Abstract

We investigate the use of polarized illumination in multiview microscopes for determining the orientation of single-molecule fluorescence transition dipoles. First, we relate the orientation of single dipoles to measurable intensities in multiview microscopes and develop an information-theoretic metric—the solid-angle uncertainty—to compare the ability of multiview microscopes to estimate the orientation of single dipoles. Next, we compare a broad class of microscopes using this metric—single- and dual-view microscopes with varying illumination polarization, illumination numerical aperture (NA), detection NA, obliquity, asymmetry, and exposure. We find that multi-view microscopes can measure all dipole orientations, while the orientations measurable with single-view microscopes is halved because of symmetries in the detection process. We also find that choosing a small illumination NA and a large detection NA are good design choices, that multiview microscopes can benefit from oblique illumination and detection, and that asymmetric NA microscopes can benefit from exposure asymmetry.

© 2017 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

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2017 (2)

M. McQuilken, M. S. Jentzsch, A. Verma, S. B. Mehta, R. Oldenbourg, and A. S. Gladfelter, “Analysis of septin reorganization at cytokinesis using polarized fluorescence microscopy,” Front. Cell Dev. Biol. 5, 42 (2017).
[Crossref] [PubMed]

A. Meurer, C. P. Smith, M. Paprocki, O. Čertík, S. B. Kirpichev, M. Rocklin, A. Kumar, S. Ivanov, J. K. Moore, S. Singh, T. Rathnayake, S. Vig, B. E. Granger, R. P. Muller, F. Bonazzi, H. Gupta, S. Vats, F. Johansson, F. Pedregosa, M. J. Curry, A. R. Terrel, v. Roučka, A. Saboo, I. Fernando, S. Kulal, R. Cimrman, and A. Scopatz, “SymPy: symbolic computing in Python,” PeerJ Computer Science 3, e103 (2017).
[Crossref]

2016 (2)

Y. Wu, P. Chandris, P. W. Winter, E. Y. Kim, V. Jaumouillé, A. Kumar, M. Guo, J. M. Leung, C. Smith, I. Rey-Suarez, H. Liu, C. M. Waterman, K. S. Ramamurthi, P. J. La Rivière, and H. Shroff, “Simultaneous multiview capture and fusion improves spatial resolution in wide-field and light-sheet microscopy,” Optica 3, 897–910 (2016).
[Crossref] [PubMed]

S. B. Mehta, M. McQuilken, P. J. La Rivière, P. Occhipinti, A. Verma, R. Oldenbourg, A. S. Gladfelter, and T. Tani, “Dissection of molecular assembly dynamics by tracking orientation and position of single molecules in live cells,” Proc. Natl. Acad. Sci. U.S.A. 113, E6352–E6361 (2016).
[Crossref] [PubMed]

2015 (1)

R. K. Chhetri, F. Amat, Y. Wan, B. Hockendorf, W. C. Lemon, and P. J. Keller, “Whole-animal functional and developmental imaging with isotropic spatial resolution,” Nat. Methods 12, 1171–1178 (2015).
[Crossref] [PubMed]

2014 (2)

A. S. Backer and W. E. Moerner, “Extending single-molecule microscopy using optical Fourier processing,” J. Phys. Chem. B 118, 8313–8329 (2014).
[Crossref] [PubMed]

M. P. Backlund, M. D. Lew, A. S. Backer, S. J. Sahl, and W. E. Moerner, “The role of molecular dipole orientation in single-molecule fluorescence microscopy and implications for super-resolution imaging,” ChemPhysChem 15, 587–599 (2014).
[Crossref] [PubMed]

2013 (1)

Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colon-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31, 1032–1038 (2013).
[Crossref] [PubMed]

2012 (1)

2011 (1)

B. DeMay, N. Noda, A. Gladfelter, and R. Oldenbourg, “Rapid and quantitative imaging of excitation polarized fluorescence reveals ordered septin dynamics in live yeast,” Biophys. J. 101, 985–994 (2011).
[Crossref] [PubMed]

2010 (1)

A. Anantharam, B. Onoa, R. H. Edwards, R. W. Holz, and D. Axelrod, “Localized topological changes of the plasma membrane upon exocytosis visualized by polarized TIRFM,” J. Cell Biol. 188, 415–428 (2010).
[Crossref] [PubMed]

2008 (2)

C.-Y. Lu and D. A. Vanden Bout, “Analysis of orientational dynamics of single fluorophore trajectories from three-angle polarization experiments,” J. Chem. Phys. 128, 244501 (2008).
[Crossref] [PubMed]

J. C. Bowman and A. Hammerlindl, “Asymptote: A vector graphics language,” TUGBOAT 29, 288–294 (2008).

2007 (1)

J. D. Hunter, “Matplotlib: A 2D graphics environment,” Comput. Sci. Eng. 9, 90–95 (2007).
[Crossref]

2006 (2)

J. S. Tyo, D. L. Goldstein, D. B. Chenault, and J. A. Shaw, “Review of passive imaging polarimetry for remote sensing applications,” Appl. Opt. 45, 5453–5469 (2006).
[Crossref] [PubMed]

E. Toprak, J. Enderlein, S. Syed, S. A. McKinney, R. G. Petschek, T. Ha, Y. E. Goldman, and P. R. Selvin, “Defocused orientation and position imaging (DOPI) of myosin V,” Proc. Natl. Acad. Sci. U.S.A. 103, 6495–6499 (2006).
[Crossref] [PubMed]

2004 (2)

A. Débarre, R. Jaffiol, C. Julien, D. Nutarelli, A. Richard, P. Tchénio, F. Chaput, and J.-P. Boilot, “Quantitative determination of the 3D dipole orientation of single molecules,” Eur. Phys. J. D. 28, 67–77 (2004).
[Crossref]

M. A. Lieb, J. M. Zavislan, and L. Novotny, “Single-molecule orientations determined by direct emission pattern imaging,” J. Opt. Soc. Am. B 21, 1210–1215 (2004).
[Crossref]

2003 (2)

J. N. Forkey, M. E. Quinlan, M. A. Shaw, J. E. T. Corrie, and Y. E. Goldman, “Three-dimensional structural dynamics of myosin V by single-molecule fluorescence polarization,” Nature 422, 399–404 (2003).
[Crossref] [PubMed]

M. Shribak and R. Oldenbourg, “Techniques for fast and sensitive measurements of two-dimensional birefringence distributions,” Appl. Opt. 42, 3009–3017 (2003).
[Crossref] [PubMed]

2001 (2)

J. T. Fourkas, “Rapid determination of the three-dimensional orientation of single molecules,” Opt. Lett. 26, 211–213 (2001).
[Crossref]

E. J. Peterman, H. Sosa, L. S. Goldstein, and W. E. Moerner, “Polarized fluorescence microscopy of individual and many kinesin motors bound to axonemal microtubules,” Biophys. J. 81, 2851–2863 (2001).
[Crossref] [PubMed]

Adams, A.

M. Levoy, R. Ng, A. Adams, M. Footer, and M. Horowitz, “Light field microscopy,” in “ACM SIGGRAPH 2006 Papers,” (ACM, New York, NY, USA, 2006), SIGGRAPH ’06, pp. 924–934.

Agrawal, A.

Amat, F.

R. K. Chhetri, F. Amat, Y. Wan, B. Hockendorf, W. C. Lemon, and P. J. Keller, “Whole-animal functional and developmental imaging with isotropic spatial resolution,” Nat. Methods 12, 1171–1178 (2015).
[Crossref] [PubMed]

Anantharam, A.

A. Anantharam, B. Onoa, R. H. Edwards, R. W. Holz, and D. Axelrod, “Localized topological changes of the plasma membrane upon exocytosis visualized by polarized TIRFM,” J. Cell Biol. 188, 415–428 (2010).
[Crossref] [PubMed]

Anderson, T. W.

T. W. Anderson, An introduction to multivariate statistical analysis (Wiley, 1958).

Ardiel, E.

Y. Wu, A. Kumar, C. Smith, E. Ardiel, P. Chandris, R. Christensen, I. Rey-Suarez, M. Guo, H. Vishwasrao, J. Chen, J. Tang, A. Upadhyaya, P. La Rivière, and H. Shroff, “Reflective imaging improves resolution, speed, and collection efficiency in light sheet microscopy,” bioRxiv (2017).

Axelrod, D.

A. Anantharam, B. Onoa, R. H. Edwards, R. W. Holz, and D. Axelrod, “Localized topological changes of the plasma membrane upon exocytosis visualized by polarized TIRFM,” J. Cell Biol. 188, 415–428 (2010).
[Crossref] [PubMed]

Backer, A. S.

M. P. Backlund, M. D. Lew, A. S. Backer, S. J. Sahl, and W. E. Moerner, “The role of molecular dipole orientation in single-molecule fluorescence microscopy and implications for super-resolution imaging,” ChemPhysChem 15, 587–599 (2014).
[Crossref] [PubMed]

A. S. Backer and W. E. Moerner, “Extending single-molecule microscopy using optical Fourier processing,” J. Phys. Chem. B 118, 8313–8329 (2014).
[Crossref] [PubMed]

A. S. Backer, M. Lee, and W. E. Moerner, “Enhanced DNA imaging using super-resolution microscopy and simultaneous single-molecule orientation measurements,” in “Conference on Lasers and Electro-Optics,” (Optical Society of America, 2016), p. JTh4B.4.

Backlund, M. P.

M. P. Backlund, M. D. Lew, A. S. Backer, S. J. Sahl, and W. E. Moerner, “The role of molecular dipole orientation in single-molecule fluorescence microscopy and implications for super-resolution imaging,” ChemPhysChem 15, 587–599 (2014).
[Crossref] [PubMed]

Bao, Z.

Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colon-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31, 1032–1038 (2013).
[Crossref] [PubMed]

Boilot, J.-P.

A. Débarre, R. Jaffiol, C. Julien, D. Nutarelli, A. Richard, P. Tchénio, F. Chaput, and J.-P. Boilot, “Quantitative determination of the 3D dipole orientation of single molecules,” Eur. Phys. J. D. 28, 67–77 (2004).
[Crossref]

Bonazzi, F.

A. Meurer, C. P. Smith, M. Paprocki, O. Čertík, S. B. Kirpichev, M. Rocklin, A. Kumar, S. Ivanov, J. K. Moore, S. Singh, T. Rathnayake, S. Vig, B. E. Granger, R. P. Muller, F. Bonazzi, H. Gupta, S. Vats, F. Johansson, F. Pedregosa, M. J. Curry, A. R. Terrel, v. Roučka, A. Saboo, I. Fernando, S. Kulal, R. Cimrman, and A. Scopatz, “SymPy: symbolic computing in Python,” PeerJ Computer Science 3, e103 (2017).
[Crossref]

Bowman, J. C.

J. C. Bowman and A. Hammerlindl, “Asymptote: A vector graphics language,” TUGBOAT 29, 288–294 (2008).

Campagnola, L.

L. Campagnola, A. Klein, C. Larson, N. P. Rossant, and Rougier, “VisPy: Harnessing The GPU For Fast, High-Level Visualization,” in Proceedings of the 14th Python in Science Conference, (2015).

Certík, O.

A. Meurer, C. P. Smith, M. Paprocki, O. Čertík, S. B. Kirpichev, M. Rocklin, A. Kumar, S. Ivanov, J. K. Moore, S. Singh, T. Rathnayake, S. Vig, B. E. Granger, R. P. Muller, F. Bonazzi, H. Gupta, S. Vats, F. Johansson, F. Pedregosa, M. J. Curry, A. R. Terrel, v. Roučka, A. Saboo, I. Fernando, S. Kulal, R. Cimrman, and A. Scopatz, “SymPy: symbolic computing in Python,” PeerJ Computer Science 3, e103 (2017).
[Crossref]

Chandris, P.

Y. Wu, P. Chandris, P. W. Winter, E. Y. Kim, V. Jaumouillé, A. Kumar, M. Guo, J. M. Leung, C. Smith, I. Rey-Suarez, H. Liu, C. M. Waterman, K. S. Ramamurthi, P. J. La Rivière, and H. Shroff, “Simultaneous multiview capture and fusion improves spatial resolution in wide-field and light-sheet microscopy,” Optica 3, 897–910 (2016).
[Crossref] [PubMed]

Y. Wu, A. Kumar, C. Smith, E. Ardiel, P. Chandris, R. Christensen, I. Rey-Suarez, M. Guo, H. Vishwasrao, J. Chen, J. Tang, A. Upadhyaya, P. La Rivière, and H. Shroff, “Reflective imaging improves resolution, speed, and collection efficiency in light sheet microscopy,” bioRxiv (2017).

Chaput, F.

A. Débarre, R. Jaffiol, C. Julien, D. Nutarelli, A. Richard, P. Tchénio, F. Chaput, and J.-P. Boilot, “Quantitative determination of the 3D dipole orientation of single molecules,” Eur. Phys. J. D. 28, 67–77 (2004).
[Crossref]

Chen, J.

Y. Wu, A. Kumar, C. Smith, E. Ardiel, P. Chandris, R. Christensen, I. Rey-Suarez, M. Guo, H. Vishwasrao, J. Chen, J. Tang, A. Upadhyaya, P. La Rivière, and H. Shroff, “Reflective imaging improves resolution, speed, and collection efficiency in light sheet microscopy,” bioRxiv (2017).

Chenault, D. B.

Chhetri, R. K.

R. K. Chhetri, F. Amat, Y. Wan, B. Hockendorf, W. C. Lemon, and P. J. Keller, “Whole-animal functional and developmental imaging with isotropic spatial resolution,” Nat. Methods 12, 1171–1178 (2015).
[Crossref] [PubMed]

Christensen, R.

Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colon-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31, 1032–1038 (2013).
[Crossref] [PubMed]

Y. Wu, A. Kumar, C. Smith, E. Ardiel, P. Chandris, R. Christensen, I. Rey-Suarez, M. Guo, H. Vishwasrao, J. Chen, J. Tang, A. Upadhyaya, P. La Rivière, and H. Shroff, “Reflective imaging improves resolution, speed, and collection efficiency in light sheet microscopy,” bioRxiv (2017).

Cimrman, R.

A. Meurer, C. P. Smith, M. Paprocki, O. Čertík, S. B. Kirpichev, M. Rocklin, A. Kumar, S. Ivanov, J. K. Moore, S. Singh, T. Rathnayake, S. Vig, B. E. Granger, R. P. Muller, F. Bonazzi, H. Gupta, S. Vats, F. Johansson, F. Pedregosa, M. J. Curry, A. R. Terrel, v. Roučka, A. Saboo, I. Fernando, S. Kulal, R. Cimrman, and A. Scopatz, “SymPy: symbolic computing in Python,” PeerJ Computer Science 3, e103 (2017).
[Crossref]

Coe, D.

D. Coe, “Fisher matrices and confidence ellipses: a quick-start guide and software,” arXiv preprint arXiv:0906.4123 (2009).

Colbert, S. C.

S. van der Walt, S. C. Colbert, and G. Varoquaux, “The NumPy array: a structure for efficient numerical computation,” CoRR abs/1102.1523 (2011).

Colon-Ramos, D. A.

Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colon-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31, 1032–1038 (2013).
[Crossref] [PubMed]

Corrie, J. E. T.

J. N. Forkey, M. E. Quinlan, M. A. Shaw, J. E. T. Corrie, and Y. E. Goldman, “Three-dimensional structural dynamics of myosin V by single-molecule fluorescence polarization,” Nature 422, 399–404 (2003).
[Crossref] [PubMed]

Curry, M. J.

A. Meurer, C. P. Smith, M. Paprocki, O. Čertík, S. B. Kirpichev, M. Rocklin, A. Kumar, S. Ivanov, J. K. Moore, S. Singh, T. Rathnayake, S. Vig, B. E. Granger, R. P. Muller, F. Bonazzi, H. Gupta, S. Vats, F. Johansson, F. Pedregosa, M. J. Curry, A. R. Terrel, v. Roučka, A. Saboo, I. Fernando, S. Kulal, R. Cimrman, and A. Scopatz, “SymPy: symbolic computing in Python,” PeerJ Computer Science 3, e103 (2017).
[Crossref]

Débarre, A.

A. Débarre, R. Jaffiol, C. Julien, D. Nutarelli, A. Richard, P. Tchénio, F. Chaput, and J.-P. Boilot, “Quantitative determination of the 3D dipole orientation of single molecules,” Eur. Phys. J. D. 28, 67–77 (2004).
[Crossref]

DeMay, B.

B. DeMay, N. Noda, A. Gladfelter, and R. Oldenbourg, “Rapid and quantitative imaging of excitation polarized fluorescence reveals ordered septin dynamics in live yeast,” Biophys. J. 101, 985–994 (2011).
[Crossref] [PubMed]

Edwards, R. H.

A. Anantharam, B. Onoa, R. H. Edwards, R. W. Holz, and D. Axelrod, “Localized topological changes of the plasma membrane upon exocytosis visualized by polarized TIRFM,” J. Cell Biol. 188, 415–428 (2010).
[Crossref] [PubMed]

Enderlein, J.

E. Toprak, J. Enderlein, S. Syed, S. A. McKinney, R. G. Petschek, T. Ha, Y. E. Goldman, and P. R. Selvin, “Defocused orientation and position imaging (DOPI) of myosin V,” Proc. Natl. Acad. Sci. U.S.A. 103, 6495–6499 (2006).
[Crossref] [PubMed]

Fernando, I.

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B. DeMay, N. Noda, A. Gladfelter, and R. Oldenbourg, “Rapid and quantitative imaging of excitation polarized fluorescence reveals ordered septin dynamics in live yeast,” Biophys. J. 101, 985–994 (2011).
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M. McQuilken, M. S. Jentzsch, A. Verma, S. B. Mehta, R. Oldenbourg, and A. S. Gladfelter, “Analysis of septin reorganization at cytokinesis using polarized fluorescence microscopy,” Front. Cell Dev. Biol. 5, 42 (2017).
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E. Toprak, J. Enderlein, S. Syed, S. A. McKinney, R. G. Petschek, T. Ha, Y. E. Goldman, and P. R. Selvin, “Defocused orientation and position imaging (DOPI) of myosin V,” Proc. Natl. Acad. Sci. U.S.A. 103, 6495–6499 (2006).
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Goldstein, L. S.

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A. Meurer, C. P. Smith, M. Paprocki, O. Čertík, S. B. Kirpichev, M. Rocklin, A. Kumar, S. Ivanov, J. K. Moore, S. Singh, T. Rathnayake, S. Vig, B. E. Granger, R. P. Muller, F. Bonazzi, H. Gupta, S. Vats, F. Johansson, F. Pedregosa, M. J. Curry, A. R. Terrel, v. Roučka, A. Saboo, I. Fernando, S. Kulal, R. Cimrman, and A. Scopatz, “SymPy: symbolic computing in Python,” PeerJ Computer Science 3, e103 (2017).
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Gupta, H.

A. Meurer, C. P. Smith, M. Paprocki, O. Čertík, S. B. Kirpichev, M. Rocklin, A. Kumar, S. Ivanov, J. K. Moore, S. Singh, T. Rathnayake, S. Vig, B. E. Granger, R. P. Muller, F. Bonazzi, H. Gupta, S. Vats, F. Johansson, F. Pedregosa, M. J. Curry, A. R. Terrel, v. Roučka, A. Saboo, I. Fernando, S. Kulal, R. Cimrman, and A. Scopatz, “SymPy: symbolic computing in Python,” PeerJ Computer Science 3, e103 (2017).
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E. Toprak, J. Enderlein, S. Syed, S. A. McKinney, R. G. Petschek, T. Ha, Y. E. Goldman, and P. R. Selvin, “Defocused orientation and position imaging (DOPI) of myosin V,” Proc. Natl. Acad. Sci. U.S.A. 103, 6495–6499 (2006).
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A. Anantharam, B. Onoa, R. H. Edwards, R. W. Holz, and D. Axelrod, “Localized topological changes of the plasma membrane upon exocytosis visualized by polarized TIRFM,” J. Cell Biol. 188, 415–428 (2010).
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A. Débarre, R. Jaffiol, C. Julien, D. Nutarelli, A. Richard, P. Tchénio, F. Chaput, and J.-P. Boilot, “Quantitative determination of the 3D dipole orientation of single molecules,” Eur. Phys. J. D. 28, 67–77 (2004).
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Jentzsch, M. S.

M. McQuilken, M. S. Jentzsch, A. Verma, S. B. Mehta, R. Oldenbourg, and A. S. Gladfelter, “Analysis of septin reorganization at cytokinesis using polarized fluorescence microscopy,” Front. Cell Dev. Biol. 5, 42 (2017).
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A. Meurer, C. P. Smith, M. Paprocki, O. Čertík, S. B. Kirpichev, M. Rocklin, A. Kumar, S. Ivanov, J. K. Moore, S. Singh, T. Rathnayake, S. Vig, B. E. Granger, R. P. Muller, F. Bonazzi, H. Gupta, S. Vats, F. Johansson, F. Pedregosa, M. J. Curry, A. R. Terrel, v. Roučka, A. Saboo, I. Fernando, S. Kulal, R. Cimrman, and A. Scopatz, “SymPy: symbolic computing in Python,” PeerJ Computer Science 3, e103 (2017).
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R. K. Chhetri, F. Amat, Y. Wan, B. Hockendorf, W. C. Lemon, and P. J. Keller, “Whole-animal functional and developmental imaging with isotropic spatial resolution,” Nat. Methods 12, 1171–1178 (2015).
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Kim, E. Y.

Kirpichev, S. B.

A. Meurer, C. P. Smith, M. Paprocki, O. Čertík, S. B. Kirpichev, M. Rocklin, A. Kumar, S. Ivanov, J. K. Moore, S. Singh, T. Rathnayake, S. Vig, B. E. Granger, R. P. Muller, F. Bonazzi, H. Gupta, S. Vats, F. Johansson, F. Pedregosa, M. J. Curry, A. R. Terrel, v. Roučka, A. Saboo, I. Fernando, S. Kulal, R. Cimrman, and A. Scopatz, “SymPy: symbolic computing in Python,” PeerJ Computer Science 3, e103 (2017).
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A. Meurer, C. P. Smith, M. Paprocki, O. Čertík, S. B. Kirpichev, M. Rocklin, A. Kumar, S. Ivanov, J. K. Moore, S. Singh, T. Rathnayake, S. Vig, B. E. Granger, R. P. Muller, F. Bonazzi, H. Gupta, S. Vats, F. Johansson, F. Pedregosa, M. J. Curry, A. R. Terrel, v. Roučka, A. Saboo, I. Fernando, S. Kulal, R. Cimrman, and A. Scopatz, “SymPy: symbolic computing in Python,” PeerJ Computer Science 3, e103 (2017).
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A. Meurer, C. P. Smith, M. Paprocki, O. Čertík, S. B. Kirpichev, M. Rocklin, A. Kumar, S. Ivanov, J. K. Moore, S. Singh, T. Rathnayake, S. Vig, B. E. Granger, R. P. Muller, F. Bonazzi, H. Gupta, S. Vats, F. Johansson, F. Pedregosa, M. J. Curry, A. R. Terrel, v. Roučka, A. Saboo, I. Fernando, S. Kulal, R. Cimrman, and A. Scopatz, “SymPy: symbolic computing in Python,” PeerJ Computer Science 3, e103 (2017).
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Y. Wu, P. Chandris, P. W. Winter, E. Y. Kim, V. Jaumouillé, A. Kumar, M. Guo, J. M. Leung, C. Smith, I. Rey-Suarez, H. Liu, C. M. Waterman, K. S. Ramamurthi, P. J. La Rivière, and H. Shroff, “Simultaneous multiview capture and fusion improves spatial resolution in wide-field and light-sheet microscopy,” Optica 3, 897–910 (2016).
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La Rivière, P.

Y. Wu, A. Kumar, C. Smith, E. Ardiel, P. Chandris, R. Christensen, I. Rey-Suarez, M. Guo, H. Vishwasrao, J. Chen, J. Tang, A. Upadhyaya, P. La Rivière, and H. Shroff, “Reflective imaging improves resolution, speed, and collection efficiency in light sheet microscopy,” bioRxiv (2017).

La Rivière, P. J.

Y. Wu, P. Chandris, P. W. Winter, E. Y. Kim, V. Jaumouillé, A. Kumar, M. Guo, J. M. Leung, C. Smith, I. Rey-Suarez, H. Liu, C. M. Waterman, K. S. Ramamurthi, P. J. La Rivière, and H. Shroff, “Simultaneous multiview capture and fusion improves spatial resolution in wide-field and light-sheet microscopy,” Optica 3, 897–910 (2016).
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S. B. Mehta, M. McQuilken, P. J. La Rivière, P. Occhipinti, A. Verma, R. Oldenbourg, A. S. Gladfelter, and T. Tani, “Dissection of molecular assembly dynamics by tracking orientation and position of single molecules in live cells,” Proc. Natl. Acad. Sci. U.S.A. 113, E6352–E6361 (2016).
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Larson, C.

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Lee, M.

A. S. Backer, M. Lee, and W. E. Moerner, “Enhanced DNA imaging using super-resolution microscopy and simultaneous single-molecule orientation measurements,” in “Conference on Lasers and Electro-Optics,” (Optical Society of America, 2016), p. JTh4B.4.

Lemon, W. C.

R. K. Chhetri, F. Amat, Y. Wan, B. Hockendorf, W. C. Lemon, and P. J. Keller, “Whole-animal functional and developmental imaging with isotropic spatial resolution,” Nat. Methods 12, 1171–1178 (2015).
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Leung, J. M.

Levoy, M.

M. Levoy, R. Ng, A. Adams, M. Footer, and M. Horowitz, “Light field microscopy,” in “ACM SIGGRAPH 2006 Papers,” (ACM, New York, NY, USA, 2006), SIGGRAPH ’06, pp. 924–934.

Lew, M. D.

M. P. Backlund, M. D. Lew, A. S. Backer, S. J. Sahl, and W. E. Moerner, “The role of molecular dipole orientation in single-molecule fluorescence microscopy and implications for super-resolution imaging,” ChemPhysChem 15, 587–599 (2014).
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E. Toprak, J. Enderlein, S. Syed, S. A. McKinney, R. G. Petschek, T. Ha, Y. E. Goldman, and P. R. Selvin, “Defocused orientation and position imaging (DOPI) of myosin V,” Proc. Natl. Acad. Sci. U.S.A. 103, 6495–6499 (2006).
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McQuilken, M.

M. McQuilken, M. S. Jentzsch, A. Verma, S. B. Mehta, R. Oldenbourg, and A. S. Gladfelter, “Analysis of septin reorganization at cytokinesis using polarized fluorescence microscopy,” Front. Cell Dev. Biol. 5, 42 (2017).
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S. B. Mehta, M. McQuilken, P. J. La Rivière, P. Occhipinti, A. Verma, R. Oldenbourg, A. S. Gladfelter, and T. Tani, “Dissection of molecular assembly dynamics by tracking orientation and position of single molecules in live cells,” Proc. Natl. Acad. Sci. U.S.A. 113, E6352–E6361 (2016).
[Crossref] [PubMed]

Mehta, S. B.

M. McQuilken, M. S. Jentzsch, A. Verma, S. B. Mehta, R. Oldenbourg, and A. S. Gladfelter, “Analysis of septin reorganization at cytokinesis using polarized fluorescence microscopy,” Front. Cell Dev. Biol. 5, 42 (2017).
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S. B. Mehta, M. McQuilken, P. J. La Rivière, P. Occhipinti, A. Verma, R. Oldenbourg, A. S. Gladfelter, and T. Tani, “Dissection of molecular assembly dynamics by tracking orientation and position of single molecules in live cells,” Proc. Natl. Acad. Sci. U.S.A. 113, E6352–E6361 (2016).
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Meurer, A.

A. Meurer, C. P. Smith, M. Paprocki, O. Čertík, S. B. Kirpichev, M. Rocklin, A. Kumar, S. Ivanov, J. K. Moore, S. Singh, T. Rathnayake, S. Vig, B. E. Granger, R. P. Muller, F. Bonazzi, H. Gupta, S. Vats, F. Johansson, F. Pedregosa, M. J. Curry, A. R. Terrel, v. Roučka, A. Saboo, I. Fernando, S. Kulal, R. Cimrman, and A. Scopatz, “SymPy: symbolic computing in Python,” PeerJ Computer Science 3, e103 (2017).
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M. P. Backlund, M. D. Lew, A. S. Backer, S. J. Sahl, and W. E. Moerner, “The role of molecular dipole orientation in single-molecule fluorescence microscopy and implications for super-resolution imaging,” ChemPhysChem 15, 587–599 (2014).
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E. J. Peterman, H. Sosa, L. S. Goldstein, and W. E. Moerner, “Polarized fluorescence microscopy of individual and many kinesin motors bound to axonemal microtubules,” Biophys. J. 81, 2851–2863 (2001).
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A. S. Backer, M. Lee, and W. E. Moerner, “Enhanced DNA imaging using super-resolution microscopy and simultaneous single-molecule orientation measurements,” in “Conference on Lasers and Electro-Optics,” (Optical Society of America, 2016), p. JTh4B.4.

Moore, J. K.

A. Meurer, C. P. Smith, M. Paprocki, O. Čertík, S. B. Kirpichev, M. Rocklin, A. Kumar, S. Ivanov, J. K. Moore, S. Singh, T. Rathnayake, S. Vig, B. E. Granger, R. P. Muller, F. Bonazzi, H. Gupta, S. Vats, F. Johansson, F. Pedregosa, M. J. Curry, A. R. Terrel, v. Roučka, A. Saboo, I. Fernando, S. Kulal, R. Cimrman, and A. Scopatz, “SymPy: symbolic computing in Python,” PeerJ Computer Science 3, e103 (2017).
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Muller, R. P.

A. Meurer, C. P. Smith, M. Paprocki, O. Čertík, S. B. Kirpichev, M. Rocklin, A. Kumar, S. Ivanov, J. K. Moore, S. Singh, T. Rathnayake, S. Vig, B. E. Granger, R. P. Muller, F. Bonazzi, H. Gupta, S. Vats, F. Johansson, F. Pedregosa, M. J. Curry, A. R. Terrel, v. Roučka, A. Saboo, I. Fernando, S. Kulal, R. Cimrman, and A. Scopatz, “SymPy: symbolic computing in Python,” PeerJ Computer Science 3, e103 (2017).
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Ng, R.

M. Levoy, R. Ng, A. Adams, M. Footer, and M. Horowitz, “Light field microscopy,” in “ACM SIGGRAPH 2006 Papers,” (ACM, New York, NY, USA, 2006), SIGGRAPH ’06, pp. 924–934.

Noda, N.

B. DeMay, N. Noda, A. Gladfelter, and R. Oldenbourg, “Rapid and quantitative imaging of excitation polarized fluorescence reveals ordered septin dynamics in live yeast,” Biophys. J. 101, 985–994 (2011).
[Crossref] [PubMed]

Novotny, L.

Nutarelli, D.

A. Débarre, R. Jaffiol, C. Julien, D. Nutarelli, A. Richard, P. Tchénio, F. Chaput, and J.-P. Boilot, “Quantitative determination of the 3D dipole orientation of single molecules,” Eur. Phys. J. D. 28, 67–77 (2004).
[Crossref]

Occhipinti, P.

S. B. Mehta, M. McQuilken, P. J. La Rivière, P. Occhipinti, A. Verma, R. Oldenbourg, A. S. Gladfelter, and T. Tani, “Dissection of molecular assembly dynamics by tracking orientation and position of single molecules in live cells,” Proc. Natl. Acad. Sci. U.S.A. 113, E6352–E6361 (2016).
[Crossref] [PubMed]

Oldenbourg, R.

M. McQuilken, M. S. Jentzsch, A. Verma, S. B. Mehta, R. Oldenbourg, and A. S. Gladfelter, “Analysis of septin reorganization at cytokinesis using polarized fluorescence microscopy,” Front. Cell Dev. Biol. 5, 42 (2017).
[Crossref] [PubMed]

S. B. Mehta, M. McQuilken, P. J. La Rivière, P. Occhipinti, A. Verma, R. Oldenbourg, A. S. Gladfelter, and T. Tani, “Dissection of molecular assembly dynamics by tracking orientation and position of single molecules in live cells,” Proc. Natl. Acad. Sci. U.S.A. 113, E6352–E6361 (2016).
[Crossref] [PubMed]

B. DeMay, N. Noda, A. Gladfelter, and R. Oldenbourg, “Rapid and quantitative imaging of excitation polarized fluorescence reveals ordered septin dynamics in live yeast,” Biophys. J. 101, 985–994 (2011).
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M. Shribak and R. Oldenbourg, “Techniques for fast and sensitive measurements of two-dimensional birefringence distributions,” Appl. Opt. 42, 3009–3017 (2003).
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Onoa, B.

A. Anantharam, B. Onoa, R. H. Edwards, R. W. Holz, and D. Axelrod, “Localized topological changes of the plasma membrane upon exocytosis visualized by polarized TIRFM,” J. Cell Biol. 188, 415–428 (2010).
[Crossref] [PubMed]

Paprocki, M.

A. Meurer, C. P. Smith, M. Paprocki, O. Čertík, S. B. Kirpichev, M. Rocklin, A. Kumar, S. Ivanov, J. K. Moore, S. Singh, T. Rathnayake, S. Vig, B. E. Granger, R. P. Muller, F. Bonazzi, H. Gupta, S. Vats, F. Johansson, F. Pedregosa, M. J. Curry, A. R. Terrel, v. Roučka, A. Saboo, I. Fernando, S. Kulal, R. Cimrman, and A. Scopatz, “SymPy: symbolic computing in Python,” PeerJ Computer Science 3, e103 (2017).
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Pedregosa, F.

A. Meurer, C. P. Smith, M. Paprocki, O. Čertík, S. B. Kirpichev, M. Rocklin, A. Kumar, S. Ivanov, J. K. Moore, S. Singh, T. Rathnayake, S. Vig, B. E. Granger, R. P. Muller, F. Bonazzi, H. Gupta, S. Vats, F. Johansson, F. Pedregosa, M. J. Curry, A. R. Terrel, v. Roučka, A. Saboo, I. Fernando, S. Kulal, R. Cimrman, and A. Scopatz, “SymPy: symbolic computing in Python,” PeerJ Computer Science 3, e103 (2017).
[Crossref]

Peterman, E. J.

E. J. Peterman, H. Sosa, L. S. Goldstein, and W. E. Moerner, “Polarized fluorescence microscopy of individual and many kinesin motors bound to axonemal microtubules,” Biophys. J. 81, 2851–2863 (2001).
[Crossref] [PubMed]

Petschek, R. G.

E. Toprak, J. Enderlein, S. Syed, S. A. McKinney, R. G. Petschek, T. Ha, Y. E. Goldman, and P. R. Selvin, “Defocused orientation and position imaging (DOPI) of myosin V,” Proc. Natl. Acad. Sci. U.S.A. 103, 6495–6499 (2006).
[Crossref] [PubMed]

Piestun, R.

Quinlan, M. E.

J. N. Forkey, M. E. Quinlan, M. A. Shaw, J. E. T. Corrie, and Y. E. Goldman, “Three-dimensional structural dynamics of myosin V by single-molecule fluorescence polarization,” Nature 422, 399–404 (2003).
[Crossref] [PubMed]

Quirin, S.

Ramamurthi, K. S.

Rathnayake, T.

A. Meurer, C. P. Smith, M. Paprocki, O. Čertík, S. B. Kirpichev, M. Rocklin, A. Kumar, S. Ivanov, J. K. Moore, S. Singh, T. Rathnayake, S. Vig, B. E. Granger, R. P. Muller, F. Bonazzi, H. Gupta, S. Vats, F. Johansson, F. Pedregosa, M. J. Curry, A. R. Terrel, v. Roučka, A. Saboo, I. Fernando, S. Kulal, R. Cimrman, and A. Scopatz, “SymPy: symbolic computing in Python,” PeerJ Computer Science 3, e103 (2017).
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Rey-Suarez, I.

Y. Wu, P. Chandris, P. W. Winter, E. Y. Kim, V. Jaumouillé, A. Kumar, M. Guo, J. M. Leung, C. Smith, I. Rey-Suarez, H. Liu, C. M. Waterman, K. S. Ramamurthi, P. J. La Rivière, and H. Shroff, “Simultaneous multiview capture and fusion improves spatial resolution in wide-field and light-sheet microscopy,” Optica 3, 897–910 (2016).
[Crossref] [PubMed]

Y. Wu, A. Kumar, C. Smith, E. Ardiel, P. Chandris, R. Christensen, I. Rey-Suarez, M. Guo, H. Vishwasrao, J. Chen, J. Tang, A. Upadhyaya, P. La Rivière, and H. Shroff, “Reflective imaging improves resolution, speed, and collection efficiency in light sheet microscopy,” bioRxiv (2017).

Richard, A.

A. Débarre, R. Jaffiol, C. Julien, D. Nutarelli, A. Richard, P. Tchénio, F. Chaput, and J.-P. Boilot, “Quantitative determination of the 3D dipole orientation of single molecules,” Eur. Phys. J. D. 28, 67–77 (2004).
[Crossref]

Rocklin, M.

A. Meurer, C. P. Smith, M. Paprocki, O. Čertík, S. B. Kirpichev, M. Rocklin, A. Kumar, S. Ivanov, J. K. Moore, S. Singh, T. Rathnayake, S. Vig, B. E. Granger, R. P. Muller, F. Bonazzi, H. Gupta, S. Vats, F. Johansson, F. Pedregosa, M. J. Curry, A. R. Terrel, v. Roučka, A. Saboo, I. Fernando, S. Kulal, R. Cimrman, and A. Scopatz, “SymPy: symbolic computing in Python,” PeerJ Computer Science 3, e103 (2017).
[Crossref]

Rossant, N. P.

L. Campagnola, A. Klein, C. Larson, N. P. Rossant, and Rougier, “VisPy: Harnessing The GPU For Fast, High-Level Visualization,” in Proceedings of the 14th Python in Science Conference, (2015).

Roucka, v.

A. Meurer, C. P. Smith, M. Paprocki, O. Čertík, S. B. Kirpichev, M. Rocklin, A. Kumar, S. Ivanov, J. K. Moore, S. Singh, T. Rathnayake, S. Vig, B. E. Granger, R. P. Muller, F. Bonazzi, H. Gupta, S. Vats, F. Johansson, F. Pedregosa, M. J. Curry, A. R. Terrel, v. Roučka, A. Saboo, I. Fernando, S. Kulal, R. Cimrman, and A. Scopatz, “SymPy: symbolic computing in Python,” PeerJ Computer Science 3, e103 (2017).
[Crossref]

Rougier,

L. Campagnola, A. Klein, C. Larson, N. P. Rossant, and Rougier, “VisPy: Harnessing The GPU For Fast, High-Level Visualization,” in Proceedings of the 14th Python in Science Conference, (2015).

Saboo, A.

A. Meurer, C. P. Smith, M. Paprocki, O. Čertík, S. B. Kirpichev, M. Rocklin, A. Kumar, S. Ivanov, J. K. Moore, S. Singh, T. Rathnayake, S. Vig, B. E. Granger, R. P. Muller, F. Bonazzi, H. Gupta, S. Vats, F. Johansson, F. Pedregosa, M. J. Curry, A. R. Terrel, v. Roučka, A. Saboo, I. Fernando, S. Kulal, R. Cimrman, and A. Scopatz, “SymPy: symbolic computing in Python,” PeerJ Computer Science 3, e103 (2017).
[Crossref]

Sahl, S. J.

M. P. Backlund, M. D. Lew, A. S. Backer, S. J. Sahl, and W. E. Moerner, “The role of molecular dipole orientation in single-molecule fluorescence microscopy and implications for super-resolution imaging,” ChemPhysChem 15, 587–599 (2014).
[Crossref] [PubMed]

Santella, A.

Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colon-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31, 1032–1038 (2013).
[Crossref] [PubMed]

Scopatz, A.

A. Meurer, C. P. Smith, M. Paprocki, O. Čertík, S. B. Kirpichev, M. Rocklin, A. Kumar, S. Ivanov, J. K. Moore, S. Singh, T. Rathnayake, S. Vig, B. E. Granger, R. P. Muller, F. Bonazzi, H. Gupta, S. Vats, F. Johansson, F. Pedregosa, M. J. Curry, A. R. Terrel, v. Roučka, A. Saboo, I. Fernando, S. Kulal, R. Cimrman, and A. Scopatz, “SymPy: symbolic computing in Python,” PeerJ Computer Science 3, e103 (2017).
[Crossref]

Selvin, P. R.

E. Toprak, J. Enderlein, S. Syed, S. A. McKinney, R. G. Petschek, T. Ha, Y. E. Goldman, and P. R. Selvin, “Defocused orientation and position imaging (DOPI) of myosin V,” Proc. Natl. Acad. Sci. U.S.A. 103, 6495–6499 (2006).
[Crossref] [PubMed]

Senseney, J.

Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colon-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31, 1032–1038 (2013).
[Crossref] [PubMed]

Shaw, J. A.

Shaw, M. A.

J. N. Forkey, M. E. Quinlan, M. A. Shaw, J. E. T. Corrie, and Y. E. Goldman, “Three-dimensional structural dynamics of myosin V by single-molecule fluorescence polarization,” Nature 422, 399–404 (2003).
[Crossref] [PubMed]

Shribak, M.

Shroff, H.

Y. Wu, P. Chandris, P. W. Winter, E. Y. Kim, V. Jaumouillé, A. Kumar, M. Guo, J. M. Leung, C. Smith, I. Rey-Suarez, H. Liu, C. M. Waterman, K. S. Ramamurthi, P. J. La Rivière, and H. Shroff, “Simultaneous multiview capture and fusion improves spatial resolution in wide-field and light-sheet microscopy,” Optica 3, 897–910 (2016).
[Crossref] [PubMed]

Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colon-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31, 1032–1038 (2013).
[Crossref] [PubMed]

Y. Wu, A. Kumar, C. Smith, E. Ardiel, P. Chandris, R. Christensen, I. Rey-Suarez, M. Guo, H. Vishwasrao, J. Chen, J. Tang, A. Upadhyaya, P. La Rivière, and H. Shroff, “Reflective imaging improves resolution, speed, and collection efficiency in light sheet microscopy,” bioRxiv (2017).

Singh, S.

A. Meurer, C. P. Smith, M. Paprocki, O. Čertík, S. B. Kirpichev, M. Rocklin, A. Kumar, S. Ivanov, J. K. Moore, S. Singh, T. Rathnayake, S. Vig, B. E. Granger, R. P. Muller, F. Bonazzi, H. Gupta, S. Vats, F. Johansson, F. Pedregosa, M. J. Curry, A. R. Terrel, v. Roučka, A. Saboo, I. Fernando, S. Kulal, R. Cimrman, and A. Scopatz, “SymPy: symbolic computing in Python,” PeerJ Computer Science 3, e103 (2017).
[Crossref]

Smith, C.

Y. Wu, P. Chandris, P. W. Winter, E. Y. Kim, V. Jaumouillé, A. Kumar, M. Guo, J. M. Leung, C. Smith, I. Rey-Suarez, H. Liu, C. M. Waterman, K. S. Ramamurthi, P. J. La Rivière, and H. Shroff, “Simultaneous multiview capture and fusion improves spatial resolution in wide-field and light-sheet microscopy,” Optica 3, 897–910 (2016).
[Crossref] [PubMed]

Y. Wu, A. Kumar, C. Smith, E. Ardiel, P. Chandris, R. Christensen, I. Rey-Suarez, M. Guo, H. Vishwasrao, J. Chen, J. Tang, A. Upadhyaya, P. La Rivière, and H. Shroff, “Reflective imaging improves resolution, speed, and collection efficiency in light sheet microscopy,” bioRxiv (2017).

Smith, C. P.

A. Meurer, C. P. Smith, M. Paprocki, O. Čertík, S. B. Kirpichev, M. Rocklin, A. Kumar, S. Ivanov, J. K. Moore, S. Singh, T. Rathnayake, S. Vig, B. E. Granger, R. P. Muller, F. Bonazzi, H. Gupta, S. Vats, F. Johansson, F. Pedregosa, M. J. Curry, A. R. Terrel, v. Roučka, A. Saboo, I. Fernando, S. Kulal, R. Cimrman, and A. Scopatz, “SymPy: symbolic computing in Python,” PeerJ Computer Science 3, e103 (2017).
[Crossref]

Sosa, H.

E. J. Peterman, H. Sosa, L. S. Goldstein, and W. E. Moerner, “Polarized fluorescence microscopy of individual and many kinesin motors bound to axonemal microtubules,” Biophys. J. 81, 2851–2863 (2001).
[Crossref] [PubMed]

Syed, S.

E. Toprak, J. Enderlein, S. Syed, S. A. McKinney, R. G. Petschek, T. Ha, Y. E. Goldman, and P. R. Selvin, “Defocused orientation and position imaging (DOPI) of myosin V,” Proc. Natl. Acad. Sci. U.S.A. 103, 6495–6499 (2006).
[Crossref] [PubMed]

Tang, J.

Y. Wu, A. Kumar, C. Smith, E. Ardiel, P. Chandris, R. Christensen, I. Rey-Suarez, M. Guo, H. Vishwasrao, J. Chen, J. Tang, A. Upadhyaya, P. La Rivière, and H. Shroff, “Reflective imaging improves resolution, speed, and collection efficiency in light sheet microscopy,” bioRxiv (2017).

Tani, T.

S. B. Mehta, M. McQuilken, P. J. La Rivière, P. Occhipinti, A. Verma, R. Oldenbourg, A. S. Gladfelter, and T. Tani, “Dissection of molecular assembly dynamics by tracking orientation and position of single molecules in live cells,” Proc. Natl. Acad. Sci. U.S.A. 113, E6352–E6361 (2016).
[Crossref] [PubMed]

Tchénio, P.

A. Débarre, R. Jaffiol, C. Julien, D. Nutarelli, A. Richard, P. Tchénio, F. Chaput, and J.-P. Boilot, “Quantitative determination of the 3D dipole orientation of single molecules,” Eur. Phys. J. D. 28, 67–77 (2004).
[Crossref]

Terrel, A. R.

A. Meurer, C. P. Smith, M. Paprocki, O. Čertík, S. B. Kirpichev, M. Rocklin, A. Kumar, S. Ivanov, J. K. Moore, S. Singh, T. Rathnayake, S. Vig, B. E. Granger, R. P. Muller, F. Bonazzi, H. Gupta, S. Vats, F. Johansson, F. Pedregosa, M. J. Curry, A. R. Terrel, v. Roučka, A. Saboo, I. Fernando, S. Kulal, R. Cimrman, and A. Scopatz, “SymPy: symbolic computing in Python,” PeerJ Computer Science 3, e103 (2017).
[Crossref]

Toprak, E.

E. Toprak, J. Enderlein, S. Syed, S. A. McKinney, R. G. Petschek, T. Ha, Y. E. Goldman, and P. R. Selvin, “Defocused orientation and position imaging (DOPI) of myosin V,” Proc. Natl. Acad. Sci. U.S.A. 103, 6495–6499 (2006).
[Crossref] [PubMed]

Tyo, J. S.

Upadhyaya, A.

Y. Wu, A. Kumar, C. Smith, E. Ardiel, P. Chandris, R. Christensen, I. Rey-Suarez, M. Guo, H. Vishwasrao, J. Chen, J. Tang, A. Upadhyaya, P. La Rivière, and H. Shroff, “Reflective imaging improves resolution, speed, and collection efficiency in light sheet microscopy,” bioRxiv (2017).

van der Walt, S.

S. van der Walt, S. C. Colbert, and G. Varoquaux, “The NumPy array: a structure for efficient numerical computation,” CoRR abs/1102.1523 (2011).

Vanden Bout, D. A.

C.-Y. Lu and D. A. Vanden Bout, “Analysis of orientational dynamics of single fluorophore trajectories from three-angle polarization experiments,” J. Chem. Phys. 128, 244501 (2008).
[Crossref] [PubMed]

Varoquaux, G.

S. van der Walt, S. C. Colbert, and G. Varoquaux, “The NumPy array: a structure for efficient numerical computation,” CoRR abs/1102.1523 (2011).

Vats, S.

A. Meurer, C. P. Smith, M. Paprocki, O. Čertík, S. B. Kirpichev, M. Rocklin, A. Kumar, S. Ivanov, J. K. Moore, S. Singh, T. Rathnayake, S. Vig, B. E. Granger, R. P. Muller, F. Bonazzi, H. Gupta, S. Vats, F. Johansson, F. Pedregosa, M. J. Curry, A. R. Terrel, v. Roučka, A. Saboo, I. Fernando, S. Kulal, R. Cimrman, and A. Scopatz, “SymPy: symbolic computing in Python,” PeerJ Computer Science 3, e103 (2017).
[Crossref]

Verma, A.

M. McQuilken, M. S. Jentzsch, A. Verma, S. B. Mehta, R. Oldenbourg, and A. S. Gladfelter, “Analysis of septin reorganization at cytokinesis using polarized fluorescence microscopy,” Front. Cell Dev. Biol. 5, 42 (2017).
[Crossref] [PubMed]

S. B. Mehta, M. McQuilken, P. J. La Rivière, P. Occhipinti, A. Verma, R. Oldenbourg, A. S. Gladfelter, and T. Tani, “Dissection of molecular assembly dynamics by tracking orientation and position of single molecules in live cells,” Proc. Natl. Acad. Sci. U.S.A. 113, E6352–E6361 (2016).
[Crossref] [PubMed]

Vig, S.

A. Meurer, C. P. Smith, M. Paprocki, O. Čertík, S. B. Kirpichev, M. Rocklin, A. Kumar, S. Ivanov, J. K. Moore, S. Singh, T. Rathnayake, S. Vig, B. E. Granger, R. P. Muller, F. Bonazzi, H. Gupta, S. Vats, F. Johansson, F. Pedregosa, M. J. Curry, A. R. Terrel, v. Roučka, A. Saboo, I. Fernando, S. Kulal, R. Cimrman, and A. Scopatz, “SymPy: symbolic computing in Python,” PeerJ Computer Science 3, e103 (2017).
[Crossref]

Vishwasrao, H.

Y. Wu, A. Kumar, C. Smith, E. Ardiel, P. Chandris, R. Christensen, I. Rey-Suarez, M. Guo, H. Vishwasrao, J. Chen, J. Tang, A. Upadhyaya, P. La Rivière, and H. Shroff, “Reflective imaging improves resolution, speed, and collection efficiency in light sheet microscopy,” bioRxiv (2017).

Wan, Y.

R. K. Chhetri, F. Amat, Y. Wan, B. Hockendorf, W. C. Lemon, and P. J. Keller, “Whole-animal functional and developmental imaging with isotropic spatial resolution,” Nat. Methods 12, 1171–1178 (2015).
[Crossref] [PubMed]

Waterman, C. M.

Y. Wu, P. Chandris, P. W. Winter, E. Y. Kim, V. Jaumouillé, A. Kumar, M. Guo, J. M. Leung, C. Smith, I. Rey-Suarez, H. Liu, C. M. Waterman, K. S. Ramamurthi, P. J. La Rivière, and H. Shroff, “Simultaneous multiview capture and fusion improves spatial resolution in wide-field and light-sheet microscopy,” Optica 3, 897–910 (2016).
[Crossref] [PubMed]

Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colon-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31, 1032–1038 (2013).
[Crossref] [PubMed]

Wawrzusin, P.

Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colon-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31, 1032–1038 (2013).
[Crossref] [PubMed]

Winter, P. W.

Y. Wu, P. Chandris, P. W. Winter, E. Y. Kim, V. Jaumouillé, A. Kumar, M. Guo, J. M. Leung, C. Smith, I. Rey-Suarez, H. Liu, C. M. Waterman, K. S. Ramamurthi, P. J. La Rivière, and H. Shroff, “Simultaneous multiview capture and fusion improves spatial resolution in wide-field and light-sheet microscopy,” Optica 3, 897–910 (2016).
[Crossref] [PubMed]

Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colon-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31, 1032–1038 (2013).
[Crossref] [PubMed]

Wu, Y.

Y. Wu, P. Chandris, P. W. Winter, E. Y. Kim, V. Jaumouillé, A. Kumar, M. Guo, J. M. Leung, C. Smith, I. Rey-Suarez, H. Liu, C. M. Waterman, K. S. Ramamurthi, P. J. La Rivière, and H. Shroff, “Simultaneous multiview capture and fusion improves spatial resolution in wide-field and light-sheet microscopy,” Optica 3, 897–910 (2016).
[Crossref] [PubMed]

Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colon-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31, 1032–1038 (2013).
[Crossref] [PubMed]

Y. Wu, A. Kumar, C. Smith, E. Ardiel, P. Chandris, R. Christensen, I. Rey-Suarez, M. Guo, H. Vishwasrao, J. Chen, J. Tang, A. Upadhyaya, P. La Rivière, and H. Shroff, “Reflective imaging improves resolution, speed, and collection efficiency in light sheet microscopy,” bioRxiv (2017).

York, A. G.

Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colon-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31, 1032–1038 (2013).
[Crossref] [PubMed]

Zavislan, J. M.

Appl. Opt. (2)

Biophys. J. (2)

E. J. Peterman, H. Sosa, L. S. Goldstein, and W. E. Moerner, “Polarized fluorescence microscopy of individual and many kinesin motors bound to axonemal microtubules,” Biophys. J. 81, 2851–2863 (2001).
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ChemPhysChem (1)

M. P. Backlund, M. D. Lew, A. S. Backer, S. J. Sahl, and W. E. Moerner, “The role of molecular dipole orientation in single-molecule fluorescence microscopy and implications for super-resolution imaging,” ChemPhysChem 15, 587–599 (2014).
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J. D. Hunter, “Matplotlib: A 2D graphics environment,” Comput. Sci. Eng. 9, 90–95 (2007).
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Eur. Phys. J. D. (1)

A. Débarre, R. Jaffiol, C. Julien, D. Nutarelli, A. Richard, P. Tchénio, F. Chaput, and J.-P. Boilot, “Quantitative determination of the 3D dipole orientation of single molecules,” Eur. Phys. J. D. 28, 67–77 (2004).
[Crossref]

Front. Cell Dev. Biol. (1)

M. McQuilken, M. S. Jentzsch, A. Verma, S. B. Mehta, R. Oldenbourg, and A. S. Gladfelter, “Analysis of septin reorganization at cytokinesis using polarized fluorescence microscopy,” Front. Cell Dev. Biol. 5, 42 (2017).
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A. Anantharam, B. Onoa, R. H. Edwards, R. W. Holz, and D. Axelrod, “Localized topological changes of the plasma membrane upon exocytosis visualized by polarized TIRFM,” J. Cell Biol. 188, 415–428 (2010).
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J. Chem. Phys. (1)

C.-Y. Lu and D. A. Vanden Bout, “Analysis of orientational dynamics of single fluorophore trajectories from three-angle polarization experiments,” J. Chem. Phys. 128, 244501 (2008).
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J. Opt. Soc. Am. B (1)

J. Phys. Chem. B (1)

A. S. Backer and W. E. Moerner, “Extending single-molecule microscopy using optical Fourier processing,” J. Phys. Chem. B 118, 8313–8329 (2014).
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Nat. Biotechnol. (1)

Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colon-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31, 1032–1038 (2013).
[Crossref] [PubMed]

Nat. Methods (1)

R. K. Chhetri, F. Amat, Y. Wan, B. Hockendorf, W. C. Lemon, and P. J. Keller, “Whole-animal functional and developmental imaging with isotropic spatial resolution,” Nat. Methods 12, 1171–1178 (2015).
[Crossref] [PubMed]

Nature (1)

J. N. Forkey, M. E. Quinlan, M. A. Shaw, J. E. T. Corrie, and Y. E. Goldman, “Three-dimensional structural dynamics of myosin V by single-molecule fluorescence polarization,” Nature 422, 399–404 (2003).
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Opt. Express (1)

Opt. Lett. (1)

Optica (1)

PeerJ Computer Science (1)

A. Meurer, C. P. Smith, M. Paprocki, O. Čertík, S. B. Kirpichev, M. Rocklin, A. Kumar, S. Ivanov, J. K. Moore, S. Singh, T. Rathnayake, S. Vig, B. E. Granger, R. P. Muller, F. Bonazzi, H. Gupta, S. Vats, F. Johansson, F. Pedregosa, M. J. Curry, A. R. Terrel, v. Roučka, A. Saboo, I. Fernando, S. Kulal, R. Cimrman, and A. Scopatz, “SymPy: symbolic computing in Python,” PeerJ Computer Science 3, e103 (2017).
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Proc. Natl. Acad. Sci. U.S.A. (2)

S. B. Mehta, M. McQuilken, P. J. La Rivière, P. Occhipinti, A. Verma, R. Oldenbourg, A. S. Gladfelter, and T. Tani, “Dissection of molecular assembly dynamics by tracking orientation and position of single molecules in live cells,” Proc. Natl. Acad. Sci. U.S.A. 113, E6352–E6361 (2016).
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Y. Wu, A. Kumar, C. Smith, E. Ardiel, P. Chandris, R. Christensen, I. Rey-Suarez, M. Guo, H. Vishwasrao, J. Chen, J. Tang, A. Upadhyaya, P. La Rivière, and H. Shroff, “Reflective imaging improves resolution, speed, and collection efficiency in light sheet microscopy,” bioRxiv (2017).

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Figures (6)

Fig. 1
Fig. 1 Coordinate systems for a) the absorption dipole moment μ̂abs, b) the polarizer transmission axis exc, and c) the dummy integration vector . d) The scene consists of a single molecule at the focal point of an objective lens with a polarizer in the aperture plane.
Fig. 2
Fig. 2 Representative examples of single intensity measurements. Black dots indicate where the Cartesian unit vectors intersect the unit sphere.
Fig. 3
Fig. 3 Single-view microscope with varying illumination and detection NA. a) Schematic of a single-view four-polarization epi-illumination microscope. The red arrows indicate the four illumination polarization orientations—one for each intensity measurement. b) Uncertainty ellipses for the microscope in a). The ellipses indicate the relative size of the uncertainty in different directions, not the absolute size of the uncertainty. c) Solid-angle uncertainty for the microscope in a). The solid-angle uncertainty is a measure of the absolute size of the uncertainty in all directions. d) Median of the solid-angle uncertainty as a function of illumination and detection NA. e) MAD of the solid-angle uncertainty as a function of illumination and detection NA. The microscope configuration in a), b), and c) is indicated by a cross in d) and e).
Fig. 4
Fig. 4 Dual-view symmetric designs with varying NA and angle between objectives. a) Schematic of the microscope. We illuminate with the first objective (red solid) and detect from the second objective (red dashed). Then we illuminate from the second objective (blue solid) and detect from the first objective (blue dashed). b) Uncertainty ellipses for the microscope in a). The ellipses indicate the relative size of the uncertainty in different directions, not the absolute size of the uncertainty. c) Solid-angle uncertainty for the microscope in a). The solid-angle uncertainty is a measure of the absolute size of the uncertainty in all directions. d) Median of the solid-angle uncertainty as a function of NA and the angle between the objectives. e) MAD of the solid-angle uncertainty as a function of NA and the angle between the objectives. The microscope configuration in a), b), and c) is indicated by a cross in d) and e). f) Median of the solid-angle uncertainty as a function of the angle between the objectives when NA=0.6. g) MAD of the solid-angle uncertainty as a function of the angle between the objectives when NA=0.6. The profile in f) and g) is taken along the purple line in d) and e).
Fig. 5
Fig. 5 Dual-view symmetric orthogonal designs with varying illumination and detection NA. a) Schematic of the microscope. b) Uncertainty ellipses for the microscope in a). The ellipses indicate the relative size of the uncertainty in different directions, not the absolute size of the uncertainty. c) Solid-angle uncertainty for the microscope in a). The solid-angle uncertainty is a measure of the absolute size of the uncertainty in all directions. d) Median of the solid-angle uncertainty as a function of illumination and detection NA. e) MAD of the solid-angle uncertainty as a function of illumination and detection NA. The microscope configuration in a), b), and c) is indicated by a cross in d) and e).
Fig. 6
Fig. 6 Dual-view asymmetric light-sheet illumination designs with varying NA and sample exposure asymmetry. a) Schematic of the microscope. b) Uncertainty ellipses for the microscope in a). The ellipses indicate the relative size of the uncertainty in different directions, not the absolute size of the uncertainty. c) Solid-angle uncertainty for the microscope in a). The solid-angle uncertainty is a measure of the absolute size of the uncertainty in all directions. d) Median of the solid-angle uncertainty as a function of NA and sample exposure asymmetry. e) MAD of the solid-angle uncertainty as a function of NA and sample exposure asymmetry. The microscope configuration in a), b), and c) is indicated by a cross in d) and e).

Tables (1)

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Table 1 Comparison of designs in each class of microscope. All solid-angle uncertainty statistics are in steradians.

Equations (28)

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μ ^ abs ( Θ , Φ ) = sin Θ cos Φ x ^ + sin Θ sin Φ y ^ cos Θ z ^ .
p ^ exc ( ϕ exc ) = cos ϕ exc x ^ + sin ϕ exc y ^ ,
r ^ ( θ , ϕ ) = sin θ cos ϕ x ^ + sin θ sin ϕ y ^ + cos θ z ^ ,
Ω = { ϕ , θ | 0 < ϕ 2 π , 0 < θ α } ,
NA = n sin α ,
R ( r ^ ) = [ cos θ cos 2 ϕ + sin 2 ϕ ( cos θ 1 ) sin ϕ cos ϕ sin θ cos ϕ ( cos θ 1 ) sin ϕ cos ϕ cos θ sin 2 ϕ + cos 2 ϕ sin θ sin ϕ sin θ cos ϕ sin θ sin ϕ cos θ ] .
η abs ray = | μ ^ abs p ^ exc | 2 .
η abs = Ω d r ^ | μ ^ abs R ( r ^ ) p ^ exc | 2 Ω d r ^ .
η abs = D { A + B sin 2 Θ + C sin 2 Θ cos [ 2 ( Φ ϕ exc ) ] }
A = 1 4 3 8 cos α + 1 8 cos 3 α
B = 3 16 cos α 3 16 cos 3 α
C = 7 32 3 32 cos α 3 32 cos 2 α 1 32 cos 3 α
D = 4 3 ( 1 cos α ) .
η abs ray = sin 2 Θ cos 2 ( Φ ϕ exc ) ,
η det pol = A + B sin 2 Θ + C sin 2 Θ cos [ 2 ( Φ ϕ det ) ] ,
η det = 2 ( A + B sin 2 Θ ) .
Θ = arccos ( sin ψ cos Φ sin Θ + cos ψ cos Θ )
Φ = { arccos ( cos ψ cos Θ sin Θ sin ψ cos Θ 1 ( sin ψ cos Φ sin Θ + cos ψ cos Θ ) 2 ) 0 Φ < π arccos ( cos ψ cos Φ sin Θ sin ψ cos Θ 1 ( sin ψ cos Θ sin Θ + cos ψ cos Θ ) 2 ) π Φ < 0
I I in η abs η det ,
F = k = 1 N 1 I k [ I k Θ I k Θ I k Θ I k Φ I k Θ I k Φ I k Φ I k Φ ]
σ Ω sin Θ det { F 1 }
( x cos γ + y sin γ ) 2 a 2 + ( x sin γ + y cos γ ) 2 b 2 = 1 .
σ x = F 0 , 0 1
σ y = sin Θ F 1 , 1 1
σ x y = sin Θ F 1 , 0 1
a 2 = σ x 2 + σ y 2 2 + ( σ x 2 + σ y 2 ) 2 4 + σ x y 2
b 2 = σ x 2 + σ y 2 2 ( σ x 2 σ y 2 ) 2 4 + σ x y 2
γ = 1 2 arctan ( 2 σ x y σ x 2 σ y 2 ) .

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