Abstract

The performance of structured illumination microscopy (SIM) is hampered in many biological applications due to the inability to modulate the light when imaging deep into the sample. This is in part because sample-induced aberration reduces the modulation contrast of the structured pattern. In this paper, we present an image restoration approach suitable for processing raw incoherent-grid-projection SIM data with a low fringe contrast. Restoration results from simulated and experimental ApoTome SIM data show results with improved signal-to-noise ratio (SNR) and optical sectioning compared to the results obtained from existing methods, such as 2D demodulation and 3D SIM deconvolution. Our proposed method provides satisfactory results (quantified by the achieved SNR and normalized mean square error) even when the modulation contrast of the illumination pattern is as low as 7%.

© 2018 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

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2018 (2)

N. Patwary, J. Sola-Pikabea, A. Doblas, G. Saavedra, and C. Preza, “Evaluation of the use of wavefront encoding to reduce depth-induced aberration in structured illumination microscopy,” Proc. SPIE 10499, 10499 (2018).

H. Shabani, A. Doblas, G. Saavedra, and C. Preza, “3D structured illumination microscopy using an incoherent illumination system based on a Fresnel biprism,” Proc. SPIE 10499, 10499 (2018).

2017 (2)

2016 (2)

N. Patwary, S. V. King, G. Saavedra, and C. Preza, “Reducing effects of aberration in 3D fluorescence imaging using wavefront coding with a radially symmetric phase mask,” Opt. Express 24(12), 12905–12921 (2016).
[Crossref] [PubMed]

Q. Yang, L. Cao, H. Zhang, H. Zhang, and G. Jin, “Method of lateral image reconstruction in structured illumination microscopy with super resolution,” J. Innov. Opt. Health Sci. 9(3), 1630002 (2016).
[Crossref]

2015 (2)

A. Jost, E. Tolstik, P. Feldmann, K. Wicker, A. Sentenac, and R. Heintzmann, “Optical sectioning and high resolution in single-slice structured illumination microscopy by thick slice blind-SIM reconstruction,” PLoS One 10(7), e0132174 (2015).
[Crossref] [PubMed]

F. Ströhl and C. F. Kaminski, “A joint Richardson-Lucy deconvolution algorithm for the reconstruction of multifocal structured illumination microscopy data,” Methods Appl. Fluoresc. 3(1), 014002 (2015).
[Crossref] [PubMed]

2014 (2)

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A. C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

S. Dong, P. Nanda, R. Shiradkar, K. Guo, and G. Zheng, “High-resolution fluorescence imaging via pattern-illuminated Fourier ptychography,” Opt. Express 22(17), 20856–20870 (2014).
[Crossref] [PubMed]

2013 (1)

2012 (4)

M. Sivaguru, L. Mander, G. Fried, and S. W. Punyasena, “Capturing the surface texture and shape of pollen: a comparison of microscopy techniques,” PLoS One 7(6), e39129 (2012).
[Crossref] [PubMed]

L. Gao, L. Shao, C. D. Higgins, J. S. Poulton, M. Peifer, M. W. Davidson, X. Wu, B. Goldstein, and E. Betzig, “Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens,” Cell 151(6), 1370–1385 (2012).
[Crossref] [PubMed]

A. G. York, S. H. Parekh, D. Dalle Nogare, R. S. Fischer, K. Temprine, M. Mione, A. B. Chitnis, C. A. Combs, and H. Shroff, “Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy,” Nat. Methods 9(7), 749–754 (2012).
[Crossref] [PubMed]

F. Orieux, E. Sepulveda, V. Loriette, B. Dubertret, and J. C. Olivo-Marin, “Bayesian estimation for optimized structured illumination microscopy,” IEEE Trans. Image Process. 21(2), 601–614 (2012).
[Crossref] [PubMed]

2011 (2)

2009 (5)

S. A. Shroff, J. R. Fienup, and D. R. Williams, “Phase-shift estimation in sinusoidally illuminated images for lateral superresolution,” J. Opt. Soc. Am. A 26(2), 413–424 (2009).
[Crossref] [PubMed]

G. Saavedra, I. Escobar, R. Martínez-Cuenca, E. Sánchez-Ortiga, and M. Martínez-Corral, “Reduction of spherical-aberration impact in microscopy by wavefront coding,” Opt. Express 17(16), 13810–13818 (2009).
[Crossref] [PubMed]

J. Huisken and D. Y. R. Stainier, “Selective plane illumination microscopy techniques in developmental biology,” Development 136(12), 1963–1975 (2009).
[Crossref] [PubMed]

M. F. Langhorst, J. Schaffer, and B. Goetze, “Structure brings clarity: structured illumination microscopy in cell biology,” Biotechnol. J. 4(6), 858–865 (2009).
[Crossref] [PubMed]

M. Bertero, P. Boccacci, G. Desiderà, and G. Vicidomini, “Image deblurring with Poisson data: from cells to galaxies,” Inverse Probl. 25(12), 123006 (2009).
[Crossref]

2008 (2)

M. G. L. Gustafsson, L. Shao, P. M. Carlton, C. J. Wang, I. N. Golubovskaya, W. Z. Cande, D. A. Agard, and J. W. Sedat, “Three-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination,” Biophys. J. 94(12), 4957–4970 (2008).
[Crossref] [PubMed]

D. Débarre, E. J. Botcherby, M. J. Booth, and T. Wilson, “Adaptive optics for structured illumination microscopy,” Opt. Express 16(13), 9290–9305 (2008).
[Crossref] [PubMed]

2004 (3)

T. Tkaczyk, M. Rahman, V. Mack, K. Sokolov, J. Rogers, R. Richards-Kortum, and M. Descour, “High resolution, molecular-specific, reflectance imaging in optically dense tissue phantoms with structured-illumination,” Opt. Express 12(16), 3745–3758 (2004).
[Crossref] [PubMed]

Z. Wang, A. C. Bovik, H. R. Sheikh, and E. P. Simoncelli, “Image quality assessment: from error visibility to structural similarity,” IEEE Trans. Image Process. 13(4), 600–612 (2004).
[Crossref] [PubMed]

L. H. Schaefer, D. Schuster, and J. Schaffer, “Structured illumination microscopy: artefact analysis and reduction utilizing a parameter optimization approach,” J. Microsc. 216(2), 165–174 (2004).
[Crossref] [PubMed]

2000 (1)

M. G. L. Gustafsson, “Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy,” J. Microsc. 198(2), 82–87 (2000).
[Crossref] [PubMed]

1999 (1)

M. G. L. Gustafsson, D. A. Agard, and J. W. Sedat, “I5M: 3D widefield light microscopy with better than 100 nm axial resolution,” J. Microsc. 195(1), 10–16 (1999).
[Crossref] [PubMed]

1998 (1)

1997 (1)

1996 (1)

J. A. Conchello and J. G. McNally, “Fast regularization technique for expectation maximization algorithm for optical sectioning microscopy,” Proc. SPIE 2655, 199–208 (1996).

1992 (1)

Agard, D. A.

M. G. L. Gustafsson, L. Shao, P. M. Carlton, C. J. Wang, I. N. Golubovskaya, W. Z. Cande, D. A. Agard, and J. W. Sedat, “Three-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination,” Biophys. J. 94(12), 4957–4970 (2008).
[Crossref] [PubMed]

M. G. L. Gustafsson, D. A. Agard, and J. W. Sedat, “I5M: 3D widefield light microscopy with better than 100 nm axial resolution,” J. Microsc. 195(1), 10–16 (1999).
[Crossref] [PubMed]

Bembenek, J. N.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A. C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Bertero, M.

M. Bertero, P. Boccacci, G. Desiderà, and G. Vicidomini, “Image deblurring with Poisson data: from cells to galaxies,” Inverse Probl. 25(12), 123006 (2009).
[Crossref]

Best, G.

Betzig, E.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A. C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

L. Gao, L. Shao, C. D. Higgins, J. S. Poulton, M. Peifer, M. W. Davidson, X. Wu, B. Goldstein, and E. Betzig, “Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens,” Cell 151(6), 1370–1385 (2012).
[Crossref] [PubMed]

Boccacci, P.

M. Bertero, P. Boccacci, G. Desiderà, and G. Vicidomini, “Image deblurring with Poisson data: from cells to galaxies,” Inverse Probl. 25(12), 123006 (2009).
[Crossref]

Böhme, R.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A. C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Booth, M. J.

Botcherby, E. J.

Bovik, A. C.

Z. Wang, A. C. Bovik, H. R. Sheikh, and E. P. Simoncelli, “Image quality assessment: from error visibility to structural similarity,” IEEE Trans. Image Process. 13(4), 600–612 (2004).
[Crossref] [PubMed]

Cande, W. Z.

M. G. L. Gustafsson, L. Shao, P. M. Carlton, C. J. Wang, I. N. Golubovskaya, W. Z. Cande, D. A. Agard, and J. W. Sedat, “Three-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination,” Biophys. J. 94(12), 4957–4970 (2008).
[Crossref] [PubMed]

Cao, L.

Q. Yang, L. Cao, H. Zhang, H. Zhang, and G. Jin, “Method of lateral image reconstruction in structured illumination microscopy with super resolution,” J. Innov. Opt. Health Sci. 9(3), 1630002 (2016).
[Crossref]

Carlton, P. M.

M. G. L. Gustafsson, L. Shao, P. M. Carlton, C. J. Wang, I. N. Golubovskaya, W. Z. Cande, D. A. Agard, and J. W. Sedat, “Three-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination,” Biophys. J. 94(12), 4957–4970 (2008).
[Crossref] [PubMed]

Chen, B.-C.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A. C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Chitnis, A. B.

A. G. York, S. H. Parekh, D. Dalle Nogare, R. S. Fischer, K. Temprine, M. Mione, A. B. Chitnis, C. A. Combs, and H. Shroff, “Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy,” Nat. Methods 9(7), 749–754 (2012).
[Crossref] [PubMed]

Combs, C. A.

A. G. York, S. H. Parekh, D. Dalle Nogare, R. S. Fischer, K. Temprine, M. Mione, A. B. Chitnis, C. A. Combs, and H. Shroff, “Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy,” Nat. Methods 9(7), 749–754 (2012).
[Crossref] [PubMed]

Conchello, J. A.

J. A. Conchello, “Superresolution and convergence properties of the expectation-maximization algorithm for maximum-likelihood deconvolution of incoherent images,” J. Opt. Soc. Am. A 15(10), 2609–2619 (1998).
[Crossref] [PubMed]

J. A. Conchello and J. G. McNally, “Fast regularization technique for expectation maximization algorithm for optical sectioning microscopy,” Proc. SPIE 2655, 199–208 (1996).

Dalle Nogare, D.

A. G. York, S. H. Parekh, D. Dalle Nogare, R. S. Fischer, K. Temprine, M. Mione, A. B. Chitnis, C. A. Combs, and H. Shroff, “Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy,” Nat. Methods 9(7), 749–754 (2012).
[Crossref] [PubMed]

Davidson, M. W.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A. C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

L. Gao, L. Shao, C. D. Higgins, J. S. Poulton, M. Peifer, M. W. Davidson, X. Wu, B. Goldstein, and E. Betzig, “Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens,” Cell 151(6), 1370–1385 (2012).
[Crossref] [PubMed]

Débarre, D.

Descour, M.

Desiderà, G.

M. Bertero, P. Boccacci, G. Desiderà, and G. Vicidomini, “Image deblurring with Poisson data: from cells to galaxies,” Inverse Probl. 25(12), 123006 (2009).
[Crossref]

Doblas, A.

H. Shabani, A. Doblas, G. Saavedra, and C. Preza, “3D structured illumination microscopy using an incoherent illumination system based on a Fresnel biprism,” Proc. SPIE 10499, 10499 (2018).

N. Patwary, J. Sola-Pikabea, A. Doblas, G. Saavedra, and C. Preza, “Evaluation of the use of wavefront encoding to reduce depth-induced aberration in structured illumination microscopy,” Proc. SPIE 10499, 10499 (2018).

N. Patwary, H. Shabani, A. Doblas, G. Saavedra, and C. Preza, “Experimental validation of a customized phase mask designed to enable efficient computational optical sectioning microscopy through wavefront encoding,” Appl. Opt. 56(9), D14–D23 (2017).
[Crossref] [PubMed]

Dong, S.

Dubertret, B.

F. Orieux, E. Sepulveda, V. Loriette, B. Dubertret, and J. C. Olivo-Marin, “Bayesian estimation for optimized structured illumination microscopy,” IEEE Trans. Image Process. 21(2), 601–614 (2012).
[Crossref] [PubMed]

English, B. P.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A. C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Escobar, I.

Feldmann, P.

A. Jost, E. Tolstik, P. Feldmann, K. Wicker, A. Sentenac, and R. Heintzmann, “Optical sectioning and high resolution in single-slice structured illumination microscopy by thick slice blind-SIM reconstruction,” PLoS One 10(7), e0132174 (2015).
[Crossref] [PubMed]

Fienup, J. R.

Fiolka, R.

Fischer, R. S.

A. G. York, S. H. Parekh, D. Dalle Nogare, R. S. Fischer, K. Temprine, M. Mione, A. B. Chitnis, C. A. Combs, and H. Shroff, “Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy,” Nat. Methods 9(7), 749–754 (2012).
[Crossref] [PubMed]

Fried, G.

M. Sivaguru, L. Mander, G. Fried, and S. W. Punyasena, “Capturing the surface texture and shape of pollen: a comparison of microscopy techniques,” PLoS One 7(6), e39129 (2012).
[Crossref] [PubMed]

Fritz-Laylin, L.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A. C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Gao, L.

L. Gao, L. Shao, C. D. Higgins, J. S. Poulton, M. Peifer, M. W. Davidson, X. Wu, B. Goldstein, and E. Betzig, “Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens,” Cell 151(6), 1370–1385 (2012).
[Crossref] [PubMed]

Gibson, S. F.

Goetze, B.

M. F. Langhorst, J. Schaffer, and B. Goetze, “Structure brings clarity: structured illumination microscopy in cell biology,” Biotechnol. J. 4(6), 858–865 (2009).
[Crossref] [PubMed]

Goldstein, B.

L. Gao, L. Shao, C. D. Higgins, J. S. Poulton, M. Peifer, M. W. Davidson, X. Wu, B. Goldstein, and E. Betzig, “Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens,” Cell 151(6), 1370–1385 (2012).
[Crossref] [PubMed]

Golubovskaya, I. N.

M. G. L. Gustafsson, L. Shao, P. M. Carlton, C. J. Wang, I. N. Golubovskaya, W. Z. Cande, D. A. Agard, and J. W. Sedat, “Three-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination,” Biophys. J. 94(12), 4957–4970 (2008).
[Crossref] [PubMed]

Grill, S. W.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A. C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Guo, K.

Gustafsson, M. G. L.

M. G. L. Gustafsson, L. Shao, P. M. Carlton, C. J. Wang, I. N. Golubovskaya, W. Z. Cande, D. A. Agard, and J. W. Sedat, “Three-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination,” Biophys. J. 94(12), 4957–4970 (2008).
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M. G. L. Gustafsson, “Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy,” J. Microsc. 198(2), 82–87 (2000).
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M. G. L. Gustafsson, D. A. Agard, and J. W. Sedat, “I5M: 3D widefield light microscopy with better than 100 nm axial resolution,” J. Microsc. 195(1), 10–16 (1999).
[Crossref] [PubMed]

Hammer, J. A.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A. C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Heintzmann, R.

A. Jost, E. Tolstik, P. Feldmann, K. Wicker, A. Sentenac, and R. Heintzmann, “Optical sectioning and high resolution in single-slice structured illumination microscopy by thick slice blind-SIM reconstruction,” PLoS One 10(7), e0132174 (2015).
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K. Wicker, O. Mandula, G. Best, R. Fiolka, and R. Heintzmann, “Phase optimisation for structured illumination microscopy,” Opt. Express 21(2), 2032–2049 (2013).
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Higgins, C. D.

L. Gao, L. Shao, C. D. Higgins, J. S. Poulton, M. Peifer, M. W. Davidson, X. Wu, B. Goldstein, and E. Betzig, “Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens,” Cell 151(6), 1370–1385 (2012).
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Huisken, J.

J. Huisken and D. Y. R. Stainier, “Selective plane illumination microscopy techniques in developmental biology,” Development 136(12), 1963–1975 (2009).
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Janetopoulos, C.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A. C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
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Jin, G.

Q. Yang, L. Cao, H. Zhang, H. Zhang, and G. Jin, “Method of lateral image reconstruction in structured illumination microscopy with super resolution,” J. Innov. Opt. Health Sci. 9(3), 1630002 (2016).
[Crossref]

Jost, A.

A. Jost, E. Tolstik, P. Feldmann, K. Wicker, A. Sentenac, and R. Heintzmann, “Optical sectioning and high resolution in single-slice structured illumination microscopy by thick slice blind-SIM reconstruction,” PLoS One 10(7), e0132174 (2015).
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Juskaitis, R.

Kaminski, C. F.

F. Ströhl and C. F. Kaminski, “A joint Richardson-Lucy deconvolution algorithm for the reconstruction of multifocal structured illumination microscopy data,” Methods Appl. Fluoresc. 3(1), 014002 (2015).
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Kiehart, D. P.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A. C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

King, S. V.

Langhorst, M. F.

M. F. Langhorst, J. Schaffer, and B. Goetze, “Structure brings clarity: structured illumination microscopy in cell biology,” Biotechnol. J. 4(6), 858–865 (2009).
[Crossref] [PubMed]

Lanni, F.

Legant, W. R.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A. C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Lippincott-Schwartz, J.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A. C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Liu, Z.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A. C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Loriette, V.

F. Orieux, E. Sepulveda, V. Loriette, B. Dubertret, and J. C. Olivo-Marin, “Bayesian estimation for optimized structured illumination microscopy,” IEEE Trans. Image Process. 21(2), 601–614 (2012).
[Crossref] [PubMed]

Mack, V.

Mander, L.

M. Sivaguru, L. Mander, G. Fried, and S. W. Punyasena, “Capturing the surface texture and shape of pollen: a comparison of microscopy techniques,” PLoS One 7(6), e39129 (2012).
[Crossref] [PubMed]

Mandula, O.

Martínez-Corral, M.

Martínez-Cuenca, R.

McNally, J. G.

J. A. Conchello and J. G. McNally, “Fast regularization technique for expectation maximization algorithm for optical sectioning microscopy,” Proc. SPIE 2655, 199–208 (1996).

Milkie, D. E.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A. C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Mimori-Kiyosue, Y.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A. C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Mione, M.

A. G. York, S. H. Parekh, D. Dalle Nogare, R. S. Fischer, K. Temprine, M. Mione, A. B. Chitnis, C. A. Combs, and H. Shroff, “Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy,” Nat. Methods 9(7), 749–754 (2012).
[Crossref] [PubMed]

Mitchell, D. M.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A. C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Mullins, R. D.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A. C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Nanda, P.

Neil, M. A. A.

Olivo-Marin, J. C.

F. Orieux, E. Sepulveda, V. Loriette, B. Dubertret, and J. C. Olivo-Marin, “Bayesian estimation for optimized structured illumination microscopy,” IEEE Trans. Image Process. 21(2), 601–614 (2012).
[Crossref] [PubMed]

Orieux, F.

F. Orieux, E. Sepulveda, V. Loriette, B. Dubertret, and J. C. Olivo-Marin, “Bayesian estimation for optimized structured illumination microscopy,” IEEE Trans. Image Process. 21(2), 601–614 (2012).
[Crossref] [PubMed]

Parekh, S. H.

A. G. York, S. H. Parekh, D. Dalle Nogare, R. S. Fischer, K. Temprine, M. Mione, A. B. Chitnis, C. A. Combs, and H. Shroff, “Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy,” Nat. Methods 9(7), 749–754 (2012).
[Crossref] [PubMed]

Patwary, N.

Peifer, M.

L. Gao, L. Shao, C. D. Higgins, J. S. Poulton, M. Peifer, M. W. Davidson, X. Wu, B. Goldstein, and E. Betzig, “Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens,” Cell 151(6), 1370–1385 (2012).
[Crossref] [PubMed]

Poulton, J. S.

L. Gao, L. Shao, C. D. Higgins, J. S. Poulton, M. Peifer, M. W. Davidson, X. Wu, B. Goldstein, and E. Betzig, “Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens,” Cell 151(6), 1370–1385 (2012).
[Crossref] [PubMed]

Preza, C.

H. Shabani, A. Doblas, G. Saavedra, and C. Preza, “3D structured illumination microscopy using an incoherent illumination system based on a Fresnel biprism,” Proc. SPIE 10499, 10499 (2018).

N. Patwary, J. Sola-Pikabea, A. Doblas, G. Saavedra, and C. Preza, “Evaluation of the use of wavefront encoding to reduce depth-induced aberration in structured illumination microscopy,” Proc. SPIE 10499, 10499 (2018).

N. Patwary, H. Shabani, A. Doblas, G. Saavedra, and C. Preza, “Experimental validation of a customized phase mask designed to enable efficient computational optical sectioning microscopy through wavefront encoding,” Appl. Opt. 56(9), D14–D23 (2017).
[Crossref] [PubMed]

N. Patwary, S. V. King, G. Saavedra, and C. Preza, “Reducing effects of aberration in 3D fluorescence imaging using wavefront coding with a radially symmetric phase mask,” Opt. Express 24(12), 12905–12921 (2016).
[Crossref] [PubMed]

C. Preza, “Simulating structured-illumination microscopy in the presence of spherical aberrations,” Proc. SPIE 7904, 79040D (2011).
[Crossref]

S. Yuan and C. Preza, “Point-spread function engineering to reduce the impact of spherical aberration on 3D computational fluorescence microscopy imaging,” Opt. Express 19(23), 23298–23314 (2011).
[Crossref] [PubMed]

Punyasena, S. W.

M. Sivaguru, L. Mander, G. Fried, and S. W. Punyasena, “Capturing the surface texture and shape of pollen: a comparison of microscopy techniques,” PLoS One 7(6), e39129 (2012).
[Crossref] [PubMed]

Rahman, M.

Reymann, A. C.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A. C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Richards-Kortum, R.

Ritter, A. T.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A. C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Rogers, J.

Romero, D. P.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A. C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Saavedra, G.

Sánchez-Ortiga, E.

Schaefer, L. H.

L. H. Schaefer, D. Schuster, and J. Schaffer, “Structured illumination microscopy: artefact analysis and reduction utilizing a parameter optimization approach,” J. Microsc. 216(2), 165–174 (2004).
[Crossref] [PubMed]

Schaffer, J.

M. F. Langhorst, J. Schaffer, and B. Goetze, “Structure brings clarity: structured illumination microscopy in cell biology,” Biotechnol. J. 4(6), 858–865 (2009).
[Crossref] [PubMed]

L. H. Schaefer, D. Schuster, and J. Schaffer, “Structured illumination microscopy: artefact analysis and reduction utilizing a parameter optimization approach,” J. Microsc. 216(2), 165–174 (2004).
[Crossref] [PubMed]

Schuster, D.

L. H. Schaefer, D. Schuster, and J. Schaffer, “Structured illumination microscopy: artefact analysis and reduction utilizing a parameter optimization approach,” J. Microsc. 216(2), 165–174 (2004).
[Crossref] [PubMed]

Sedat, J. W.

M. G. L. Gustafsson, L. Shao, P. M. Carlton, C. J. Wang, I. N. Golubovskaya, W. Z. Cande, D. A. Agard, and J. W. Sedat, “Three-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination,” Biophys. J. 94(12), 4957–4970 (2008).
[Crossref] [PubMed]

M. G. L. Gustafsson, D. A. Agard, and J. W. Sedat, “I5M: 3D widefield light microscopy with better than 100 nm axial resolution,” J. Microsc. 195(1), 10–16 (1999).
[Crossref] [PubMed]

Sentenac, A.

A. Jost, E. Tolstik, P. Feldmann, K. Wicker, A. Sentenac, and R. Heintzmann, “Optical sectioning and high resolution in single-slice structured illumination microscopy by thick slice blind-SIM reconstruction,” PLoS One 10(7), e0132174 (2015).
[Crossref] [PubMed]

Sepulveda, E.

F. Orieux, E. Sepulveda, V. Loriette, B. Dubertret, and J. C. Olivo-Marin, “Bayesian estimation for optimized structured illumination microscopy,” IEEE Trans. Image Process. 21(2), 601–614 (2012).
[Crossref] [PubMed]

Seydoux, G.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A. C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Shabani, H.

H. Shabani, A. Doblas, G. Saavedra, and C. Preza, “3D structured illumination microscopy using an incoherent illumination system based on a Fresnel biprism,” Proc. SPIE 10499, 10499 (2018).

N. Patwary, H. Shabani, A. Doblas, G. Saavedra, and C. Preza, “Experimental validation of a customized phase mask designed to enable efficient computational optical sectioning microscopy through wavefront encoding,” Appl. Opt. 56(9), D14–D23 (2017).
[Crossref] [PubMed]

Shao, L.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A. C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

L. Gao, L. Shao, C. D. Higgins, J. S. Poulton, M. Peifer, M. W. Davidson, X. Wu, B. Goldstein, and E. Betzig, “Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens,” Cell 151(6), 1370–1385 (2012).
[Crossref] [PubMed]

M. G. L. Gustafsson, L. Shao, P. M. Carlton, C. J. Wang, I. N. Golubovskaya, W. Z. Cande, D. A. Agard, and J. W. Sedat, “Three-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination,” Biophys. J. 94(12), 4957–4970 (2008).
[Crossref] [PubMed]

Sheikh, H. R.

Z. Wang, A. C. Bovik, H. R. Sheikh, and E. P. Simoncelli, “Image quality assessment: from error visibility to structural similarity,” IEEE Trans. Image Process. 13(4), 600–612 (2004).
[Crossref] [PubMed]

Shiradkar, R.

Shroff, H.

A. G. York, S. H. Parekh, D. Dalle Nogare, R. S. Fischer, K. Temprine, M. Mione, A. B. Chitnis, C. A. Combs, and H. Shroff, “Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy,” Nat. Methods 9(7), 749–754 (2012).
[Crossref] [PubMed]

Shroff, S. A.

Simoncelli, E. P.

Z. Wang, A. C. Bovik, H. R. Sheikh, and E. P. Simoncelli, “Image quality assessment: from error visibility to structural similarity,” IEEE Trans. Image Process. 13(4), 600–612 (2004).
[Crossref] [PubMed]

Sivaguru, M.

M. Sivaguru, L. Mander, G. Fried, and S. W. Punyasena, “Capturing the surface texture and shape of pollen: a comparison of microscopy techniques,” PLoS One 7(6), e39129 (2012).
[Crossref] [PubMed]

Sokolov, K.

Sola-Pikabea, J.

N. Patwary, J. Sola-Pikabea, A. Doblas, G. Saavedra, and C. Preza, “Evaluation of the use of wavefront encoding to reduce depth-induced aberration in structured illumination microscopy,” Proc. SPIE 10499, 10499 (2018).

Stainier, D. Y. R.

J. Huisken and D. Y. R. Stainier, “Selective plane illumination microscopy techniques in developmental biology,” Development 136(12), 1963–1975 (2009).
[Crossref] [PubMed]

Ströhl, F.

F. Ströhl and C. F. Kaminski, “A joint Richardson-Lucy deconvolution algorithm for the reconstruction of multifocal structured illumination microscopy data,” Methods Appl. Fluoresc. 3(1), 014002 (2015).
[Crossref] [PubMed]

Temprine, K.

A. G. York, S. H. Parekh, D. Dalle Nogare, R. S. Fischer, K. Temprine, M. Mione, A. B. Chitnis, C. A. Combs, and H. Shroff, “Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy,” Nat. Methods 9(7), 749–754 (2012).
[Crossref] [PubMed]

Tian, L.

Tkaczyk, T.

Tolstik, E.

A. Jost, E. Tolstik, P. Feldmann, K. Wicker, A. Sentenac, and R. Heintzmann, “Optical sectioning and high resolution in single-slice structured illumination microscopy by thick slice blind-SIM reconstruction,” PLoS One 10(7), e0132174 (2015).
[Crossref] [PubMed]

Tulu, U. S.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A. C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Vicidomini, G.

M. Bertero, P. Boccacci, G. Desiderà, and G. Vicidomini, “Image deblurring with Poisson data: from cells to galaxies,” Inverse Probl. 25(12), 123006 (2009).
[Crossref]

Waller, L.

Wang, C. J.

M. G. L. Gustafsson, L. Shao, P. M. Carlton, C. J. Wang, I. N. Golubovskaya, W. Z. Cande, D. A. Agard, and J. W. Sedat, “Three-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination,” Biophys. J. 94(12), 4957–4970 (2008).
[Crossref] [PubMed]

Wang, J. T.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A. C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Wang, K.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A. C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Wang, Z.

Z. Wang, A. C. Bovik, H. R. Sheikh, and E. P. Simoncelli, “Image quality assessment: from error visibility to structural similarity,” IEEE Trans. Image Process. 13(4), 600–612 (2004).
[Crossref] [PubMed]

Wicker, K.

A. Jost, E. Tolstik, P. Feldmann, K. Wicker, A. Sentenac, and R. Heintzmann, “Optical sectioning and high resolution in single-slice structured illumination microscopy by thick slice blind-SIM reconstruction,” PLoS One 10(7), e0132174 (2015).
[Crossref] [PubMed]

K. Wicker, O. Mandula, G. Best, R. Fiolka, and R. Heintzmann, “Phase optimisation for structured illumination microscopy,” Opt. Express 21(2), 2032–2049 (2013).
[Crossref] [PubMed]

Williams, D. R.

Wilson, T.

Wu, X.

L. Gao, L. Shao, C. D. Higgins, J. S. Poulton, M. Peifer, M. W. Davidson, X. Wu, B. Goldstein, and E. Betzig, “Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens,” Cell 151(6), 1370–1385 (2012).
[Crossref] [PubMed]

Wu, X. S.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A. C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Yang, Q.

Q. Yang, L. Cao, H. Zhang, H. Zhang, and G. Jin, “Method of lateral image reconstruction in structured illumination microscopy with super resolution,” J. Innov. Opt. Health Sci. 9(3), 1630002 (2016).
[Crossref]

Yeh, L.-H.

York, A. G.

A. G. York, S. H. Parekh, D. Dalle Nogare, R. S. Fischer, K. Temprine, M. Mione, A. B. Chitnis, C. A. Combs, and H. Shroff, “Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy,” Nat. Methods 9(7), 749–754 (2012).
[Crossref] [PubMed]

Yuan, S.

Zhang, H.

Q. Yang, L. Cao, H. Zhang, H. Zhang, and G. Jin, “Method of lateral image reconstruction in structured illumination microscopy with super resolution,” J. Innov. Opt. Health Sci. 9(3), 1630002 (2016).
[Crossref]

Q. Yang, L. Cao, H. Zhang, H. Zhang, and G. Jin, “Method of lateral image reconstruction in structured illumination microscopy with super resolution,” J. Innov. Opt. Health Sci. 9(3), 1630002 (2016).
[Crossref]

Zheng, G.

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Cell (1)

L. Gao, L. Shao, C. D. Higgins, J. S. Poulton, M. Peifer, M. W. Davidson, X. Wu, B. Goldstein, and E. Betzig, “Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens,” Cell 151(6), 1370–1385 (2012).
[Crossref] [PubMed]

Development (1)

J. Huisken and D. Y. R. Stainier, “Selective plane illumination microscopy techniques in developmental biology,” Development 136(12), 1963–1975 (2009).
[Crossref] [PubMed]

IEEE Trans. Image Process. (2)

F. Orieux, E. Sepulveda, V. Loriette, B. Dubertret, and J. C. Olivo-Marin, “Bayesian estimation for optimized structured illumination microscopy,” IEEE Trans. Image Process. 21(2), 601–614 (2012).
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Z. Wang, A. C. Bovik, H. R. Sheikh, and E. P. Simoncelli, “Image quality assessment: from error visibility to structural similarity,” IEEE Trans. Image Process. 13(4), 600–612 (2004).
[Crossref] [PubMed]

Inverse Probl. (1)

M. Bertero, P. Boccacci, G. Desiderà, and G. Vicidomini, “Image deblurring with Poisson data: from cells to galaxies,” Inverse Probl. 25(12), 123006 (2009).
[Crossref]

J. Innov. Opt. Health Sci. (1)

Q. Yang, L. Cao, H. Zhang, H. Zhang, and G. Jin, “Method of lateral image reconstruction in structured illumination microscopy with super resolution,” J. Innov. Opt. Health Sci. 9(3), 1630002 (2016).
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[Crossref] [PubMed]

Nat. Methods (1)

A. G. York, S. H. Parekh, D. Dalle Nogare, R. S. Fischer, K. Temprine, M. Mione, A. B. Chitnis, C. A. Combs, and H. Shroff, “Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy,” Nat. Methods 9(7), 749–754 (2012).
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S. Yuan and C. Preza, “Point-spread function engineering to reduce the impact of spherical aberration on 3D computational fluorescence microscopy imaging,” Opt. Express 19(23), 23298–23314 (2011).
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K. Wicker, O. Mandula, G. Best, R. Fiolka, and R. Heintzmann, “Phase optimisation for structured illumination microscopy,” Opt. Express 21(2), 2032–2049 (2013).
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S. Dong, P. Nanda, R. Shiradkar, K. Guo, and G. Zheng, “High-resolution fluorescence imaging via pattern-illuminated Fourier ptychography,” Opt. Express 22(17), 20856–20870 (2014).
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Proc. SPIE (4)

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Figures (7)

Fig. 1
Fig. 1 Demonstration of the improved OS capability of the proposed method. XZ cross-sectional image of (a) the true thin fluorescent layer; (b) its simulated raw image at φ = 0 deg; (c) corresponding demodulated image using the 2D-DMOD method; (d) the restored image from the 3D-DCV method; and (e) the restored image from the proposed method. (f) The m(z; f M ,d) in Eq. (6) and the corresponding m ˜ (z; f M ,d) in Eq. (13) computed for fM = 0.2fc at a depth d = 30 µm from the coverslip (w40 = −1.08). (g) Intensity profile along the dashed horizontal line as shown in the raw image in panel (b), and after applying the Wiener filter to the raw data. (h) The axial profile is taken along the dashed vertical line (as shown in panel c) from the true object and the restored images. (i) XZ cross-sectional image of an object with two fluorescent layers separated by 0.5 µm and corresponding restored images obtained with the three methods. (j) Normalized intensity profiles through the center of the XZ view images shown in (i). Lens: 63 × /1.4 NA oil immersion; emission wavelength is 515 nm, RI of the sample mounting medium is 1.47.
Fig. 2
Fig. 2 Effect of illumination fringe frequency and depth-induced SA on simulated ApoTome-based SIM imaging. (a) XZ cross-sectional view image of the test object (top) and its corresponding SIM raw image at depth 30 µm with modulation frequency fM = 0.5 µm−1. XZ cross-sections from restored SIM images when: (b) fM = 0.5 µm−1; (c) fM = 1.0 µm−1; and (d) fM = 1.5 µm−1. For each case, results are shown at different depths below the coverslip: 0 µm (top row), 30 µm (middle row), and 60 µm (bottom row). The SIM restored images from: (i) the 2D-DMOD method, (ii) the 3D-DCV method, and (iii) the proposed method. Lens: 63 × /1.4 NA oil immersion. RI of the specimen-embedding medium is 1.47. The emission wavelength is 515 nm. SA coefficient, w40, for the three different depths: 0, −1.08, and −2.16, respectively.
Fig. 3
Fig. 3 The experimental validation of the proposed method. (a) XZ cross-sectional view image of the raw SIM data captured from 50 µm depth below the cover slip; (b) XZ cross-sectional image of the restored images (white scale bar is equal to 3 µm) from depth locations 3 µm, 24 µm, and 50 µm using the: (i) ZEN-OS, (ii) ZEN-DCV, and (iii) the proposed method; (c) Intensity profiles along the red dashed vertical line shown in panel (b) when the spherical shell is located at 50 µm below the coverslip. Lens: 63 × /1.4 NA oil immersion, emission wavelength: 515 nm, RI of the specimen-embedding medium: 1.47. Depth-induced SA coefficient w40: −0.11, −0.86, −1.80. ApoTome grid L with modulation frequency 0.17fc.
Fig. 4
Fig. 4 Improvement in the optical sectioned image obtained with magnitude demodulation when the Wiener filter is applied to the raw data. XY cross-sections of images (shown with the same color scale) after applying the magnitude demodulation technique [Eq. (8)] to SIM raw and Wiener filtered image of: (a-b) the Glioblastoma cell and (c-d) a zoomed ROI from the pollen grain images, respectively. (e-f) Intensity profiles through the raw and the Wiener filtered image (inset image) along the dashed vertical lines shown in the insets. Lens: 63 × /1.4 NA oil immersion and the emission wavelength is 515 nm. ApoTome grid L and M with modulation frequency 0.09fc, and 0.17fc, respectively in the case of the Glioblastoma cell and the pollen grain.
Fig. 5
Fig. 5 Experimental validation of the improved OS capability of the proposed method through the restoration of a 3D image from a Glioblastoma cell. The top three rows of (a)-(c) are three axial planes while the last row shows an XZ cross-sectional view from the reconstructed image obtained using 3 methods: ZEN-OS, ZEN-DCV, and the proposed one. (i)-(iii) are zoomed ROI of the image planes at d0 + 0.3 μm as shown by the red rectangle (scale bar is equal to 2 µm); (iv)-(vi) are the zoomed areas shown in the rectangular-bound area of XZ view images (scale bar is equal to 2 µm). (d) Axial intensity profile through the dashed vertical line shown in panel (vi). Lens: 63 × /14 NA oil immersion; emission wavelength 515 nm.
Fig. 6
Fig. 6 Evaluation of the proposed method in restoring a 3D image from a thick biological sample, such as the pollen grain. The top three rows of (a)-(c) are the axial planes while the last row shows the XZ cross-sectional view from the reconstructed image obtained using 3 methods: ZEN-OS, ZEN-DCV, and the proposed one. (i)-(iii) zoomed ROI of the image plane at d0 as shown by the red rectangles (scale bar is equal to 5 µm). (iv)-(vi) further zoom of the images shown in (i)-(iii) as shown by the blue rectangles (scale bar is equal to 1 µm); (d) Intensity profile through the arrow shown in (iii). Lens: 63 × /1.4 NA oil immersion, emission wavelength 515 nm.
Fig. 7
Fig. 7 Impact of different steps used in the proposed restoration method. XY cross-sections of a zoomed ROI from restored images of the pollen grain obtained with different steps of the proposed method: (a) using all the steps; (b) IGF step skipped; (c) Wiener filter step skipped; and (d) EM restoration and IGF step skipped. All panels have been displayed using the same color scale for direct comparison of signal strength. Residual fringes shown by a red arrow in (b) are not evident in (a) due to the IGF step. The dashed red rectangles highlight signal enhancement due to the Wiener filter and further signal and contrast improvement due to the EM restoration step.

Tables (2)

Tables Icon

Table 1 Comparison between the restored images shown in Fig. 2(b)-(d) using different metrics: Peak SNR, NMSE and S-SIM. Raw SIM image SNR = 29 dB.

Tables Icon

Table 2 Dimensions (mean ± standard deviation) of spherical shells approximated by FWHM distances in restored images from experimental data shown in Fig. 3

Equations (15)

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

s i (x)=δ(z) [ 1+cos(2π f M x+ φ i ) ], i=1,2,....N ,
g i (x;d)= o( x 1 ) h D (x x 1 ;d) s i ( x 1 x 0 , y 1 y 0 ,z z 1 z 0 ) h I ( x 0 ;d) d x 0 d x 1 ,
m c = | H bf (u,v; f M ,d) | 2 ,
g i (x;d)=o(x) 3 h D (x;d)+ m c [ o c ( x )cos( φ i )+ o s ( x )sin( φ i ) ] 3 h SIM (x;d),
h SIM (x;d)
m(z; f M ,d)= cos(2π f M x 0 ) ( h I ( x 0 , y 0 ,z;d) d y 0 ) d x 0
g m,i (x,y; z j ,d)χ[ o c ( x,y; z j )cos( φ i )+ o s ( x,y; z j )sin( φ i ) ] 2 h D ( x,y; z bf ,d )
o os (x,y; z j )= [ o c (x,y; z j ) ] 2 + [ o s (x,y; z j ) ] 2 .
o ˜ os ( x,y; z j )=iFT[ O os (u,v; z j ) H G (u,v) ],
H G ( u,v )=1[ e [ (u u r ) 2 + v 2 ]/(2 σ 2 ) + e [ (u+ u r ) 2 + v 2 ]/(2 σ 2 ) ],
o ˜ os (x)o(x) 3 h ˜ SIM (x; f M ,d),
h ˜ SIM (x; f M ,d)= m ˜ (x,z; f M ,d) h D (x;d),
m ˜ (z; f M ,d)= [ o TL,c (x,z; f M ,d) ] 2 + [ o TL,s (x,z; f M ,d) ] 2 ,
o TL,c ( x,z; f M ,d )= m c cos[ 2π f M ( x x 0 ) ] h SIM ( x 0 , y 0 ,z; f M ,d )d y 0 d x 0 ,
o TL,s ( x,z; f M ,d )= m c sin[ 2π f M ( x x 0 ) ] h SIM ( x 0 , y 0 ,z; f M ,d )d y 0 d x 0 .

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