Abstract

Three-dimensional microscopy suffers from sample-induced aberrations that reduce the resolution and lead to misinterpretations of the object distribution. In this paper, the resolution of a three-dimensional fluorescent microscope is significantly improved by introducing an amplitude diversity in the form of a binary amplitude mask positioned in several different orientations within the pupil, followed by computer processing of the diversity images. The method has proved to be fast, easy to implement, and cost-effective in high-resolution imaging of casper fli:GFP zebrafish.

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References

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2017 (1)

2016 (1)

2015 (2)

2014 (2)

2012 (1)

2011 (1)

X. Tao, B. Fernandez, O. Azucena, M. Fu, D. Garcia, Y. Zuo, D. C. Chen, and J. Kubby, “Adaptive optics confocal microscopy using direct wavefront sensing,” Opt. letters 36, 1062–1064 (2011).
[Crossref]

2010 (1)

2007 (3)

2004 (1)

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

2001 (1)

B. C. Platt and R. Shack, “History and principles of shack-hartmann wavefront sensing,” J. Refract. Surg. 17, S573–S577 (2001).
[PubMed]

1999 (1)

J. G. McNally, T. Karpova, J. Cooper, and J. A. Conchello, “Three-dimensional imaging by deconvolution microscopy,” Methods. 19, 373–385 (1999).
[Crossref] [PubMed]

1996 (1)

A. Pakhomov and K. Losin, “Processing of short sets of bright speckle images distorted by the turbulent earth’s athmosphere,” Opt. Commun. 125, 5–12 (1996).
[Crossref]

1994 (1)

1993 (1)

A. Voie, D. Burns, and F. Spelman, “Orthogonal-plane fluorescence optical sectioning: Three-dimensional imaging of macroscopic biological specimens,” J. Microsc. 170, 229–236 (1993).
[Crossref] [PubMed]

1988 (1)

Ayers, G.

Azucena, O.

X. Tao, B. Fernandez, O. Azucena, M. Fu, D. Garcia, Y. Zuo, D. C. Chen, and J. Kubby, “Adaptive optics confocal microscopy using direct wavefront sensing,” Opt. letters 36, 1062–1064 (2011).
[Crossref]

Booth, M. J.

M. J. Booth, “Adaptive optical microscopy: the ongoing quest for a perfect image,” Light. Sci. Appl. 3, e165 (2014).
[Crossref]

Bourgenot, C.

Burns, D.

A. Voie, D. Burns, and F. Spelman, “Orthogonal-plane fluorescence optical sectioning: Three-dimensional imaging of macroscopic biological specimens,” J. Microsc. 170, 229–236 (1993).
[Crossref] [PubMed]

Caulfield, H. J.

Chen, D. C.

X. Tao, B. Fernandez, O. Azucena, M. Fu, D. Garcia, Y. Zuo, D. C. Chen, and J. Kubby, “Adaptive optics confocal microscopy using direct wavefront sensing,” Opt. letters 36, 1062–1064 (2011).
[Crossref]

Chenegros, G.

Conchello, J. A.

J. G. McNally, T. Karpova, J. Cooper, and J. A. Conchello, “Three-dimensional imaging by deconvolution microscopy,” Methods. 19, 373–385 (1999).
[Crossref] [PubMed]

Cooper, J.

J. G. McNally, T. Karpova, J. Cooper, and J. A. Conchello, “Three-dimensional imaging by deconvolution microscopy,” Methods. 19, 373–385 (1999).
[Crossref] [PubMed]

Dainty, J. C.

Del Bene, F.

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

Doelman, N.

Fernandez, B.

X. Tao, B. Fernandez, O. Azucena, M. Fu, D. Garcia, Y. Zuo, D. C. Chen, and J. Kubby, “Adaptive optics confocal microscopy using direct wavefront sensing,” Opt. letters 36, 1062–1064 (2011).
[Crossref]

Flannery, B. P.

W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery, Numerical Recipes 3rd Edition: The Art of Scientific Computing (Cambridge University, 2007).

Fu, M.

X. Tao, B. Fernandez, O. Azucena, M. Fu, D. Garcia, Y. Zuo, D. C. Chen, and J. Kubby, “Adaptive optics confocal microscopy using direct wavefront sensing,” Opt. letters 36, 1062–1064 (2011).
[Crossref]

Garcia, D.

X. Tao, B. Fernandez, O. Azucena, M. Fu, D. Garcia, Y. Zuo, D. C. Chen, and J. Kubby, “Adaptive optics confocal microscopy using direct wavefront sensing,” Opt. letters 36, 1062–1064 (2011).
[Crossref]

Girkin, J. M.

Glanc, M.

Greger, K.

J. Swoger, P. Verveer, K. Greger, J. Huisken, and E. H. Stelzer, “Multi-view image fusion improves resolution in three-dimensional microscopy,” Opt. Express 15, 8029–8042 (2007).
[Crossref] [PubMed]

P. J. Verveer, J. Swoger, F. Pampaloni, K. Greger, M. Marcello, and E. H. Stelzer, “High-resolution three-dimensional imaging of large specimens with light sheet–based microscopy,” Nat. Methods 4, 311 (2007).
[Crossref]

Holy, T. E.

Huisken, J.

J. Swoger, P. Verveer, K. Greger, J. Huisken, and E. H. Stelzer, “Multi-view image fusion improves resolution in three-dimensional microscopy,” Opt. Express 15, 8029–8042 (2007).
[Crossref] [PubMed]

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

Kalkman, J.

Karpova, T.

J. G. McNally, T. Karpova, J. Cooper, and J. A. Conchello, “Three-dimensional imaging by deconvolution microscopy,” Methods. 19, 373–385 (1999).
[Crossref] [PubMed]

Keller, C. U.

Kenworthy, M.

Korkiakoski, V.

Kubby, J.

X. Tao, B. Fernandez, O. Azucena, M. Fu, D. Garcia, Y. Zuo, D. C. Chen, and J. Kubby, “Adaptive optics confocal microscopy using direct wavefront sensing,” Opt. letters 36, 1062–1064 (2011).
[Crossref]

Lacombe, F.

Loktev, M.

M. Loktev, G. Vdovin, O. Soloviev, and S. Savenko, “Experiments on speckle imaging using projection methods,” in “SPIE Optical Engineering+ Applications,” J. J. Dolne, T. J. Karr, V. L. Gamiz, S. Rogers, and D. P. Casasent, eds. (International Society for Optics and Photonics, 2011), pp. 81650M.

Losin, K.

A. Pakhomov and K. Losin, “Processing of short sets of bright speckle images distorted by the turbulent earth’s athmosphere,” Opt. Commun. 125, 5–12 (1996).
[Crossref]

Love, G. D.

Marcello, M.

P. J. Verveer, J. Swoger, F. Pampaloni, K. Greger, M. Marcello, and E. H. Stelzer, “High-resolution three-dimensional imaging of large specimens with light sheet–based microscopy,” Nat. Methods 4, 311 (2007).
[Crossref]

McNally, J. G.

J. G. McNally, T. Karpova, J. Cooper, and J. A. Conchello, “Three-dimensional imaging by deconvolution microscopy,” Methods. 19, 373–385 (1999).
[Crossref] [PubMed]

Mugnier, L. M.

Otten, G.

Pakhomov, A.

A. Pakhomov and K. Losin, “Processing of short sets of bright speckle images distorted by the turbulent earth’s athmosphere,” Opt. Commun. 125, 5–12 (1996).
[Crossref]

Pampaloni, F.

P. J. Verveer, J. Swoger, F. Pampaloni, K. Greger, M. Marcello, and E. H. Stelzer, “High-resolution three-dimensional imaging of large specimens with light sheet–based microscopy,” Nat. Methods 4, 311 (2007).
[Crossref]

Platt, B. C.

B. C. Platt and R. Shack, “History and principles of shack-hartmann wavefront sensing,” J. Refract. Surg. 17, S573–S577 (2001).
[PubMed]

Pozzi, P.

Press, W. H.

W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery, Numerical Recipes 3rd Edition: The Art of Scientific Computing (Cambridge University, 2007).

Saunter, C. D.

Savenko, S.

M. Loktev, G. Vdovin, O. Soloviev, and S. Savenko, “Experiments on speckle imaging using projection methods,” in “SPIE Optical Engineering+ Applications,” J. J. Dolne, T. J. Karr, V. L. Gamiz, S. Rogers, and D. P. Casasent, eds. (International Society for Optics and Photonics, 2011), pp. 81650M.

Shack, R.

B. C. Platt and R. Shack, “History and principles of shack-hartmann wavefront sensing,” J. Refract. Surg. 17, S573–S577 (2001).
[PubMed]

Soloviev, O.

Spelman, F.

A. Voie, D. Burns, and F. Spelman, “Orthogonal-plane fluorescence optical sectioning: Three-dimensional imaging of macroscopic biological specimens,” J. Microsc. 170, 229–236 (1993).
[Crossref] [PubMed]

Stelzer, E. H.

P. J. Verveer, J. Swoger, F. Pampaloni, K. Greger, M. Marcello, and E. H. Stelzer, “High-resolution three-dimensional imaging of large specimens with light sheet–based microscopy,” Nat. Methods 4, 311 (2007).
[Crossref]

J. Swoger, P. Verveer, K. Greger, J. Huisken, and E. H. Stelzer, “Multi-view image fusion improves resolution in three-dimensional microscopy,” Opt. Express 15, 8029–8042 (2007).
[Crossref] [PubMed]

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

Swoger, J.

P. J. Verveer, J. Swoger, F. Pampaloni, K. Greger, M. Marcello, and E. H. Stelzer, “High-resolution three-dimensional imaging of large specimens with light sheet–based microscopy,” Nat. Methods 4, 311 (2007).
[Crossref]

J. Swoger, P. Verveer, K. Greger, J. Huisken, and E. H. Stelzer, “Multi-view image fusion improves resolution in three-dimensional microscopy,” Opt. Express 15, 8029–8042 (2007).
[Crossref] [PubMed]

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

Tao, X.

X. Tao, B. Fernandez, O. Azucena, M. Fu, D. Garcia, Y. Zuo, D. C. Chen, and J. Kubby, “Adaptive optics confocal microscopy using direct wavefront sensing,” Opt. letters 36, 1062–1064 (2011).
[Crossref]

Taylor, J. M.

Teukolsky, S. A.

W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery, Numerical Recipes 3rd Edition: The Art of Scientific Computing (Cambridge University, 2007).

Turaga, D.

Vdovin, G.

D. Wilding, O. Soloviev, P. Pozzi, G. Vdovin, and M. Verhaegen, “Blind multi-frame deconvolution by tangential iterative projections (TIP),” Opt. Express 25, 32305 (2017).
[Crossref]

D. Wilding, P. Pozzi, O. Soloviev, G. Vdovin, and M. Verhaegen, “Adaptive illumination based on direct wavefront sensing in a light-sheet fluorescence microscope,” Opt. Express 24, 24896–24906 (2016).
[Crossref] [PubMed]

M. Loktev, G. Vdovin, O. Soloviev, and S. Savenko, “Experiments on speckle imaging using projection methods,” in “SPIE Optical Engineering+ Applications,” J. J. Dolne, T. J. Karr, V. L. Gamiz, S. Rogers, and D. P. Casasent, eds. (International Society for Optics and Photonics, 2011), pp. 81650M.

Verhaegen, M.

Verstraete, H. R.

Verveer, P.

Verveer, P. J.

P. J. Verveer, J. Swoger, F. Pampaloni, K. Greger, M. Marcello, and E. H. Stelzer, “High-resolution three-dimensional imaging of large specimens with light sheet–based microscopy,” Nat. Methods 4, 311 (2007).
[Crossref]

Vetterling, W. T.

W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery, Numerical Recipes 3rd Edition: The Art of Scientific Computing (Cambridge University, 2007).

Voie, A.

A. Voie, D. Burns, and F. Spelman, “Orthogonal-plane fluorescence optical sectioning: Three-dimensional imaging of macroscopic biological specimens,” J. Microsc. 170, 229–236 (1993).
[Crossref] [PubMed]

Wahls, S.

Wilding, D.

Wittbrodt, J.

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

Yang, H.

Yaroslavsky, L. P.

Zuo, Y.

X. Tao, B. Fernandez, O. Azucena, M. Fu, D. Garcia, Y. Zuo, D. C. Chen, and J. Kubby, “Adaptive optics confocal microscopy using direct wavefront sensing,” Opt. letters 36, 1062–1064 (2011).
[Crossref]

Appl. Opt. (3)

J. Microsc. (1)

A. Voie, D. Burns, and F. Spelman, “Orthogonal-plane fluorescence optical sectioning: Three-dimensional imaging of macroscopic biological specimens,” J. Microsc. 170, 229–236 (1993).
[Crossref] [PubMed]

J. Opt. Soc. Am. A (1)

J. Refract. Surg. (1)

B. C. Platt and R. Shack, “History and principles of shack-hartmann wavefront sensing,” J. Refract. Surg. 17, S573–S577 (2001).
[PubMed]

Light. Sci. Appl. (1)

M. J. Booth, “Adaptive optical microscopy: the ongoing quest for a perfect image,” Light. Sci. Appl. 3, e165 (2014).
[Crossref]

Methods. (1)

J. G. McNally, T. Karpova, J. Cooper, and J. A. Conchello, “Three-dimensional imaging by deconvolution microscopy,” Methods. 19, 373–385 (1999).
[Crossref] [PubMed]

Nat. Methods (1)

P. J. Verveer, J. Swoger, F. Pampaloni, K. Greger, M. Marcello, and E. H. Stelzer, “High-resolution three-dimensional imaging of large specimens with light sheet–based microscopy,” Nat. Methods 4, 311 (2007).
[Crossref]

Opt. Commun. (1)

A. Pakhomov and K. Losin, “Processing of short sets of bright speckle images distorted by the turbulent earth’s athmosphere,” Opt. Commun. 125, 5–12 (1996).
[Crossref]

Opt. Express (5)

Opt. Lett. (2)

Opt. letters (1)

X. Tao, B. Fernandez, O. Azucena, M. Fu, D. Garcia, Y. Zuo, D. C. Chen, and J. Kubby, “Adaptive optics confocal microscopy using direct wavefront sensing,” Opt. letters 36, 1062–1064 (2011).
[Crossref]

Science. (1)

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

Other (2)

W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery, Numerical Recipes 3rd Edition: The Art of Scientific Computing (Cambridge University, 2007).

M. Loktev, G. Vdovin, O. Soloviev, and S. Savenko, “Experiments on speckle imaging using projection methods,” in “SPIE Optical Engineering+ Applications,” J. J. Dolne, T. J. Karr, V. L. Gamiz, S. Rogers, and D. P. Casasent, eds. (International Society for Optics and Photonics, 2011), pp. 81650M.

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Figures (3)

Fig. 1
Fig. 1 The experimental setup used for the imaging. The incident light path has an SLM for the excitation beam shaping and in the detection path a rotating pupil mask is placed close to the back aperture of the objective.
Fig. 2
Fig. 2 (a) the evolution of the image acquisition and reconstruction for a plane 75μm inside the zebrafish (b) a ROI at plane 135μm with no mask compared with the first object reconstruction and the last. (c) the wedge positions for images 1–4. (d) the experimental wedge with the pupil size overlayed. (e) the line profile labelled LP in (b). The red arrow shows a feature not present in the original LSFM image that is now clearly resolved. All images are normalised to a 16-bit range minimum to maximum with the colour-scale as shown.
Fig. 3
Fig. 3 (a) A xy maximum intensity projection of the three-dimensional dataset of the zebrafish larvae head with the standard LSFM (8 datasets) and the diversity processed set plane-by-plane in the xy direction. (b) A slice through the zebrafish in the yz-plane showing the comparison between xy processing and yz processing. (c) A plot of the line profile in (b). All images are normalised to a 16-bit range minimum to maximum with the colour-scale as shown.

Tables (1)

Tables Icon

Table 1 Steps of the rTIP algorithm with their descriptions in schematic form. After the second acquisition the steps 1 to 5 are repeated with every subsequent acquisition to update the object estimate Ô(k).

Equations (7)

Equations on this page are rendered with MathJax. Learn more.

i ( x ) = | { 𝒫 ( x ) } | 2 * o + w ,
min h ( x ) , o i ( x ) h ( x ) * o 2 ,
O = I r ( x ) + W H ( x ) ,
| H ( ν φ ) | 0 | O ( ν φ ) | | 0 + W 0 | = .
I m = H ^ m ( k ) O ^ ( k ) + W m ,
H ^ m ( k ) = 𝒫 { I m O ^ ( k 1 ) } ,
O ^ ( k ) = α 𝒫 𝒪 { m = k n k I m × H ^ ¯ m ( k ) m = k n k | H ^ m ( k ) | 2 } O ˜ ( k ) + ( 1 α ) O ^ ( k 1 ) ,

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