Abstract

A new single-aperture 3D particle-localization and tracking technique is presented that demonstrates an increase in depth range by more than an order of magnitude without compromising optical resolution and throughput. We exploit the extended depth range and depth-dependent translation of an Airy-beam PSF for 3D localization over an extended volume in a single snapshot. The technique is applicable to all bright-field and fluorescence modalities for particle localization and tracking, ranging from super-resolution microscopy through to the tracking of fluorescent beads and endogenous particles within cells. We demonstrate and validate its application to real-time 3D velocity imaging of fluid flow in capillaries using fluorescent tracer beads. An axial localization precision of 50 nm was obtained over a depth range of 120μm using a 0.4NA, 20× microscope objective. We believe this to be the highest ratio of axial range-to-precision reported to date.

Published by The Optical Society under the terms of the Creative Commons Attribution 4.0 License. Further distribution of this work must maintain attribution to the author(s) and the published article's title, journal citation, and DOI.

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References

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2016 (3)

F. Huang, G. Sirinakis, E. S. Allgeyer, L. K. Schroeder, W. C. Duim, E. B. Kromann, T. Phan, F. E. Rivera-Molina, J. R. Myers, I. Irnov, M. Lessard, Y. Zhang, M. Handel, C. Jacobs-Wagner, C. P. Lusk, J. E. Rothman, D. Toomre, M. J. Booth, and J. Bewersdorf, “Ultra-high resolution 3D imaging of whole cells,” Cell 166(4), 1028–1040 (2016).
[Crossref] [PubMed]

B. Yu, J. Yu, W. Li, B. Cao, H. Li, D. Chen, and H. Niu, “Nanoscale three-dimensional single particle tracking by light-sheet-based double-helix point spread function microscopy,” Appl. Opt. 55(3), 449–453 (2016).
[Crossref] [PubMed]

Y. Wu, L. Dong, Y. Zhao, M. Liu, X. Chu, W. Jia, X. Guo, and Y. Feng, “Analysis of wavefront coding imaging with cubic phase mask decenter and tilt,” Appl. Opt. 55(25), 7009–7017 (2016).
[Crossref] [PubMed]

2015 (1)

Y. Shechtman, L. E. Weiss, A. S. Backer, S. J. Sahl, and W. E. Moerner, “Precise three-dimensional scan-free multiple-particle tracking over large axial ranges with tetrapod point spread functions,” Nano Lett. 15(6), 4194–4199 (2015).
[Crossref] [PubMed]

2014 (6)

Y. Shechtman, S. J. Sahl, A. S. Backer, and W. E. Moerner, “Optimal point spread function design for 3D imaging,” Phys. Rev. Lett. 113(13), 133902 (2014).
[Crossref] [PubMed]

P. Zammit, A. R. Harvey, and G. Carles, “Extended depth-of-field imaging and ranging in a snapshot,” Optica 1(4), 209–216 (2014).
[Crossref]

B. Shuang, J. Chen, L. Kisley, and C. F. Landes, “Troika of single particle tracking programing: SNR enhancement, particle identification, and mapping,” Phys. Chem. Chem. Phys. 16(2), 624–634 (2014).
[Crossref]

A. S. Backer, M. P. Backlund, A. R. Von Diezmann, S. J. Sahl, and W. E. Moerner, “A bisected pupil for studying single-molecule orientational dynamics and its application to three-dimensional super-resolution microscopy,” Appl. Phys. Lett. 104(19), 161103 (2014).
[Crossref]

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

J. Štigler, “Analytical velocity profile in tube for laminar and turbulent flow,” Engineer. Mechan. 21(6), 371–379 (2014).

2013 (1)

C. P. Calderon, M. A. Thompson, J. M. Casolari, R. C. Paffenroth, and W. E. Moerner, “Quantifying transient 3D dynamical phenomena of single mRNA particles in live yeast cell measurements,” J. Phys. Chem. B 117(49), 15701–15713 (2013).
[Crossref] [PubMed]

2012 (4)

H. D. Lee, S. J. Sahl, M. D. Lew, and W. E. Moerner, “The double-helix microscope super-resolves extended biological structures by localizing single blinking molecules in three dimensions with nanoscale precision,” Appl. Phys. Lett. 100(15), 153701 (2012).
[Crossref] [PubMed]

M. A. Thompson, M. D. Lew, and W. E. Moerner, “Extending microscopic resolution with single-molecule imaging and active control,” Ann. Rev. Biophys. 41(1), 321–342 (2012).
[Crossref]

W. E. Moerner, “Microscopy beyond the diffraction limit using actively controlled single molecules,” J. Microsc. 246(3), 213–220 (2012).
[Crossref] [PubMed]

C. Cierpka and C. J. Kähler, “Particle imaging techniques for volumetric three-component (3D3C) velocity measurements in microfluidics,” J. Visual. 15(1), 1–31 (2012).
[Crossref]

2011 (1)

2010 (1)

2009 (3)

Y. Sun, J. D. McKenna, J. M. Murray, E. M. Ostap, and Y. E. Goldman, “Parallax: High accuracy three-dimensional single molecule tracking using split images,” Nano Lett. 9(7), 2676–2682 (2009).
[Crossref] [PubMed]

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. U.S.A. 106(9), 2995–2999 (2009).
[Crossref] [PubMed]

S. Chen, N. Angarita-Jaimes, D. Angarita-Jaimes, B. Pelc, A. H. Greenaway, C. E. Towers, D. Lin, and D. P. Towers, “Wavefront sensing for three-component three-dimensional flow velocimetry in microfluidics,” Exp. Fluids 47(4), 849–863 (2009).
[Crossref]

2008 (7)

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[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. Methods 5(6), 527–529 (2008).
[Crossref] [PubMed]

J. Yajima, K. Mizutani, and T. Nishizaka, “A torque component present in mitotic kinesin Eg5 revealed by three-dimensional tracking,” Nat. Struct. Mol. Biol. 15(10), 1119–1121 (2008).
[Crossref] [PubMed]

S. R. P. Pavani and R. Piestun, “High-efficiency rotating point spread functions,” Opt. Express 16(5), 3484–3489 (2008).
[Crossref] [PubMed]

J. Lu, F. Pereira, S. E. Fraser, and M. Gharib, “Three-dimensional real-time imaging of cardiac cell motions in living embryos,” J. Biomed. Opt. 13(1), 014006 (2008).
[Crossref] [PubMed]

K. Jaqaman, D. Loerke, M. Mettlen, H. Kuwata, S. Grinstein, S. L. Schmid, and G. Danuser, “Robust single-particle tracking in live-cell time-lapse sequences,” Nat. methods 5(8), 695–702 (2008).
[Crossref] [PubMed]

D. Lin, N. C. Angarita-Jaimes, S. Chen, A. H. Greenaway, C. E. Towers, and D. P. Towers, “Three-dimensional particle imaging by defocusing method with an annular aperture,” Opt. Lett. 33(9), 905–907 (2008).
[Crossref] [PubMed]

2007 (4)

G. A. Siviloglou, J. Broky, A. Dogariu, and D. N. Christodoulides, “Observation of accelerating airy beams,” Phys. Rev. Lett. 99(21), 213901 (2007).
[Crossref]

L. Holtzer, T. Meckel, and T. Schmidt, “Nanometric three-dimensional tracking of individual quantum dots in cells,” Appl. Phys. Lett. 90(5), 053902 (2007).
[Crossref]

E. Toprak, H. Balci, B. H. Blehm, and P. R. Selvin, “Three-dimensional particle tracking via bifocal imaging,” Nano Lett. 7(7), 2043–2045 (2007).
[Crossref] [PubMed]

V. Levi and E. Gratton, “Exploring dynamics in living cells by tracking single particles,” Cell Biochem. Biophys. 48(1), 1–15 (2007).
[Crossref] [PubMed]

2006 (4)

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006).
[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,” Science 313(5793), 1642–1645 (2006).
[Crossref] [PubMed]

C. E. Towers, D. P. Towers, H. I. Campbell, S. Zhang, and A. H. Greenaway, “Three-dimensional particle imaging by wavefront sensing,” Opt. Lett. 31(9), 1220–1222 (2006).
[Crossref] [PubMed]

S. Y. Yoon and K. C. Kim, “3D particle position and 3D velocity field measurement in a microvolume via the defocusing concept,” Meas. Sci. Technol. 17(11), 2897–2905 (2006).
[Crossref]

2005 (1)

2002 (1)

F. Pereira and M. Gharib, “Defocusing digital particle image velocimetry and the three-dimensional characterization of two-phase flows,” Meas. Sci. Technol. 13(5), 683–694 (2002).
[Crossref]

2000 (3)

C. Bustamante, S. B. Smith, J. Liphardt, and D. Smith, “Single-molecule studies of DNA mechanics,” Curr. Opin. Struc. Biol. 10(3), 279–285 (2000).
[Crossref]

R. Piestun, Y. Y. Schechner, and J. Shamir, “Propagation-invariant wave fields with finite energy,” J. Opt. Soc. Am. A 17(2), 294–303 (2000).
[Crossref]

F. Pereira, M. Gharib, D. Dabiri, and D. Modarress, “Defocusing digital particle image velocimetry: a 3-component 3-dimensional DPIV measurement technique. application to bubbly flows,” Exp. Fluids 29(1), S078–S084 (2000).
[Crossref]

1996 (1)

J. C. Crocker and D. G. Grier, “Methods of digital video microscopy for colloidal studies,” J. Colloid Interf. Sci. 179(1), 298–310 (1996).
[Crossref]

1995 (1)

1994 (1)

H. P. Kao and A. S. Verkman, “Tracking of single fluorescent particles in three dimensions: use of cylindrical optics to encode particle position,” Biophys. J. 67(3), 1291–1300 (1994).
[Crossref] [PubMed]

1992 (1)

C. E. Willert and M. Gharib, “Three-dimensional particle imaging with a single camera,” Exp. Fluids 12(6), 353–358 (1992).
[Crossref]

1979 (1)

M. V. Berry and N. L. Balazs, “Nonspreading wave packets,” Am. J. Phys. 47(3), 264–267 (1979).
[Crossref]

Adelsberger, K.

K. Adelsberger, “Design guidelines for wavefront coding in broadband optical systems,” Ph.D. thesis, University of Rochester (2014).

Allgeyer, E. S.

F. Huang, G. Sirinakis, E. S. Allgeyer, L. K. Schroeder, W. C. Duim, E. B. Kromann, T. Phan, F. E. Rivera-Molina, J. R. Myers, I. Irnov, M. Lessard, Y. Zhang, M. Handel, C. Jacobs-Wagner, C. P. Lusk, J. E. Rothman, D. Toomre, M. J. Booth, and J. Bewersdorf, “Ultra-high resolution 3D imaging of whole cells,” Cell 166(4), 1028–1040 (2016).
[Crossref] [PubMed]

Angarita-Jaimes, D.

S. Chen, N. Angarita-Jaimes, D. Angarita-Jaimes, B. Pelc, A. H. Greenaway, C. E. Towers, D. Lin, and D. P. Towers, “Wavefront sensing for three-component three-dimensional flow velocimetry in microfluidics,” Exp. Fluids 47(4), 849–863 (2009).
[Crossref]

Angarita-Jaimes, N.

S. Chen, N. Angarita-Jaimes, D. Angarita-Jaimes, B. Pelc, A. H. Greenaway, C. E. Towers, D. Lin, and D. P. Towers, “Wavefront sensing for three-component three-dimensional flow velocimetry in microfluidics,” Exp. Fluids 47(4), 849–863 (2009).
[Crossref]

Angarita-Jaimes, N. C.

Backer, A. S.

Y. Shechtman, L. E. Weiss, A. S. Backer, S. J. Sahl, and W. E. Moerner, “Precise three-dimensional scan-free multiple-particle tracking over large axial ranges with tetrapod point spread functions,” Nano Lett. 15(6), 4194–4199 (2015).
[Crossref] [PubMed]

Y. Shechtman, S. J. Sahl, A. S. Backer, and W. E. Moerner, “Optimal point spread function design for 3D imaging,” Phys. Rev. Lett. 113(13), 133902 (2014).
[Crossref] [PubMed]

A. S. Backer, M. P. Backlund, A. R. Von Diezmann, S. J. Sahl, and W. E. Moerner, “A bisected pupil for studying single-molecule orientational dynamics and its application to three-dimensional super-resolution microscopy,” Appl. Phys. Lett. 104(19), 161103 (2014).
[Crossref]

Backlund, M. P.

A. S. Backer, M. P. Backlund, A. R. Von Diezmann, S. J. Sahl, and W. E. Moerner, “A bisected pupil for studying single-molecule orientational dynamics and its application to three-dimensional super-resolution microscopy,” Appl. Phys. Lett. 104(19), 161103 (2014).
[Crossref]

Balazs, N. L.

M. V. Berry and N. L. Balazs, “Nonspreading wave packets,” Am. J. Phys. 47(3), 264–267 (1979).
[Crossref]

Balci, H.

E. Toprak, H. Balci, B. H. Blehm, and P. R. Selvin, “Three-dimensional particle tracking via bifocal imaging,” Nano Lett. 7(7), 2043–2045 (2007).
[Crossref] [PubMed]

Bates, M.

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006).
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Bennett, B. T.

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Muyo, G.

Myers, J. R.

F. Huang, G. Sirinakis, E. S. Allgeyer, L. K. Schroeder, W. C. Duim, E. B. Kromann, T. Phan, F. E. Rivera-Molina, J. R. Myers, I. Irnov, M. Lessard, Y. Zhang, M. Handel, C. Jacobs-Wagner, C. P. Lusk, J. E. Rothman, D. Toomre, M. J. Booth, and J. Bewersdorf, “Ultra-high resolution 3D imaging of whole cells,” Cell 166(4), 1028–1040 (2016).
[Crossref] [PubMed]

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. Methods 5(6), 527–529 (2008).
[Crossref] [PubMed]

Nishizaka, T.

J. Yajima, K. Mizutani, and T. Nishizaka, “A torque component present in mitotic kinesin Eg5 revealed by three-dimensional tracking,” Nat. Struct. Mol. Biol. 15(10), 1119–1121 (2008).
[Crossref] [PubMed]

Niu, H.

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,” Science 313(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Ostap, E. M.

Y. Sun, J. D. McKenna, J. M. Murray, E. M. Ostap, and Y. E. Goldman, “Parallax: High accuracy three-dimensional single molecule tracking using split images,” Nano Lett. 9(7), 2676–2682 (2009).
[Crossref] [PubMed]

Paffenroth, R. C.

C. P. Calderon, M. A. Thompson, J. M. Casolari, R. C. Paffenroth, and W. E. Moerner, “Quantifying transient 3D dynamical phenomena of single mRNA particles in live yeast cell measurements,” J. Phys. Chem. B 117(49), 15701–15713 (2013).
[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,” Science 313(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Pavani, S. R. P.

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. U.S.A. 106(9), 2995–2999 (2009).
[Crossref] [PubMed]

S. R. P. Pavani and R. Piestun, “High-efficiency rotating point spread functions,” Opt. Express 16(5), 3484–3489 (2008).
[Crossref] [PubMed]

Pelc, B.

S. Chen, N. Angarita-Jaimes, D. Angarita-Jaimes, B. Pelc, A. H. Greenaway, C. E. Towers, D. Lin, and D. P. Towers, “Wavefront sensing for three-component three-dimensional flow velocimetry in microfluidics,” Exp. Fluids 47(4), 849–863 (2009).
[Crossref]

Pereira, F.

J. Lu, F. Pereira, S. E. Fraser, and M. Gharib, “Three-dimensional real-time imaging of cardiac cell motions in living embryos,” J. Biomed. Opt. 13(1), 014006 (2008).
[Crossref] [PubMed]

F. Pereira and M. Gharib, “Defocusing digital particle image velocimetry and the three-dimensional characterization of two-phase flows,” Meas. Sci. Technol. 13(5), 683–694 (2002).
[Crossref]

F. Pereira, M. Gharib, D. Dabiri, and D. Modarress, “Defocusing digital particle image velocimetry: a 3-component 3-dimensional DPIV measurement technique. application to bubbly flows,” Exp. Fluids 29(1), S078–S084 (2000).
[Crossref]

Phan, T.

F. Huang, G. Sirinakis, E. S. Allgeyer, L. K. Schroeder, W. C. Duim, E. B. Kromann, T. Phan, F. E. Rivera-Molina, J. R. Myers, I. Irnov, M. Lessard, Y. Zhang, M. Handel, C. Jacobs-Wagner, C. P. Lusk, J. E. Rothman, D. Toomre, M. J. Booth, and J. Bewersdorf, “Ultra-high resolution 3D imaging of whole cells,” Cell 166(4), 1028–1040 (2016).
[Crossref] [PubMed]

Piestun, R.

Quirin, S.

Rivera-Molina, F. E.

F. Huang, G. Sirinakis, E. S. Allgeyer, L. K. Schroeder, W. C. Duim, E. B. Kromann, T. Phan, F. E. Rivera-Molina, J. R. Myers, I. Irnov, M. Lessard, Y. Zhang, M. Handel, C. Jacobs-Wagner, C. P. Lusk, J. E. Rothman, D. Toomre, M. J. Booth, and J. Bewersdorf, “Ultra-high resolution 3D imaging of whole cells,” Cell 166(4), 1028–1040 (2016).
[Crossref] [PubMed]

Rothman, J. E.

F. Huang, G. Sirinakis, E. S. Allgeyer, L. K. Schroeder, W. C. Duim, E. B. Kromann, T. Phan, F. E. Rivera-Molina, J. R. Myers, I. Irnov, M. Lessard, Y. Zhang, M. Handel, C. Jacobs-Wagner, C. P. Lusk, J. E. Rothman, D. Toomre, M. J. Booth, and J. Bewersdorf, “Ultra-high resolution 3D imaging of whole cells,” Cell 166(4), 1028–1040 (2016).
[Crossref] [PubMed]

Rust, M. J.

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006).
[Crossref] [PubMed]

Sahl, S. J.

Y. Shechtman, L. E. Weiss, A. S. Backer, S. J. Sahl, and W. E. Moerner, “Precise three-dimensional scan-free multiple-particle tracking over large axial ranges with tetrapod point spread functions,” Nano Lett. 15(6), 4194–4199 (2015).
[Crossref] [PubMed]

Y. Shechtman, S. J. Sahl, A. S. Backer, and W. E. Moerner, “Optimal point spread function design for 3D imaging,” Phys. Rev. Lett. 113(13), 133902 (2014).
[Crossref] [PubMed]

A. S. Backer, M. P. Backlund, A. R. Von Diezmann, S. J. Sahl, and W. E. Moerner, “A bisected pupil for studying single-molecule orientational dynamics and its application to three-dimensional super-resolution microscopy,” Appl. Phys. Lett. 104(19), 161103 (2014).
[Crossref]

H. D. Lee, S. J. Sahl, M. D. Lew, and W. E. Moerner, “The double-helix microscope super-resolves extended biological structures by localizing single blinking molecules in three dimensions with nanoscale precision,” Appl. Phys. Lett. 100(15), 153701 (2012).
[Crossref] [PubMed]

Schechner, Y. Y.

Schmid, S. L.

K. Jaqaman, D. Loerke, M. Mettlen, H. Kuwata, S. Grinstein, S. L. Schmid, and G. Danuser, “Robust single-particle tracking in live-cell time-lapse sequences,” Nat. methods 5(8), 695–702 (2008).
[Crossref] [PubMed]

Schmidt, T.

L. Holtzer, T. Meckel, and T. Schmidt, “Nanometric three-dimensional tracking of individual quantum dots in cells,” Appl. Phys. Lett. 90(5), 053902 (2007).
[Crossref]

Schroeder, L. K.

F. Huang, G. Sirinakis, E. S. Allgeyer, L. K. Schroeder, W. C. Duim, E. B. Kromann, T. Phan, F. E. Rivera-Molina, J. R. Myers, I. Irnov, M. Lessard, Y. Zhang, M. Handel, C. Jacobs-Wagner, C. P. Lusk, J. E. Rothman, D. Toomre, M. J. Booth, and J. Bewersdorf, “Ultra-high resolution 3D imaging of whole cells,” Cell 166(4), 1028–1040 (2016).
[Crossref] [PubMed]

Selvin, P. R.

E. Toprak, H. Balci, B. H. Blehm, and P. R. Selvin, “Three-dimensional particle tracking via bifocal imaging,” Nano Lett. 7(7), 2043–2045 (2007).
[Crossref] [PubMed]

Shamir, J.

Shechtman, Y.

Y. Shechtman, L. E. Weiss, A. S. Backer, S. J. Sahl, and W. E. Moerner, “Precise three-dimensional scan-free multiple-particle tracking over large axial ranges with tetrapod point spread functions,” Nano Lett. 15(6), 4194–4199 (2015).
[Crossref] [PubMed]

Y. Shechtman, S. J. Sahl, A. S. Backer, and W. E. Moerner, “Optimal point spread function design for 3D imaging,” Phys. Rev. Lett. 113(13), 133902 (2014).
[Crossref] [PubMed]

Shuang, B.

B. Shuang, J. Chen, L. Kisley, and C. F. Landes, “Troika of single particle tracking programing: SNR enhancement, particle identification, and mapping,” Phys. Chem. Chem. Phys. 16(2), 624–634 (2014).
[Crossref]

Sirinakis, G.

F. Huang, G. Sirinakis, E. S. Allgeyer, L. K. Schroeder, W. C. Duim, E. B. Kromann, T. Phan, F. E. Rivera-Molina, J. R. Myers, I. Irnov, M. Lessard, Y. Zhang, M. Handel, C. Jacobs-Wagner, C. P. Lusk, J. E. Rothman, D. Toomre, M. J. Booth, and J. Bewersdorf, “Ultra-high resolution 3D imaging of whole cells,” Cell 166(4), 1028–1040 (2016).
[Crossref] [PubMed]

Siviloglou, G. A.

G. A. Siviloglou, J. Broky, A. Dogariu, and D. N. Christodoulides, “Observation of accelerating airy beams,” Phys. Rev. Lett. 99(21), 213901 (2007).
[Crossref]

Smith, D.

C. Bustamante, S. B. Smith, J. Liphardt, and D. Smith, “Single-molecule studies of DNA mechanics,” Curr. Opin. Struc. Biol. 10(3), 279–285 (2000).
[Crossref]

Smith, S. B.

C. Bustamante, S. B. Smith, J. Liphardt, and D. Smith, “Single-molecule studies of DNA mechanics,” Curr. Opin. Struc. Biol. 10(3), 279–285 (2000).
[Crossref]

Sougrat, R.

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,” Science 313(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Štigler, J.

J. Štigler, “Analytical velocity profile in tube for laminar and turbulent flow,” Engineer. Mechan. 21(6), 371–379 (2014).

Sun, Y.

Y. Sun, J. D. McKenna, J. M. Murray, E. M. Ostap, and Y. E. Goldman, “Parallax: High accuracy three-dimensional single molecule tracking using split images,” Nano Lett. 9(7), 2676–2682 (2009).
[Crossref] [PubMed]

Thompson, M. A.

C. P. Calderon, M. A. Thompson, J. M. Casolari, R. C. Paffenroth, and W. E. Moerner, “Quantifying transient 3D dynamical phenomena of single mRNA particles in live yeast cell measurements,” J. Phys. Chem. B 117(49), 15701–15713 (2013).
[Crossref] [PubMed]

M. A. Thompson, M. D. Lew, and W. E. Moerner, “Extending microscopic resolution with single-molecule imaging and active control,” Ann. Rev. Biophys. 41(1), 321–342 (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. U.S.A. 106(9), 2995–2999 (2009).
[Crossref] [PubMed]

Toomre, D.

F. Huang, G. Sirinakis, E. S. Allgeyer, L. K. Schroeder, W. C. Duim, E. B. Kromann, T. Phan, F. E. Rivera-Molina, J. R. Myers, I. Irnov, M. Lessard, Y. Zhang, M. Handel, C. Jacobs-Wagner, C. P. Lusk, J. E. Rothman, D. Toomre, M. J. Booth, and J. Bewersdorf, “Ultra-high resolution 3D imaging of whole cells,” Cell 166(4), 1028–1040 (2016).
[Crossref] [PubMed]

Toprak, E.

E. Toprak, H. Balci, B. H. Blehm, and P. R. Selvin, “Three-dimensional particle tracking via bifocal imaging,” Nano Lett. 7(7), 2043–2045 (2007).
[Crossref] [PubMed]

Towers, C. E.

Towers, D. P.

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. U.S.A. 106(9), 2995–2999 (2009).
[Crossref] [PubMed]

Vaughan, J. C.

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

Verkman, A. S.

H. P. Kao and A. S. Verkman, “Tracking of single fluorescent particles in three dimensions: use of cylindrical optics to encode particle position,” Biophys. J. 67(3), 1291–1300 (1994).
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Vettenburg, T.

Von Diezmann, A. R.

A. S. Backer, M. P. Backlund, A. R. Von Diezmann, S. J. Sahl, and W. E. Moerner, “A bisected pupil for studying single-molecule orientational dynamics and its application to three-dimensional super-resolution microscopy,” Appl. Phys. Lett. 104(19), 161103 (2014).
[Crossref]

Wang, W.

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

Weiss, L. E.

Y. Shechtman, L. E. Weiss, A. S. Backer, S. J. Sahl, and W. E. Moerner, “Precise three-dimensional scan-free multiple-particle tracking over large axial ranges with tetrapod point spread functions,” Nano Lett. 15(6), 4194–4199 (2015).
[Crossref] [PubMed]

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C. E. Willert and M. Gharib, “Three-dimensional particle imaging with a single camera,” Exp. Fluids 12(6), 353–358 (1992).
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Yajima, J.

J. Yajima, K. Mizutani, and T. Nishizaka, “A torque component present in mitotic kinesin Eg5 revealed by three-dimensional tracking,” Nat. Struct. Mol. Biol. 15(10), 1119–1121 (2008).
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Yoon, S. Y.

S. Y. Yoon and K. C. Kim, “3D particle position and 3D velocity field measurement in a microvolume via the defocusing concept,” Meas. Sci. Technol. 17(11), 2897–2905 (2006).
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P. Zammit, A. R. Harvey, and G. Carles, “Extended depth-of-field imaging and ranging in a snapshot,” Optica 1(4), 209–216 (2014).
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P. Zammit, “Extended depth-of-field imaging and ranging in microscopy,” Ph.D. thesis, University of Glasgow (2016).

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F. Huang, G. Sirinakis, E. S. Allgeyer, L. K. Schroeder, W. C. Duim, E. B. Kromann, T. Phan, F. E. Rivera-Molina, J. R. Myers, I. Irnov, M. Lessard, Y. Zhang, M. Handel, C. Jacobs-Wagner, C. P. Lusk, J. E. Rothman, D. Toomre, M. J. Booth, and J. Bewersdorf, “Ultra-high resolution 3D imaging of whole cells,” Cell 166(4), 1028–1040 (2016).
[Crossref] [PubMed]

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Zhuang, X.

S. Jia, J. C. Vaughan, and X. Zhuang, “Isotropic three-dimensional super-resolution imaging with a self-bending point spread function,” Nat. Photonics 8, 302–306 (2014).
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B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
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M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006).
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M. A. Thompson, M. D. Lew, and W. E. Moerner, “Extending microscopic resolution with single-molecule imaging and active control,” Ann. Rev. Biophys. 41(1), 321–342 (2012).
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Appl. Opt. (3)

Appl. Phys. Lett. (3)

A. S. Backer, M. P. Backlund, A. R. Von Diezmann, S. J. Sahl, and W. E. Moerner, “A bisected pupil for studying single-molecule orientational dynamics and its application to three-dimensional super-resolution microscopy,” Appl. Phys. Lett. 104(19), 161103 (2014).
[Crossref]

H. D. Lee, S. J. Sahl, M. D. Lew, and W. E. Moerner, “The double-helix microscope super-resolves extended biological structures by localizing single blinking molecules in three dimensions with nanoscale precision,” Appl. Phys. Lett. 100(15), 153701 (2012).
[Crossref] [PubMed]

L. Holtzer, T. Meckel, and T. Schmidt, “Nanometric three-dimensional tracking of individual quantum dots in cells,” Appl. Phys. Lett. 90(5), 053902 (2007).
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Biomed. Opt. Express (1)

Biophys. J. (1)

H. P. Kao and A. S. Verkman, “Tracking of single fluorescent particles in three dimensions: use of cylindrical optics to encode particle position,” Biophys. J. 67(3), 1291–1300 (1994).
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Cell (1)

F. Huang, G. Sirinakis, E. S. Allgeyer, L. K. Schroeder, W. C. Duim, E. B. Kromann, T. Phan, F. E. Rivera-Molina, J. R. Myers, I. Irnov, M. Lessard, Y. Zhang, M. Handel, C. Jacobs-Wagner, C. P. Lusk, J. E. Rothman, D. Toomre, M. J. Booth, and J. Bewersdorf, “Ultra-high resolution 3D imaging of whole cells,” Cell 166(4), 1028–1040 (2016).
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Curr. Opin. Struc. Biol. (1)

C. Bustamante, S. B. Smith, J. Liphardt, and D. Smith, “Single-molecule studies of DNA mechanics,” Curr. Opin. Struc. Biol. 10(3), 279–285 (2000).
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Engineer. Mechan. (1)

J. Štigler, “Analytical velocity profile in tube for laminar and turbulent flow,” Engineer. Mechan. 21(6), 371–379 (2014).

Exp. Fluids (3)

F. Pereira, M. Gharib, D. Dabiri, and D. Modarress, “Defocusing digital particle image velocimetry: a 3-component 3-dimensional DPIV measurement technique. application to bubbly flows,” Exp. Fluids 29(1), S078–S084 (2000).
[Crossref]

S. Chen, N. Angarita-Jaimes, D. Angarita-Jaimes, B. Pelc, A. H. Greenaway, C. E. Towers, D. Lin, and D. P. Towers, “Wavefront sensing for three-component three-dimensional flow velocimetry in microfluidics,” Exp. Fluids 47(4), 849–863 (2009).
[Crossref]

C. E. Willert and M. Gharib, “Three-dimensional particle imaging with a single camera,” Exp. Fluids 12(6), 353–358 (1992).
[Crossref]

J. Biomed. Opt. (1)

J. Lu, F. Pereira, S. E. Fraser, and M. Gharib, “Three-dimensional real-time imaging of cardiac cell motions in living embryos,” J. Biomed. Opt. 13(1), 014006 (2008).
[Crossref] [PubMed]

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J. C. Crocker and D. G. Grier, “Methods of digital video microscopy for colloidal studies,” J. Colloid Interf. Sci. 179(1), 298–310 (1996).
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W. E. Moerner, “Microscopy beyond the diffraction limit using actively controlled single molecules,” J. Microsc. 246(3), 213–220 (2012).
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J. Opt. Soc. Am. A (1)

J. Phys. Chem. B (1)

C. P. Calderon, M. A. Thompson, J. M. Casolari, R. C. Paffenroth, and W. E. Moerner, “Quantifying transient 3D dynamical phenomena of single mRNA particles in live yeast cell measurements,” J. Phys. Chem. B 117(49), 15701–15713 (2013).
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C. Cierpka and C. J. Kähler, “Particle imaging techniques for volumetric three-component (3D3C) velocity measurements in microfluidics,” J. Visual. 15(1), 1–31 (2012).
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Meas. Sci. Technol. (2)

F. Pereira and M. Gharib, “Defocusing digital particle image velocimetry and the three-dimensional characterization of two-phase flows,” Meas. Sci. Technol. 13(5), 683–694 (2002).
[Crossref]

S. Y. Yoon and K. C. Kim, “3D particle position and 3D velocity field measurement in a microvolume via the defocusing concept,” Meas. Sci. Technol. 17(11), 2897–2905 (2006).
[Crossref]

Nano Lett. (3)

Y. Sun, J. D. McKenna, J. M. Murray, E. M. Ostap, and Y. E. Goldman, “Parallax: High accuracy three-dimensional single molecule tracking using split images,” Nano Lett. 9(7), 2676–2682 (2009).
[Crossref] [PubMed]

Y. Shechtman, L. E. Weiss, A. S. Backer, S. J. Sahl, and W. E. Moerner, “Precise three-dimensional scan-free multiple-particle tracking over large axial ranges with tetrapod point spread functions,” Nano Lett. 15(6), 4194–4199 (2015).
[Crossref] [PubMed]

E. Toprak, H. Balci, B. H. Blehm, and P. R. Selvin, “Three-dimensional particle tracking via bifocal imaging,” Nano Lett. 7(7), 2043–2045 (2007).
[Crossref] [PubMed]

Nat. Methods (2)

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(6), 527–529 (2008).
[Crossref] [PubMed]

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006).
[Crossref] [PubMed]

K. Jaqaman, D. Loerke, M. Mettlen, H. Kuwata, S. Grinstein, S. L. Schmid, and G. Danuser, “Robust single-particle tracking in live-cell time-lapse sequences,” Nat. methods 5(8), 695–702 (2008).
[Crossref] [PubMed]

Nat. Photonics (1)

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

Nat. Struct. Mol. Biol. (1)

J. Yajima, K. Mizutani, and T. Nishizaka, “A torque component present in mitotic kinesin Eg5 revealed by three-dimensional tracking,” Nat. Struct. Mol. Biol. 15(10), 1119–1121 (2008).
[Crossref] [PubMed]

Opt. Express (2)

Opt. Lett. (3)

Optica (1)

Phys. Chem. Chem. Phys. (1)

B. Shuang, J. Chen, L. Kisley, and C. F. Landes, “Troika of single particle tracking programing: SNR enhancement, particle identification, and mapping,” Phys. Chem. Chem. Phys. 16(2), 624–634 (2014).
[Crossref]

Phys. Rev. Lett. (2)

Y. Shechtman, S. J. Sahl, A. S. Backer, and W. E. Moerner, “Optimal point spread function design for 3D imaging,” Phys. Rev. Lett. 113(13), 133902 (2014).
[Crossref] [PubMed]

G. A. Siviloglou, J. Broky, A. Dogariu, and D. N. Christodoulides, “Observation of accelerating airy beams,” Phys. Rev. Lett. 99(21), 213901 (2007).
[Crossref]

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

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. U.S.A. 106(9), 2995–2999 (2009).
[Crossref] [PubMed]

Science (2)

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[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,” Science 313(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Other (3)

P. Zammit, “Extended depth-of-field imaging and ranging in microscopy,” Ph.D. thesis, University of Glasgow (2016).

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Supplementary Material (1)

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» Visualization 1       Flow tracking in twisted FEP capillaries. The raw data (PSF encoded) is displayed on the right while reconstructed 3D trajectories are shown on the left. The capillary had an inner diameter of about 50 microns and an outer diameter of about 140 micro

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Figures (10)

Fig. 1
Fig. 1 (a) Simulated Airy-beam PSFs with α = 7. (b) Corresponding recovered images (i.e., Wiener deconvolution with an in-focus PSF, ψr = 0). Colors from dark blue to dark red denote the defocus from 0 to 10 waves.
Fig. 2
Fig. 2 (a) Schematic of the experimental setup used for three-dimensional particle localization and tracking with Airy-CKM method. CPM: cubic-phase mask; LBS: lateral beam splitter; PI: image plane of the positive imaging channel; NI: image plane of the negative imaging channel. The displacement between PI and NI for our setup was set to be 32 μm (approximately 4.9 waves). (b) Images of the modified objective, the refractive phase mask was 7×7 mm and mounted on a 3D printed holder with a circular aperture.
Fig. 3
Fig. 3 Three-dimensional particle localization algorithm using Airy-CKM method. I C + and I C are coded images captured by the two imaging channels; PSF+(k) and PSF(k) are the pre-recorded PSF sequences; *−1 refers to the deconvolution operation using a Wiener filter [40]; I R + ( k ) and I R ( k ) are the recovered images; P+(k, i) and P(k, i) refer to the xy centroids of the ith particle when recovered with the kth PSF; D(k, i) is the disparity of the ith particle in two recovered images; X(i), Y(i) and Z(i) are the coordinates of the ith particle.
Fig. 4
Fig. 4 (a) Image of a single in-focus bead (i.e. PSF). (b) Superimposed images of the same bead with z displacements Δz =0 (blue), 30 μm (green) and 60 μm (red) respectively. (c) Recovered images of the same bead at the mentioned depths with an in-focus PSF as the recovery kernel. (d) Comparison of the diffraction-limited PSFs, the astigmatic PSFs, the Airy-beam PSFs and the deconvolved PSFs over a depth range of 150 μm, the depth of each PSF can be read from the x axis in (e). Note that the intensity of the diffraction-limited PSFs were rescaled non-linearly to make the patterns visible. The cylindrical lens has a focal length of 1000 mm. (e) SNR comparison of the different PSFs in dB.
Fig. 5
Fig. 5 (a) A snapshot of a steady laminar flow seeded with 0.96 μm fluorescent beads in an FEP capillary with a nominal inner diameter of 150 μm. The image is coded with the Airy-beam PSF and the scale bar is 50 μm. (b) Recovered images I R + and I R (deconvolved with the in-focus kernel) superimposed after two-channel mapping with magenta spots denoting the images recovered from positive imaging channel and green spots from the negative, 20 times zoomed in. The red arrows are the calculated image disparities.
Fig. 6
Fig. 6 Examples of the z localization process by matching the disparity of two channels. Different color corresponds to beads at different depths with scatters being the raw data, solid lines being the linear-fit results. The errors in the image disparity measurements are displayed as asterisk which were estimated within 100 frames of an immobilized bead.
Fig. 7
Fig. 7 The lateral translation curves for both the imaging channels when recovered with PSFs recoded at different depths. The actual x and y coordinates can be determined from these curves once z is obtained. Blue and red curves correspond to the x and y coordinates respectively with scatters being the raw data, solid lines being the linear-fit results. PI: positive imaging plane, NI: negative imaging plane.
Fig. 8
Fig. 8 Repeatability analysis from 100 measurements for each z position and each SNR. (a) Standard deviations of the x, y and z localizations of the same bead at the focal plane as a function of SNR. (b) (c) (d) Histograms of the x, y and z coordinates of the same bead at focal plane with SNR=43.6dB. (e) x, y and z standard deviations of the same bead throughout a depth range of 160 μm with an in-focus SNR of 46.5dB.
Fig. 9
Fig. 9 3D velocity field of a steady laminar flow generated in an FEP capillary with a nominal inner diameter of 150 μm, obtained by averaging 4000 frames at a frame rate of about 9 fps. Vectors on two perpendicular slices are shown, and the color map indicates velocities from 0 to 600 μm/s. The parabolic curve is a least-squares fit to the velocity vectors at that cross-section with its three projections shown below.
Fig. 10
Fig. 10 Flow tracking in a twisted FEP capillary. (a) Twisted capillary configuration. The capillary had an inner diameter of about 50 μm and an outer diameter of about 140 μm. The capillary was immersed in salt water to match its refractive index. (b) fluorescent bead trajectories in twisted capillary within 100 successive frames. Different color denotes the time with dark blue being the first frame and dark red being the last frame. (c) image of the last frame captured by the positive imaging channel.

Equations (7)

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H ( u , ψ ) ( π 12 | α u | ) 1 / 2 exp ( j α u 3 4 ) exp ( j ψ 2 u 3 α ) , u 0 ,
T ( ψ r ) = ψ r 2 ψ 2 6 π α ,
D ( ψ r , ψ ) = T ( ψ r + Δ ψ ) T ( ψ r Δ ψ ) = 2 Δ ψ ( ψ r ψ ) 3 π α ,
R = 2 Δ ψ 3 π α ,
( u v ) = A ( u + v + ) + c ,
x x 0 = y y 0 ( ψ r 2 ψ 2 ) / 6 π α ,
v ( r ) = v m ( 1 r 2 / R 2 ) ,

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