. Khuon, T. L. Chew, V. Backman, C. Sun, and H. F. Zhang, “Super-resolution spectroscopic microscopy via photon localization,” Nat. Commun. 7, 12290 (2016).
[Crossref]

Aquino, D.

D. Aquino, A. Schonle, C. Geisler, C. V. Middendorff, C. A. Wurm, Y. Okamura, T. Lang, S. W. Hell, and A. Egner, “Two-color nanoscopy of three-dimensional volumes by 4Pi detection of stochastically switched fluorophores,” Nat. Methods 8, 353–359 (2011).
[Crossref]

Aristov, A.

A. Aristov, B. Lelandais, E. Rensen, and C. Zimmer, “ZOLA-3D allows flexible 3D localization microscopy over an adjustable axial range,” Nat. Commun. 9, 2409 (2018).
[Crossref]

Babcock, H. P.

K. Xu, H. P. Babcock, and X. Zhuang, “Dual-objective STORM reveals three-dimensional filament organization in the actin cytoskeleton,” Nat. Methods 9, 185–188 (2012).
[Crossref]

Backman, V.

B. Dong, B. T. Soetikno, X. Chen, V. Backman, C. Sun, and H. F. Zhang, “Parallel three-dimensional tracking of quantum rods using polarization-sensitive spectroscopic photon localization microscopy,” ACS Photon. 4, 1747–1752 (2017).
[Crossref]

B. Dong, L. Almassalha, B. E. Urban, T. Q. Nguyen, S. Khuon, T. L. Chew, V. Backman, C. Sun, and H. F. Zhang, “Super-resolution spectroscopic microscopy via photon localization,” Nat. Commun. 7, 12290 (2016).
[Crossref]

Bates, M.

G. T. Dempsey, J. C. Vaughan, K. H. Chen, M. Bates, and X. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat. Methods 8, 1027–1036 (2011).
[Crossref]

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional Super-resolution Imaging by Stochastic Optical Reconstruction Microscopy,” Science 319, 810–813 (2008).
[Crossref]

Beane, G. L.

Bemiller, S. M.

M. J. Mlodzianoski, P. J. Cheng-Hathaway, S. M. Bemiller, T. J. McCray, S. Liu, D. A. Miller, B. T. Lamb, G. E. Landreth, and F. Huang, “Active PSF shaping and adaptive optics enable volumetric localization microscopy through brain sections,” Nat. Methods 15, 583–586(2018).
[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. Methods 5, 527–529 (2008).
[Crossref]

Bewersdorf, J.

M. J. Mlodzianoski, M. F. Juette, G. L. Beane, and J. Bewersdorf, “Experimental characterization of 3D localization techniques for particle-tracking and super-resolution microscopy,” Opt. Express 17, 8264–8277 (2009).
[Crossref]

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. Methods 5, 527–529 (2008).
[Crossref]

Biteen, J. S.

S. R. P. Pavani, M. A. Thompson, J. S. Biteen, S. J. Lord, N. Liu, R. J. Twieg, R. Piestun, and W. E. Moerner, “Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function,” Proc. Natl. Acad. Sci. USA 106, 2995–2999 (2009).
[Crossref]

Bittel, A.

T. Huang, C. Phelps, J. Wang, L. J. Lin, A. Bittel, Z. Scott, S. Jacques, S. L. Gibbs, J. W. Gray, and X. Nan, “Simultaneous multicolor single-molecule tracking with single-laser excitation via spectral imaging,” Biophys. J. 114, 301–310 (2018).
[Crossref]

Bongiovanni, M. N.

M. N. Bongiovanni, J. Godet, M. H. Horrocks, L. Tosatto, A. R. Carr, D. C. Wirthensohn, R. T. Ranasinghe, J. E. Lee, A. Ponjavic, J. V. Fritz, C. M. Dobson, D. Klenerman, and S. F. Lee, “Multi-dimensional super-resolution imaging enables surface hydrophobicity mapping,” Nat. Commun. 7, 13544 (2016).
[Crossref]

Borkovec, J.

M. Ovesny, P. Krizek, J. Borkovec, Z. Svindrych, and G. M. Hagen, “ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging,” Bioinformatics 30, 2389–2390 (2014).
[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. Methods 5, 1047–1052 (2008).
[Crossref]

Broeken, J.

Carr, A. R.

M. N. Bongiovanni, J. Godet, M. H. Horrocks, L. Tosatto, A. R. Carr, D. C. Wirthensohn, R. T. Ranasinghe, J. E. Lee, A. Ponjavic, J. V. Fritz, C. M. Dobson, D. Klenerman, and S. F. Lee, “Multi-dimensional super-resolution imaging enables surface hydrophobicity mapping,” Nat. Commun. 7, 13544 (2016).
[Crossref]

Carter, S.

M. J. Mlodzianoski, N. M. Curthoys, M. S. Gunewardene, S. Carter, and S. T. Hess, “Super-resolution imaging of molecular emission spectra and single molecule spectral fluctuations,” PLoS One 11, e0147506 (2016).
[Crossref]

Chao, J.

S. Ram, P. Prabhat, J. Chao, E. S. Ward, and R. J. Ober, “High accuracy 3D quantum dot tracking with multifocal plane microscopy for the study of fast intracellular dynamics in live cells,” Biophys. J 95, 6025–6043 (2008).
[Crossref]

Chen, K. H.

G. T. Dempsey, J. C. Vaughan, K. H. Chen, M. Bates, and X. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat. Methods 8, 1027–1036 (2011).
[Crossref]

Chen, X.

B. Dong, B. T. Soetikno, X. Chen, V. Backman, C. Sun, and H. F. Zhang, “Parallel three-dimensional tracking of quantum rods using polarization-sensitive spectroscopic photon localization microscopy,” ACS Photon. 4, 1747–1752 (2017).
[Crossref]

Cheng-Hathaway, P. J.

M. J. Mlodzianoski, P. J. Cheng-Hathaway, S. M. Bemiller, T. J. McCray, S. Liu, D. A. Miller, B. T. Lamb, G. E. Landreth, and F. Huang, “Active PSF shaping and adaptive optics enable volumetric localization microscopy through brain sections,” Nat. Methods 15, 583–586(2018).
[Crossref]

Chew, T. L.

B. Dong, L. Almassalha, B. E. Urban, T. Q. Nguyen, S. Khuon, T. L. Chew, V. Backman, C. Sun, and H. F. Zhang, “Super-resolution spectroscopic microscopy via photon localization,” Nat. Commun. 7, 12290 (2016).
[Crossref]

Curthoys, N. M.

M. J. Mlodzianoski, N. M. Curthoys, M. S. Gunewardene, S. Carter, and S. T. Hess, “Super-resolution imaging of molecular emission spectra and single molecule spectral fluctuations,” PLoS One 11, e0147506 (2016).
[Crossref]

Cusido, J.

Y. Zhang, K.-H. Song, S. Tang, L. Ravelo, J. Cusido, C. Sun, H. F. Zhang, and F. M. Raymo, “Far-red photoactivatable BODIPYs for the super-resolution imaging of live cells,” J. Am. Chem. Soc. 140, 12741–12745 (2018).
[Crossref]

Davidson, M. W.

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S. Quirin, S. R. Pavani, and R. Piestun, “Optimal 3D single-molecule localization for superresolution microscopy with aberrations and engineered point spread functions,” Proc. Natl. Acad. Sci. USA 109, 675–679 (2012).
[Crossref]

G. Grover, K. DeLuca, S. Quirin, J. DeLuca, and R. Piestun, “Super-resolution photon-efficient imaging by nanometric double-helix point spread function localization of emitters (SPINDLE),” Opt. Express 20, 26681–26695 (2012).
[Crossref]

S. R. P. Pavani, M. A. Thompson, J. S. Biteen, S. J. Lord, N. Liu, R. J. Twieg, R. Piestun, and W. E. Moerner, “Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function,” Proc. Natl. Acad. Sci. USA 106, 2995–2999 (2009).
[Crossref]

Platonova, E.

C. M. Winterflood, E. Platonova, D. Albrecht, and H. Ewers, “Dual-color 3D superresolution microscopy by combined spectral-demixing and biplane imaging,” Biophys. J. 109, 3–6 (2015).
[Crossref]

Ponjavic, A.

M. N. Bongiovanni, J. Godet, M. H. Horrocks, L. Tosatto, A. R. Carr, D. C. Wirthensohn, R. T. Ranasinghe, J. E. Lee, A. Ponjavic, J. V. Fritz, C. M. Dobson, D. Klenerman, and S. F. Lee, “Multi-dimensional super-resolution imaging enables surface hydrophobicity mapping,” Nat. Commun. 7, 13544 (2016).
[Crossref]

Prabhat, P.

S. Ram, P. Prabhat, J. Chao, E. S. Ward, and R. J. Ober, “High accuracy 3D quantum dot tracking with multifocal plane microscopy for the study of fast intracellular dynamics in live cells,” Biophys. J 95, 6025–6043 (2008).
[Crossref]

Quirin, S.

S. Quirin, S. R. Pavani, and R. Piestun, “Optimal 3D single-molecule localization for superresolution microscopy with aberrations and engineered point spread functions,” Proc. Natl. Acad. Sci. USA 109, 675–679 (2012).
[Crossref]

G. Grover, K. DeLuca, S. Quirin, J. DeLuca, and R. Piestun, “Super-resolution photon-efficient imaging by nanometric double-helix point spread function localization of emitters (SPINDLE),” Opt. Express 20, 26681–26695 (2012).
[Crossref]

Ram, S.

S. Ram, P. Prabhat, J. Chao, E. S. Ward, and R. J. Ober, “High accuracy 3D quantum dot tracking with multifocal plane microscopy for the study of fast intracellular dynamics in live cells,” Biophys. J 95, 6025–6043 (2008).
[Crossref]

Ranasinghe, R. T.

M. N. Bongiovanni, J. Godet, M. H. Horrocks, L. Tosatto, A. R. Carr, D. C. Wirthensohn, R. T. Ranasinghe, J. E. Lee, A. Ponjavic, J. V. Fritz, C. M. Dobson, D. Klenerman, and S. F. Lee, “Multi-dimensional super-resolution imaging enables surface hydrophobicity mapping,” Nat. Commun. 7, 13544 (2016).
[Crossref]

Ravelo, L.

Y. Zhang, K.-H. Song, S. Tang, L. Ravelo, J. Cusido, C. Sun, H. F. Zhang, and F. M. Raymo, “Far-red photoactivatable BODIPYs for the super-resolution imaging of live cells,” J. Am. Chem. Soc. 140, 12741–12745 (2018).
[Crossref]

Raymo, F. M.

Y. Zhang, K.-H. Song, S. Tang, L. Ravelo, J. Cusido, C. Sun, H. F. Zhang, and F. M. Raymo, “Far-red photoactivatable BODIPYs for the super-resolution imaging of live cells,” J. Am. Chem. Soc. 140, 12741–12745 (2018).
[Crossref]

Rensen, E.

A. Aristov, B. Lelandais, E. Rensen, and C. Zimmer, “ZOLA-3D allows flexible 3D localization microscopy over an adjustable axial range,” Nat. Commun. 9, 2409 (2018).
[Crossref]

Rieger, B.

Schonle, A.

D. Aquino, A. Schonle, C. Geisler, C. V. Middendorff, C. A. Wurm, Y. Okamura, T. Lang, S. W. Hell, and A. Egner, “Two-color nanoscopy of three-dimensional volumes by 4Pi detection of stochastically switched fluorophores,” Nat. Methods 8, 353–359 (2011).
[Crossref]

Scott, Z.

T. Huang, C. Phelps, J. Wang, L. J. Lin, A. Bittel, Z. Scott, S. Jacques, S. L. Gibbs, J. W. Gray, and X. Nan, “Simultaneous multicolor single-molecule tracking with single-laser excitation via spectral imaging,” Biophys. J. 114, 301–310 (2018).
[Crossref]

Shao, G.

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. USA 106, 3125–3130 (2009).
[Crossref]

Shyu, Y.

S. Moon, R. Yan, S. J. Kenny, Y. Shyu, L. Xiang, W. Li, and K. Xu, “Spectrally resolved, functional super-resolution microscopy reveals nanoscale compositional heterogeneity in live-cell membranes,” J. Am. Chem. Soc. 139, 10944–10947 (2017).
[Crossref]

Siemons, M.

Smith, C.

Soetikno, B. T.

B. Dong, B. T. Soetikno, X. Chen, V. Backman, C. Sun, and H. F. Zhang, “Parallel three-dimensional tracking of quantum rods using polarization-sensitive spectroscopic photon localization microscopy,” ACS Photon. 4, 1747–1752 (2017).
[Crossref]

Song, K.

K. Song, B. Dong, C. Sun, and H. F. Zhang, “Theoretical analysis of spectral precision in spectroscopic single-molecule localization microscopy,” Rev. Sci. Instrum. 89, 123703 (2018).
[Crossref]

Song, K.-H.

Y. Zhang, K.-H. Song, B. Dong, J. L. Davis, G. Shao, C. Sun, and H. F. Zhang, “Multicolor super-resolution imaging using spectroscopic single-molecule localization microscopy with optimal spectral dispersion,” Appl. Opt. 58, 2248–2255 (2019).
[Crossref]

Y. Zhang, K.-H. Song, S. Tang, L. Ravelo, J. Cusido, C. Sun, H. F. Zhang, and F. M. Raymo, “Far-red photoactivatable BODIPYs for the super-resolution imaging of live cells,” J. Am. Chem. Soc. 140, 12741–12745 (2018).
[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. USA 106, 3125–3130 (2009).
[Crossref]

Stallinga, S.

Sun, C.

Y. Zhang, K.-H. Song, B. Dong, J. L. Davis, G. Shao, C. Sun, and H. F. Zhang, “Multicolor super-resolution imaging using spectroscopic single-molecule localization microscopy with optimal spectral dispersion,” Appl. Opt. 58, 2248–2255 (2019).
[Crossref]

K. Song, B. Dong, C. Sun, and H. F. Zhang, “Theoretical analysis of spectral precision in spectroscopic single-molecule localization microscopy,” Rev. Sci. Instrum. 89, 123703 (2018).
[Crossref]

Y. Zhang, K.-H. Song, S. Tang, L. Ravelo, J. Cusido, C. Sun, H. F. Zhang, and F. M. Raymo, “Far-red photoactivatable BODIPYs for the super-resolution imaging of live cells,” J. Am. Chem. Soc. 140, 12741–12745 (2018).
[Crossref]

J. L. Davis, B. Dong, C. Sun, and H. F. Zhang, “Method to identify and minimize artifacts induced by fluorescent impurities in single-molecule localization microscopy,” J. Biomed. Opt. 23, 1–14 (2018).
[Crossref]

B. Dong, B. T. Soetikno, X. Chen, V. Backman, C. Sun, and H. F. Zhang, “Parallel three-dimensional tracking of quantum rods using polarization-sensitive spectroscopic photon localization microscopy,” ACS Photon. 4, 1747–1752 (2017).
[Crossref]

B. Dong, L. Almassalha, B. E. Urban, T. Q. Nguyen, S. Khuon, T. L. Chew, V. Backman, C. Sun, and H. F. Zhang, “Super-resolution spectroscopic microscopy via photon localization,” Nat. Commun. 7, 12290 (2016).
[Crossref]

Svindrych, Z.

M. Ovesny, P. Krizek, J. Borkovec, Z. Svindrych, and G. M. Hagen, “ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging,” Bioinformatics 30, 2389–2390 (2014).
[Crossref]

Tang, S.

Y. Zhang, K.-H. Song, S. Tang, L. Ravelo, J. Cusido, C. Sun, H. F. Zhang, and F. M. Raymo, “Far-red photoactivatable BODIPYs for the super-resolution imaging of live cells,” J. Am. Chem. Soc. 140, 12741–12745 (2018).
[Crossref]

Thompson, M. A.

S. R. P. Pavani, M. A. Thompson, J. S. Biteen, S. J. Lord, N. Liu, R. J. Twieg, R. Piestun, and W. E. Moerner, “Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function,” Proc. Natl. Acad. Sci. USA 106, 2995–2999 (2009).
[Crossref]

Tosatto, L.

M. N. Bongiovanni, J. Godet, M. H. Horrocks, L. Tosatto, A. R. Carr, D. C. Wirthensohn, R. T. Ranasinghe, J. E. Lee, A. Ponjavic, J. V. Fritz, C. M. Dobson, D. Klenerman, and S. F. Lee, “Multi-dimensional super-resolution imaging enables surface hydrophobicity mapping,” Nat. Commun. 7, 13544 (2016).
[Crossref]

Twieg, R. J.

S. R. P. Pavani, M. A. Thompson, J. S. Biteen, S. J. Lord, N. Liu, R. J. Twieg, R. Piestun, and W. E. Moerner, “Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function,” Proc. Natl. Acad. Sci. USA 106, 2995–2999 (2009).
[Crossref]

Urban, B. E.

B. Dong, L. Almassalha, B. E. Urban, T. Q. Nguyen, S. Khuon, T. L. Chew, V. Backman, C. Sun, and H. F. Zhang, “Super-resolution spectroscopic microscopy via photon localization,” Nat. Commun. 7, 12290 (2016).
[Crossref]

Vaughan, J. C.

S. Jia, J. C. Vaughan, and X. Zhuang, “Isotropic 3D super-resolution imaging with a self-bending point spread function,” Nat. Photonics 8, 302–306 (2014).
[Crossref]

G. T. Dempsey, J. C. Vaughan, K. H. Chen, M. Bates, and X. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat. Methods 8, 1027–1036 (2011).
[Crossref]

Wang, J.

T. Huang, C. Phelps, J. Wang, L. J. Lin, A. Bittel, Z. Scott, S. Jacques, S. L. Gibbs, J. W. Gray, and X. Nan, “Simultaneous multicolor single-molecule tracking with single-laser excitation via spectral imaging,” Biophys. J. 114, 301–310 (2018).
[Crossref]

Wang, W.

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional Super-resolution Imaging by Stochastic Optical Reconstruction Microscopy,” Science 319, 810–813 (2008).
[Crossref]

Ward, E. S.

S. Ram, P. Prabhat, J. Chao, E. S. Ward, and R. J. Ober, “High accuracy 3D quantum dot tracking with multifocal plane microscopy for the study of fast intracellular dynamics in live cells,” Biophys. J 95, 6025–6043 (2008).
[Crossref]

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. USA 106, 3125–3130 (2009).
[Crossref]

Winterflood, C. M.

C. M. Winterflood, E. Platonova, D. Albrecht, and H. Ewers, “Dual-color 3D superresolution microscopy by combined spectral-demixing and biplane imaging,” Biophys. J. 109, 3–6 (2015).
[Crossref]

Wirthensohn, D. C.

M. N. Bongiovanni, J. Godet, M. H. Horrocks, L. Tosatto, A. R. Carr, D. C. Wirthensohn, R. T. Ranasinghe, J. E. Lee, A. Ponjavic, J. V. Fritz, C. M. Dobson, D. Klenerman, and S. F. Lee, “Multi-dimensional super-resolution imaging enables surface hydrophobicity mapping,” Nat. Commun. 7, 13544 (2016).
[Crossref]

Wojcik, M.

L. Xiang, M. Wojcik, S. J. Kenny, R. Yan, S. Moon, W. Li, and K. Xu, “Optical characterization of surface adlayers and their compositional demixing at the nanoscale,” Nat. Commun. 9, 1435 (2018).
[Crossref]

Wurm, C. A.

D. Aquino, A. Schonle, C. Geisler, C. V. Middendorff, C. A. Wurm, Y. Okamura, T. Lang, S. W. Hell, and A. Egner, “Two-color nanoscopy of three-dimensional volumes by 4Pi detection of stochastically switched fluorophores,” Nat. Methods 8, 353–359 (2011).
[Crossref]

Xiang, L.

L. Xiang, M. Wojcik, S. J. Kenny, R. Yan, S. Moon, W. Li, and K. Xu, “Optical characterization of surface adlayers and their compositional demixing at the nanoscale,” Nat. Commun. 9, 1435 (2018).
[Crossref]

S. Moon, R. Yan, S. J. Kenny, Y. Shyu, L. Xiang, W. Li, and K. Xu, “Spectrally resolved, functional super-resolution microscopy reveals nanoscale compositional heterogeneity in live-cell membranes,” J. Am. Chem. Soc. 139, 10944–10947 (2017).
[Crossref]

Xu, K.

L. Xiang, M. Wojcik, S. J. Kenny, R. Yan, S. Moon, W. Li, and K. Xu, “Optical characterization of surface adlayers and their compositional demixing at the nanoscale,” Nat. Commun. 9, 1435 (2018).
[Crossref]

D. Kim, Z. Zhang, and K. Xu, “Spectrally resolved super-resolution microscopy unveils multipath reaction pathways of single spiropyran molecules,” J. Am. Chem. Soc. 139, 9447–9450 (2017).
[Crossref]

S. Moon, R. Yan, S. J. Kenny, Y. Shyu, L. Xiang, W. Li, and K. Xu, “Spectrally resolved, functional super-resolution microscopy reveals nanoscale compositional heterogeneity in live-cell membranes,” J. Am. Chem. Soc. 139, 10944–10947 (2017).
[Crossref]

Z. Zhang, S. J. Kenny, M. Hauser, W. Li, and K. Xu, “Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-resolution microscopy,” Nat. Methods 12, 935–938 (2015).
[Crossref]

K. Xu, H. P. Babcock, and X. Zhuang, “Dual-objective STORM reveals three-dimensional filament organization in the actin cytoskeleton,” Nat. Methods 9, 185–188 (2012).
[Crossref]

Yan, R.

L. Xiang, M. Wojcik, S. J. Kenny, R. Yan, S. Moon, W. Li, and K. Xu, “Optical characterization of surface adlayers and their compositional demixing at the nanoscale,” Nat. Commun. 9, 1435 (2018).
[Crossref]

S. Moon, R. Yan, S. J. Kenny, Y. Shyu, L. Xiang, W. Li, and K. Xu, “Spectrally resolved, functional super-resolution microscopy reveals nanoscale compositional heterogeneity in live-cell membranes,” J. Am. Chem. Soc. 139, 10944–10947 (2017).
[Crossref]

Zhang, H. F.

Y. Zhang, K.-H. Song, B. Dong, J. L. Davis, G. Shao, C. Sun, and H. F. Zhang, “Multicolor super-resolution imaging using spectroscopic single-molecule localization microscopy with optimal spectral dispersion,” Appl. Opt. 58, 2248–2255 (2019).
[Crossref]

K. Song, B. Dong, C. Sun, and H. F. Zhang, “Theoretical analysis of spectral precision in spectroscopic single-molecule localization microscopy,” Rev. Sci. Instrum. 89, 123703 (2018).
[Crossref]

J. L. Davis, B. Dong, C. Sun, and H. F. Zhang, “Method to identify and minimize artifacts induced by fluorescent impurities in single-molecule localization microscopy,” J. Biomed. Opt. 23, 1–14 (2018).
[Crossref]

Y. Zhang, K.-H. Song, S. Tang, L. Ravelo, J. Cusido, C. Sun, H. F. Zhang, and F. M. Raymo, “Far-red photoactivatable BODIPYs for the super-resolution imaging of live cells,” J. Am. Chem. Soc. 140, 12741–12745 (2018).
[Crossref]

B. Dong, B. T. Soetikno, X. Chen, V. Backman, C. Sun, and H. F. Zhang, “Parallel three-dimensional tracking of quantum rods using polarization-sensitive spectroscopic photon localization microscopy,” ACS Photon. 4, 1747–1752 (2017).
[Crossref]

B. Dong, L. Almassalha, B. E. Urban, T. Q. Nguyen, S. Khuon, T. L. Chew, V. Backman, C. Sun, and H. F. Zhang, “Super-resolution spectroscopic microscopy via photon localization,” Nat. Commun. 7, 12290 (2016).
[Crossref]

Zhang, Y.

Y. Zhang, K.-H. Song, B. Dong, J. L. Davis, G. Shao, C. Sun, and H. F. Zhang, “Multicolor super-resolution imaging using spectroscopic single-molecule localization microscopy with optimal spectral dispersion,” Appl. Opt. 58, 2248–2255 (2019).
[Crossref]

Y. Zhang, K.-H. Song, S. Tang, L. Ravelo, J. Cusido, C. Sun, H. F. Zhang, and F. M. Raymo, “Far-red photoactivatable BODIPYs for the super-resolution imaging of live cells,” J. Am. Chem. Soc. 140, 12741–12745 (2018).
[Crossref]

Zhang, Z.

D. Kim, Z. Zhang, and K. Xu, “Spectrally resolved super-resolution microscopy unveils multipath reaction pathways of single spiropyran molecules,” J. Am. Chem. Soc. 139, 9447–9450 (2017).
[Crossref]

Z. Zhang, S. J. Kenny, M. Hauser, W. Li, and K. Xu, “Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-resolution microscopy,” Nat. Methods 12, 935–938 (2015).
[Crossref]

Zhuang, X.

S. Jia, J. C. Vaughan, and X. Zhuang, “Isotropic 3D super-resolution imaging with a self-bending point spread function,” Nat. Photonics 8, 302–306 (2014).
[Crossref]

K. Xu, H. P. Babcock, and X. Zhuang, “Dual-objective STORM reveals three-dimensional filament organization in the actin cytoskeleton,” Nat. Methods 9, 185–188 (2012).
[Crossref]

G. T. Dempsey, J. C. Vaughan, K. H. Chen, M. Bates, and X. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat. Methods 8, 1027–1036 (2011).
[Crossref]

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional Super-resolution Imaging by Stochastic Optical Reconstruction Microscopy,” Science 319, 810–813 (2008).
[Crossref]

B. Huang, S. A. Jones, B. Brandenburg, and X. Zhuang, “Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution,” Nat. Methods 5, 1047–1052 (2008).
[Crossref]

Zimmer, C.

A. Aristov, B. Lelandais, E. Rensen, and C. Zimmer, “ZOLA-3D allows flexible 3D localization microscopy over an adjustable axial range,” Nat. Commun. 9, 2409 (2018).
[Crossref]

ACS Photon. (1)

B. Dong, B. T. Soetikno, X. Chen, V. Backman, C. Sun, and H. F. Zhang, “Parallel three-dimensional tracking of quantum rods using polarization-sensitive spectroscopic photon localization microscopy,” ACS Photon. 4, 1747–1752 (2017).
[Crossref]

Appl. Opt. (1)

Bioinformatics (1)

M. Ovesny, P. Krizek, J. Borkovec, Z. Svindrych, and G. M. Hagen, “ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging,” Bioinformatics 30, 2389–2390 (2014).
[Crossref]

Biophys. J (1)

S. Ram, P. Prabhat, J. Chao, E. S. Ward, and R. J. Ober, “High accuracy 3D quantum dot tracking with multifocal plane microscopy for the study of fast intracellular dynamics in live cells,” Biophys. J 95, 6025–6043 (2008).
[Crossref]

Biophys. J. (2)

C. M. Winterflood, E. Platonova, D. Albrecht, and H. Ewers, “Dual-color 3D superresolution microscopy by combined spectral-demixing and biplane imaging,” Biophys. J. 109, 3–6 (2015).
[Crossref]

T. Huang, C. Phelps, J. Wang, L. J. Lin, A. Bittel, Z. Scott, S. Jacques, S. L. Gibbs, J. W. Gray, and X. Nan, “Simultaneous multicolor single-molecule tracking with single-laser excitation via spectral imaging,” Biophys. J. 114, 301–310 (2018).
[Crossref]

J. Am. Chem. Soc. (3)

Y. Zhang, K.-H. Song, S. Tang, L. Ravelo, J. Cusido, C. Sun, H. F. Zhang, and F. M. Raymo, “Far-red photoactivatable BODIPYs for the super-resolution imaging of live cells,” J. Am. Chem. Soc. 140, 12741–12745 (2018).
[Crossref]

D. Kim, Z. Zhang, and K. Xu, “Spectrally resolved super-resolution microscopy unveils multipath reaction pathways of single spiropyran molecules,” J. Am. Chem. Soc. 139, 9447–9450 (2017).
[Crossref]

S. Moon, R. Yan, S. J. Kenny, Y. Shyu, L. Xiang, W. Li, and K. Xu, “Spectrally resolved, functional super-resolution microscopy reveals nanoscale compositional heterogeneity in live-cell membranes,” J. Am. Chem. Soc. 139, 10944–10947 (2017).
[Crossref]

J. Biomed. Opt. (1)

J. L. Davis, B. Dong, C. Sun, and H. F. Zhang, “Method to identify and minimize artifacts induced by fluorescent impurities in single-molecule localization microscopy,” J. Biomed. Opt. 23, 1–14 (2018).
[Crossref]

Nat. Commun. (4)

L. Xiang, M. Wojcik, S. J. Kenny, R. Yan, S. Moon, W. Li, and K. Xu, “Optical characterization of surface adlayers and their compositional demixing at the nanoscale,” Nat. Commun. 9, 1435 (2018).
[Crossref]

B. Dong, L. Almassalha, B. E. Urban, T. Q. Nguyen, S. Khuon, T. L. Chew, V. Backman, C. Sun, and H. F. Zhang, “Super-resolution spectroscopic microscopy via photon localization,” Nat. Commun. 7, 12290 (2016).
[Crossref]

M. N. Bongiovanni, J. Godet, M. H. Horrocks, L. Tosatto, A. R. Carr, D. C. Wirthensohn, R. T. Ranasinghe, J. E. Lee, A. Ponjavic, J. V. Fritz, C. M. Dobson, D. Klenerman, and S. F. Lee, “Multi-dimensional super-resolution imaging enables surface hydrophobicity mapping,” Nat. Commun. 7, 13544 (2016).
[Crossref]

A. Aristov, B. Lelandais, E. Rensen, and C. Zimmer, “ZOLA-3D allows flexible 3D localization microscopy over an adjustable axial range,” Nat. Commun. 9, 2409 (2018).
[Crossref]

Nat. Methods (7)

M. J. Mlodzianoski, P. J. Cheng-Hathaway, S. M. Bemiller, T. J. McCray, S. Liu, D. A. Miller, B. T. Lamb, G. E. Landreth, and F. Huang, “Active PSF shaping and adaptive optics enable volumetric localization microscopy through brain sections,” Nat. Methods 15, 583–586(2018).
[Crossref]

D. Aquino, A. Schonle, C. Geisler, C. V. Middendorff, C. A. Wurm, Y. Okamura, T. Lang, S. W. Hell, and A. Egner, “Two-color nanoscopy of three-dimensional volumes by 4Pi detection of stochastically switched fluorophores,” Nat. Methods 8, 353–359 (2011).
[Crossref]

K. Xu, H. P. Babcock, and X. Zhuang, “Dual-objective STORM reveals three-dimensional filament organization in the actin cytoskeleton,” Nat. Methods 9, 185–188 (2012).
[Crossref]

G. T. Dempsey, J. C. Vaughan, K. H. Chen, M. Bates, and X. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat. Methods 8, 1027–1036 (2011).
[Crossref]

Z. Zhang, S. J. Kenny, M. Hauser, W. Li, and K. Xu, “Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-resolution microscopy,” Nat. Methods 12, 935–938 (2015).
[Crossref]

B. Huang, S. A. Jones, B. Brandenburg, and X. Zhuang, “Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution,” Nat. Methods 5, 1047–1052 (2008).
[Crossref]

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. Methods 5, 527–529 (2008).
[Crossref]

Nat. Photonics (1)

S. Jia, J. C. Vaughan, and X. Zhuang, “Isotropic 3D super-resolution imaging with a self-bending point spread function,” Nat. Photonics 8, 302–306 (2014).
[Crossref]

Opt. Express (3)

Opt. Lett. (1)

PLoS One (1)

M. J. Mlodzianoski, N. M. Curthoys, M. S. Gunewardene, S. Carter, and S. T. Hess, “Super-resolution imaging of molecular emission spectra and single molecule spectral fluctuations,” PLoS One 11, e0147506 (2016).
[Crossref]

Proc. Natl. Acad. Sci. USA (3)

S. R. P. Pavani, M. A. Thompson, J. S. Biteen, S. J. Lord, N. Liu, R. J. Twieg, R. Piestun, and W. E. Moerner, “Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function,” Proc. Natl. Acad. Sci. USA 106, 2995–2999 (2009).
[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. USA 106, 3125–3130 (2009).
[Crossref]

S. Quirin, S. R. Pavani, and R. Piestun, “Optimal 3D single-molecule localization for superresolution microscopy with aberrations and engineered point spread functions,” Proc. Natl. Acad. Sci. USA 109, 675–679 (2012).
[Crossref]

Rev. Sci. Instrum. (1)

K. Song, B. Dong, C. Sun, and H. F. Zhang, “Theoretical analysis of spectral precision in spectroscopic single-molecule localization microscopy,” Rev. Sci. Instrum. 89, 123703 (2018).
[Crossref]

Science (1)

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional Super-resolution Imaging by Stochastic Optical Reconstruction Microscopy,” Science 319, 810–813 (2008).
[Crossref]

Supplementary Material (1)

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Figures (4)

Fig. 1.
Fig. 1. (a) Schematic and (b–f) working principle of 3D biplane sSMLM. (b) The detected spatial image and (c) the spectral image of a single-molecule emission. (c) The spectral image is the result of the convolution of the diffraction-limited PSF of individual stochastic fluorescent-emitting molecules in the spectral imaging plane and (d) the linearly spread spectroscopic signature. By integrating the spectral and spatial images along the x axis, (e), (f) 1D PSF y s are retrieved from both images and used for biplane imaging. (g) The experimentally acquired spatial (top row) and spectral (bottom) images at the different axial positions from single emitters. (h) The experimentally obtained depth calibration curve.
Fig. 2.
Fig. 2. (a) Overall projection image of the reconstructed 3D sSMLM with pseudocolors corresponding to the z -axis positions of individual molecules. (b–d) The projection images from three 200 nm thick sections as highlighted in (a). The cross-sectional images in (e) the y z plane and (f)  x z plane corresponding to the three magenta-dashed lines as highlighted in (a). (g–j) Spectral analyses of same single AF647 molecules. (g) The scatterplot of the photo count versus the spectral centroids. (h) and (i) respectively show the statistics of the emission photon count versus the number of emission events and centroid wavelengths versus the number of emission events. (j) The averaged spectrum of AF647 of all emission events in (g).
Fig. 3.
Fig. 3. (a) Normalized emission spectra of AF647 (red) and CF660C (green) with their centroids (686 nm for AF647 and 695 nm for CF660C), respectively. (b) The histogram of spectral centroid of multi-color 3D sSMLM image of tubulin and TOM20, labeled with AF647 and CF660C, respectively. To separate the two dyes, we defined two different color channels: (1) 674 to 689 nm for AF647 and (2) 692 nm to 707 nm for CF660C.
Fig. 4.
Fig. 4. (a) Overall 2D projection view over a whole depth range of 1.75 μm. The red and green colors represent AF647-labeled microtubules and CF660C-labeled mitochondria, respectively. (a) The projection images for different axial ranges from (b) 1.0 to 1.3 μm and from (c) 0.5 to 0.8 μm [color-coded along the spectral centroid in (a–c)]. The separated 3D sSMLM images for different color channels, (d) 692 to 707 nm for mitochondria and (e) 674–689 nm for microtubules [color-coded along the axial axis in (d–e)]. (f) The magnified view of the region indicated by the yellow-dashed box in (a). (g) The cross-section image corresponding to the white-dashed lines in (f). (h–j) The cross-section images corresponding to the three white-solid lines in (f) [color-coded along the spectral centroid in (f–j)]. (k) The volumetric rendering of the region covering (h–j). The rendering was visualized with the interpolation for a microtubule.

Equations (1)

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Δ λ = W p × R d = W p × d cos θ f × m ,

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