Abstract

The performance of a tunable three-dimensional (3D) structured illumination microscope (SIM) system and its ability to provide simultaneously super-resolution (SR) and optical-sectioning (OS) capabilities are investigated. Numerical results show that the performance of our 3D-SIM system is comparable with the one provided by a three-wave interference SIM, while requiring 40% fewer images for the reconstruction and providing frequency tunability in a cost-effective implementation. The performance of the system has been validated experimentally with images from test samples, which were also imaged with a commercial SIM based on incoherent-grid projection for comparison. Restored images from data acquired from an axially-thin fluorescent layer show a 1.6× improvement in OS capability compared to the commercial instrument while results from a fluorescent tilted USAF target show the OS and SR capabilities achieved by our system.

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

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2018 (7)

H. Shabani, A. Doblas, G. Saavedra, E. Sanchez-Ortiga, and C. Preza, “Improvement of two-dimensional structured illumination microscopy with an incoherent illumination pattern of tunable frequency,” Appl. Opt. 57(7), B92–B101 (2018).
[Crossref] [PubMed]

J. Boulanger, N. Pustelnik, L. Condat, L. Sengmanivong, and T. Piolot, “Nonsmooth convex optimization for structured illumination microscopy image reconstruction,” Inverse Probl. 34(9), 095004 (2018).
[Crossref] [PubMed]

A. Lal, C. Shan, K. Zhao, W. Liu, X. Huang, W. Zong, L. Chen, and P. Xi, “A Frequency Domain SIM Reconstruction Algorithm Using Reduced Number of Images,” IEEE Trans. Image Process. 27(9), 4555–4570 (2018).
[Crossref] [PubMed]

H. Shabani, A. Doblas, G. Saavedra, and C. Preza, “Preprocessing method to correct illumination pattern in sinusoidal-based structured illumination microscopy,” Proc. SPIE 10499, 104991Z (2018).
[Crossref]

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, 1049903 (2018).
[Crossref]

N. Patwary, A. Doblas, and C. Preza, “Image restoration approach to address reduced modulation contrast in structured illumination microscopy,” Biomed. Opt. Express 9(4), 1630–1647 (2018).
[Crossref] [PubMed]

C. Karras, M. Smedh, R. Förster, H. Deschout, J. Fernandez-Rodriguez, and R. Heintzmann, “Successful optimization of reconstruction parameters in structured illumination microscopy - a practical guide,” bioRxiv 402115, 1–13 (2018).

2017 (2)

H. Shabani, N. Patwary, A. Doblas, G. Saavedra, and C. Preza, “Comparison of two structured illumination techniques based on different 3D illumination patterns,” Proc. SPIE 10070, 1007013 (2017).
[Crossref]

F. Orieux, V. Loriette, J. C. Olivo-Marin, E. Sepulveda, and A. Fragola, “Fast myopic 2D-SIM super resolution microscopy with joint modulation pattern estimation,” Inverse Probl. 33(12), 1–22 (2017).
[Crossref]

2016 (1)

V. O. Chagin, C. S. Casas-Delucchi, M. Reinhart, L. Schermelleh, Y. Markaki, A. Maiser, J. J. Bolius, A. Bensimon, M. Fillies, P. Domaing, Y. M. Rozanov, H. Leonhardt, and M. C. Cardoso, “4D Visualization of replication foci in mammalian cells corresponding to individual replicons,” Nat. Commun. 7, 11231 (2016).
[Crossref] [PubMed]

2015 (2)

S. Dong, J. Liao, K. Guo, L. Bian, J. Suo, and G. Zheng, “Resolution doubling with a reduced number of image acquisitions,” Biomed. Opt. Express 6(8), 2946–2952 (2015).
[Crossref] [PubMed]

P. Vermeulen, H. Zhan, F. Orieux, J. C. Olivo-Marin, Z. Lenkei, V. Loriette, and A. Fragola, “Out-of-focus background subtraction for fast structured illumination super-resolution microscopy of optically thick samples,” J. Microsc. 259(3), 257–268 (2015).
[Crossref] [PubMed]

2014 (2)

V. W. Rowlett and W. Margolin, “3D-SIM super-resolution of FtsZ and its membrane tethers in Escherichia coli cells,” Biophys. J. 107(8), L17–L20 (2014).
[Crossref] [PubMed]

C. Lesterlin, G. Ball, L. Schermelleh, and D. J. Sherratt, “RecA bundles mediate homology pairing between distant sisters during DNA break repair,” Nature 506(7487), 249–253 (2014).
[Crossref] [PubMed]

2013 (2)

J. Tilsner, O. Linnik, M. Louveaux, I. M. Roberts, S. N. Chapman, and K. J. Oparka, “Replication and trafficking of a plant virus are coupled at the entrances of plasmodesmata,” J. Cell Biol. 201(7), 981–995 (2013).
[Crossref] [PubMed]

A. Doblas, G. Saavedra, M. Martinez-Corral, J. C. Barreiro, E. Sanchez-Ortiga, and A. Llavador, “Axial resonance of periodic patterns by using a Fresnel biprism,” J. Opt. Soc. Am. A 30(1), 140–148 (2013).
[Crossref] [PubMed]

2012 (3)

K. F. Sonnen, L. Schermelleh, H. Leonhardt, and E. A. Nigg, “3D-structured illumination microscopy provides novel insight into architecture of human centrosomes,” Biol. Open 1(10), 965–976 (2012).
[Crossref] [PubMed]

R. Fiolka, L. Shao, E. H. Rego, M. W. Davidson, and M. G. L. Gustafsson, “Time-lapse two-color 3D imaging of live cells with doubled resolution using structured illumination,” Proc. Natl. Acad. Sci. U.S.A. 109(14), 5311–5315 (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 (1)

A. C. N. Brown, S. Oddos, I. M. Dobbie, J. M. Alakoskela, R. M. Parton, P. Eissmann, M. A. A. Neil, C. Dunsby, P. M. W. French, I. Davis, and D. M. Davis, “Remodelling of cortical actin where lytic granules dock at Natural Killer cell immune synapses revealed by super-resolution microscopy,” PLoS Biol. 9(9), e1001152 (2011).
[Crossref] [PubMed]

2010 (1)

V. C. Cogger, G. P. McNerney, T. Nyunt, L. D. DeLeve, P. McCourt, B. Smedsrød, D. G. Le Couteur, and T. R. Huser, “Three-dimensional structured illumination microscopy of liver sinusoidal endothelial cell fenestrations,” J. Struct. Biol. 171(3), 382–388 (2010).
[Crossref] [PubMed]

2009 (7)

C. J. R. Wang, P. M. Carlton, I. N. Golubovskaya, and W. Z. Cande, “Interlock formation and coiling of meiotic chromosome axes during synapsis,” Genetics 183(3), 905–915 (2009).
[Crossref] [PubMed]

L. M. Hirvonen, K. Wicker, O. Mandula, and R. Heintzmann, “Structured illumination microscopy of a living cell,” Eur. Biophys. J. 38(6), 807–812 (2009).
[Crossref] [PubMed]

P. Kner, B. B. Chhun, E. R. Griffis, L. Winoto, and M. G. L. Gustafsson, “Super-resolution video microscopy of live cells by structured illumination,” Nat. Methods 6(5), 339–342 (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]

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

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]

M. Martínez-Corral and G. Saavedra, “The Resolution Challenge in 3D Optical Microscopy,” Prog. Opt. 53, 1–67 (2009).
[Crossref]

2008 (1)

M. G. L. Gustafsson, L. Shao, P. M. Carlton, C. J. R. 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]

2003 (1)

R. Heintzmann, “Saturated patterned excitation microscopy with two-dimensional excitation patterns,” Micron 34(6-7), 283–291 (2003).
[Crossref] [PubMed]

1997 (2)

Agard, D. A.

M. G. L. Gustafsson, L. Shao, P. M. Carlton, C. J. R. 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]

Alakoskela, J. M.

A. C. N. Brown, S. Oddos, I. M. Dobbie, J. M. Alakoskela, R. M. Parton, P. Eissmann, M. A. A. Neil, C. Dunsby, P. M. W. French, I. Davis, and D. M. Davis, “Remodelling of cortical actin where lytic granules dock at Natural Killer cell immune synapses revealed by super-resolution microscopy,” PLoS Biol. 9(9), e1001152 (2011).
[Crossref] [PubMed]

Ball, G.

C. Lesterlin, G. Ball, L. Schermelleh, and D. J. Sherratt, “RecA bundles mediate homology pairing between distant sisters during DNA break repair,” Nature 506(7487), 249–253 (2014).
[Crossref] [PubMed]

Barreiro, J. C.

Bensimon, A.

V. O. Chagin, C. S. Casas-Delucchi, M. Reinhart, L. Schermelleh, Y. Markaki, A. Maiser, J. J. Bolius, A. Bensimon, M. Fillies, P. Domaing, Y. M. Rozanov, H. Leonhardt, and M. C. Cardoso, “4D Visualization of replication foci in mammalian cells corresponding to individual replicons,” Nat. Commun. 7, 11231 (2016).
[Crossref] [PubMed]

Bertero, M.

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

Bian, L.

Boccacci, P.

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

Bolius, J. J.

V. O. Chagin, C. S. Casas-Delucchi, M. Reinhart, L. Schermelleh, Y. Markaki, A. Maiser, J. J. Bolius, A. Bensimon, M. Fillies, P. Domaing, Y. M. Rozanov, H. Leonhardt, and M. C. Cardoso, “4D Visualization of replication foci in mammalian cells corresponding to individual replicons,” Nat. Commun. 7, 11231 (2016).
[Crossref] [PubMed]

Boulanger, J.

J. Boulanger, N. Pustelnik, L. Condat, L. Sengmanivong, and T. Piolot, “Nonsmooth convex optimization for structured illumination microscopy image reconstruction,” Inverse Probl. 34(9), 095004 (2018).
[Crossref] [PubMed]

Brown, A. C. N.

A. C. N. Brown, S. Oddos, I. M. Dobbie, J. M. Alakoskela, R. M. Parton, P. Eissmann, M. A. A. Neil, C. Dunsby, P. M. W. French, I. Davis, and D. M. Davis, “Remodelling of cortical actin where lytic granules dock at Natural Killer cell immune synapses revealed by super-resolution microscopy,” PLoS Biol. 9(9), e1001152 (2011).
[Crossref] [PubMed]

Cande, W. Z.

C. J. R. Wang, P. M. Carlton, I. N. Golubovskaya, and W. Z. Cande, “Interlock formation and coiling of meiotic chromosome axes during synapsis,” Genetics 183(3), 905–915 (2009).
[Crossref] [PubMed]

M. G. L. Gustafsson, L. Shao, P. M. Carlton, C. J. R. 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]

Cardoso, M. C.

V. O. Chagin, C. S. Casas-Delucchi, M. Reinhart, L. Schermelleh, Y. Markaki, A. Maiser, J. J. Bolius, A. Bensimon, M. Fillies, P. Domaing, Y. M. Rozanov, H. Leonhardt, and M. C. Cardoso, “4D Visualization of replication foci in mammalian cells corresponding to individual replicons,” Nat. Commun. 7, 11231 (2016).
[Crossref] [PubMed]

Carlton, P. M.

C. J. R. Wang, P. M. Carlton, I. N. Golubovskaya, and W. Z. Cande, “Interlock formation and coiling of meiotic chromosome axes during synapsis,” Genetics 183(3), 905–915 (2009).
[Crossref] [PubMed]

M. G. L. Gustafsson, L. Shao, P. M. Carlton, C. J. R. 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]

Casas-Delucchi, C. S.

V. O. Chagin, C. S. Casas-Delucchi, M. Reinhart, L. Schermelleh, Y. Markaki, A. Maiser, J. J. Bolius, A. Bensimon, M. Fillies, P. Domaing, Y. M. Rozanov, H. Leonhardt, and M. C. Cardoso, “4D Visualization of replication foci in mammalian cells corresponding to individual replicons,” Nat. Commun. 7, 11231 (2016).
[Crossref] [PubMed]

Chagin, V. O.

V. O. Chagin, C. S. Casas-Delucchi, M. Reinhart, L. Schermelleh, Y. Markaki, A. Maiser, J. J. Bolius, A. Bensimon, M. Fillies, P. Domaing, Y. M. Rozanov, H. Leonhardt, and M. C. Cardoso, “4D Visualization of replication foci in mammalian cells corresponding to individual replicons,” Nat. Commun. 7, 11231 (2016).
[Crossref] [PubMed]

Chang, T. Y.

Chapman, S. N.

J. Tilsner, O. Linnik, M. Louveaux, I. M. Roberts, S. N. Chapman, and K. J. Oparka, “Replication and trafficking of a plant virus are coupled at the entrances of plasmodesmata,” J. Cell Biol. 201(7), 981–995 (2013).
[Crossref] [PubMed]

Chen, L.

A. Lal, C. Shan, K. Zhao, W. Liu, X. Huang, W. Zong, L. Chen, and P. Xi, “A Frequency Domain SIM Reconstruction Algorithm Using Reduced Number of Images,” IEEE Trans. Image Process. 27(9), 4555–4570 (2018).
[Crossref] [PubMed]

Chhun, B. B.

P. Kner, B. B. Chhun, E. R. Griffis, L. Winoto, and M. G. L. Gustafsson, “Super-resolution video microscopy of live cells by structured illumination,” Nat. Methods 6(5), 339–342 (2009).
[Crossref] [PubMed]

Choe, J. Y.

Cogger, V. C.

V. C. Cogger, G. P. McNerney, T. Nyunt, L. D. DeLeve, P. McCourt, B. Smedsrød, D. G. Le Couteur, and T. R. Huser, “Three-dimensional structured illumination microscopy of liver sinusoidal endothelial cell fenestrations,” J. Struct. Biol. 171(3), 382–388 (2010).
[Crossref] [PubMed]

Condat, L.

J. Boulanger, N. Pustelnik, L. Condat, L. Sengmanivong, and T. Piolot, “Nonsmooth convex optimization for structured illumination microscopy image reconstruction,” Inverse Probl. 34(9), 095004 (2018).
[Crossref] [PubMed]

Davidson, M. W.

R. Fiolka, L. Shao, E. H. Rego, M. W. Davidson, and M. G. L. Gustafsson, “Time-lapse two-color 3D imaging of live cells with doubled resolution using structured illumination,” Proc. Natl. Acad. Sci. U.S.A. 109(14), 5311–5315 (2012).
[Crossref] [PubMed]

Davis, D. M.

A. C. N. Brown, S. Oddos, I. M. Dobbie, J. M. Alakoskela, R. M. Parton, P. Eissmann, M. A. A. Neil, C. Dunsby, P. M. W. French, I. Davis, and D. M. Davis, “Remodelling of cortical actin where lytic granules dock at Natural Killer cell immune synapses revealed by super-resolution microscopy,” PLoS Biol. 9(9), e1001152 (2011).
[Crossref] [PubMed]

Davis, I.

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V. C. Cogger, G. P. McNerney, T. Nyunt, L. D. DeLeve, P. McCourt, B. Smedsrød, D. G. Le Couteur, and T. R. Huser, “Three-dimensional structured illumination microscopy of liver sinusoidal endothelial cell fenestrations,” J. Struct. Biol. 171(3), 382–388 (2010).
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C. Karras, M. Smedh, R. Förster, H. Deschout, J. Fernandez-Rodriguez, and R. Heintzmann, “Successful optimization of reconstruction parameters in structured illumination microscopy - a practical guide,” bioRxiv 402115, 1–13 (2018).

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A. C. N. Brown, S. Oddos, I. M. Dobbie, J. M. Alakoskela, R. M. Parton, P. Eissmann, M. A. A. Neil, C. Dunsby, P. M. W. French, I. Davis, and D. M. Davis, “Remodelling of cortical actin where lytic granules dock at Natural Killer cell immune synapses revealed by super-resolution microscopy,” PLoS Biol. 9(9), e1001152 (2011).
[Crossref] [PubMed]

Doblas, A.

H. Shabani, A. Doblas, G. Saavedra, and C. Preza, “Preprocessing method to correct illumination pattern in sinusoidal-based structured illumination microscopy,” Proc. SPIE 10499, 104991Z (2018).
[Crossref]

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, 1049903 (2018).
[Crossref]

H. Shabani, A. Doblas, G. Saavedra, E. Sanchez-Ortiga, and C. Preza, “Improvement of two-dimensional structured illumination microscopy with an incoherent illumination pattern of tunable frequency,” Appl. Opt. 57(7), B92–B101 (2018).
[Crossref] [PubMed]

N. Patwary, A. Doblas, and C. Preza, “Image restoration approach to address reduced modulation contrast in structured illumination microscopy,” Biomed. Opt. Express 9(4), 1630–1647 (2018).
[Crossref] [PubMed]

H. Shabani, N. Patwary, A. Doblas, G. Saavedra, and C. Preza, “Comparison of two structured illumination techniques based on different 3D illumination patterns,” Proc. SPIE 10070, 1007013 (2017).
[Crossref]

A. Doblas, G. Saavedra, M. Martinez-Corral, J. C. Barreiro, E. Sanchez-Ortiga, and A. Llavador, “Axial resonance of periodic patterns by using a Fresnel biprism,” J. Opt. Soc. Am. A 30(1), 140–148 (2013).
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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).
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A. C. N. Brown, S. Oddos, I. M. Dobbie, J. M. Alakoskela, R. M. Parton, P. Eissmann, M. A. A. Neil, C. Dunsby, P. M. W. French, I. Davis, and D. M. Davis, “Remodelling of cortical actin where lytic granules dock at Natural Killer cell immune synapses revealed by super-resolution microscopy,” PLoS Biol. 9(9), e1001152 (2011).
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A. C. N. Brown, S. Oddos, I. M. Dobbie, J. M. Alakoskela, R. M. Parton, P. Eissmann, M. A. A. Neil, C. Dunsby, P. M. W. French, I. Davis, and D. M. Davis, “Remodelling of cortical actin where lytic granules dock at Natural Killer cell immune synapses revealed by super-resolution microscopy,” PLoS Biol. 9(9), e1001152 (2011).
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Fernandez-Rodriguez, J.

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Fienup, J. R.

Fillies, M.

V. O. Chagin, C. S. Casas-Delucchi, M. Reinhart, L. Schermelleh, Y. Markaki, A. Maiser, J. J. Bolius, A. Bensimon, M. Fillies, P. Domaing, Y. M. Rozanov, H. Leonhardt, and M. C. Cardoso, “4D Visualization of replication foci in mammalian cells corresponding to individual replicons,” Nat. Commun. 7, 11231 (2016).
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R. Fiolka, L. Shao, E. H. Rego, M. W. Davidson, and M. G. L. Gustafsson, “Time-lapse two-color 3D imaging of live cells with doubled resolution using structured illumination,” Proc. Natl. Acad. Sci. U.S.A. 109(14), 5311–5315 (2012).
[Crossref] [PubMed]

Förster, R.

C. Karras, M. Smedh, R. Förster, H. Deschout, J. Fernandez-Rodriguez, and R. Heintzmann, “Successful optimization of reconstruction parameters in structured illumination microscopy - a practical guide,” bioRxiv 402115, 1–13 (2018).

Fragola, A.

F. Orieux, V. Loriette, J. C. Olivo-Marin, E. Sepulveda, and A. Fragola, “Fast myopic 2D-SIM super resolution microscopy with joint modulation pattern estimation,” Inverse Probl. 33(12), 1–22 (2017).
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P. Vermeulen, H. Zhan, F. Orieux, J. C. Olivo-Marin, Z. Lenkei, V. Loriette, and A. Fragola, “Out-of-focus background subtraction for fast structured illumination super-resolution microscopy of optically thick samples,” J. Microsc. 259(3), 257–268 (2015).
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A. C. N. Brown, S. Oddos, I. M. Dobbie, J. M. Alakoskela, R. M. Parton, P. Eissmann, M. A. A. Neil, C. Dunsby, P. M. W. French, I. Davis, and D. M. Davis, “Remodelling of cortical actin where lytic granules dock at Natural Killer cell immune synapses revealed by super-resolution microscopy,” PLoS Biol. 9(9), e1001152 (2011).
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Griffis, E. R.

P. Kner, B. B. Chhun, E. R. Griffis, L. Winoto, and M. G. L. Gustafsson, “Super-resolution video microscopy of live cells by structured illumination,” Nat. Methods 6(5), 339–342 (2009).
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Guo, K.

Gustafsson, M. G. L.

R. Fiolka, L. Shao, E. H. Rego, M. W. Davidson, and M. G. L. Gustafsson, “Time-lapse two-color 3D imaging of live cells with doubled resolution using structured illumination,” Proc. Natl. Acad. Sci. U.S.A. 109(14), 5311–5315 (2012).
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P. Kner, B. B. Chhun, E. R. Griffis, L. Winoto, and M. G. L. Gustafsson, “Super-resolution video microscopy of live cells by structured illumination,” Nat. Methods 6(5), 339–342 (2009).
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M. G. L. Gustafsson, L. Shao, P. M. Carlton, C. J. R. 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]

Heintzmann, R.

C. Karras, M. Smedh, R. Förster, H. Deschout, J. Fernandez-Rodriguez, and R. Heintzmann, “Successful optimization of reconstruction parameters in structured illumination microscopy - a practical guide,” bioRxiv 402115, 1–13 (2018).

L. M. Hirvonen, K. Wicker, O. Mandula, and R. Heintzmann, “Structured illumination microscopy of a living cell,” Eur. Biophys. J. 38(6), 807–812 (2009).
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R. Heintzmann, “Saturated patterned excitation microscopy with two-dimensional excitation patterns,” Micron 34(6-7), 283–291 (2003).
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Hirvonen, L. M.

L. M. Hirvonen, K. Wicker, O. Mandula, and R. Heintzmann, “Structured illumination microscopy of a living cell,” Eur. Biophys. J. 38(6), 807–812 (2009).
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Hong, J. H.

Huang, X.

A. Lal, C. Shan, K. Zhao, W. Liu, X. Huang, W. Zong, L. Chen, and P. Xi, “A Frequency Domain SIM Reconstruction Algorithm Using Reduced Number of Images,” IEEE Trans. Image Process. 27(9), 4555–4570 (2018).
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Huser, T. R.

V. C. Cogger, G. P. McNerney, T. Nyunt, L. D. DeLeve, P. McCourt, B. Smedsrød, D. G. Le Couteur, and T. R. Huser, “Three-dimensional structured illumination microscopy of liver sinusoidal endothelial cell fenestrations,” J. Struct. Biol. 171(3), 382–388 (2010).
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Juskaitis, R.

Karras, C.

C. Karras, M. Smedh, R. Förster, H. Deschout, J. Fernandez-Rodriguez, and R. Heintzmann, “Successful optimization of reconstruction parameters in structured illumination microscopy - a practical guide,” bioRxiv 402115, 1–13 (2018).

Kner, P.

P. Kner, B. B. Chhun, E. R. Griffis, L. Winoto, and M. G. L. Gustafsson, “Super-resolution video microscopy of live cells by structured illumination,” Nat. Methods 6(5), 339–342 (2009).
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Lal, A.

A. Lal, C. Shan, K. Zhao, W. Liu, X. Huang, W. Zong, L. Chen, and P. Xi, “A Frequency Domain SIM Reconstruction Algorithm Using Reduced Number of Images,” IEEE Trans. Image Process. 27(9), 4555–4570 (2018).
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Le Couteur, D. G.

V. C. Cogger, G. P. McNerney, T. Nyunt, L. D. DeLeve, P. McCourt, B. Smedsrød, D. G. Le Couteur, and T. R. Huser, “Three-dimensional structured illumination microscopy of liver sinusoidal endothelial cell fenestrations,” J. Struct. Biol. 171(3), 382–388 (2010).
[Crossref] [PubMed]

Lenkei, Z.

P. Vermeulen, H. Zhan, F. Orieux, J. C. Olivo-Marin, Z. Lenkei, V. Loriette, and A. Fragola, “Out-of-focus background subtraction for fast structured illumination super-resolution microscopy of optically thick samples,” J. Microsc. 259(3), 257–268 (2015).
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Leonhardt, H.

V. O. Chagin, C. S. Casas-Delucchi, M. Reinhart, L. Schermelleh, Y. Markaki, A. Maiser, J. J. Bolius, A. Bensimon, M. Fillies, P. Domaing, Y. M. Rozanov, H. Leonhardt, and M. C. Cardoso, “4D Visualization of replication foci in mammalian cells corresponding to individual replicons,” Nat. Commun. 7, 11231 (2016).
[Crossref] [PubMed]

K. F. Sonnen, L. Schermelleh, H. Leonhardt, and E. A. Nigg, “3D-structured illumination microscopy provides novel insight into architecture of human centrosomes,” Biol. Open 1(10), 965–976 (2012).
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C. Lesterlin, G. Ball, L. Schermelleh, and D. J. Sherratt, “RecA bundles mediate homology pairing between distant sisters during DNA break repair,” Nature 506(7487), 249–253 (2014).
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Liao, J.

Linnik, O.

J. Tilsner, O. Linnik, M. Louveaux, I. M. Roberts, S. N. Chapman, and K. J. Oparka, “Replication and trafficking of a plant virus are coupled at the entrances of plasmodesmata,” J. Cell Biol. 201(7), 981–995 (2013).
[Crossref] [PubMed]

Liu, W.

A. Lal, C. Shan, K. Zhao, W. Liu, X. Huang, W. Zong, L. Chen, and P. Xi, “A Frequency Domain SIM Reconstruction Algorithm Using Reduced Number of Images,” IEEE Trans. Image Process. 27(9), 4555–4570 (2018).
[Crossref] [PubMed]

Llavador, A.

Loriette, V.

F. Orieux, V. Loriette, J. C. Olivo-Marin, E. Sepulveda, and A. Fragola, “Fast myopic 2D-SIM super resolution microscopy with joint modulation pattern estimation,” Inverse Probl. 33(12), 1–22 (2017).
[Crossref]

P. Vermeulen, H. Zhan, F. Orieux, J. C. Olivo-Marin, Z. Lenkei, V. Loriette, and A. Fragola, “Out-of-focus background subtraction for fast structured illumination super-resolution microscopy of optically thick samples,” J. Microsc. 259(3), 257–268 (2015).
[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]

Louveaux, M.

J. Tilsner, O. Linnik, M. Louveaux, I. M. Roberts, S. N. Chapman, and K. J. Oparka, “Replication and trafficking of a plant virus are coupled at the entrances of plasmodesmata,” J. Cell Biol. 201(7), 981–995 (2013).
[Crossref] [PubMed]

Maiser, A.

V. O. Chagin, C. S. Casas-Delucchi, M. Reinhart, L. Schermelleh, Y. Markaki, A. Maiser, J. J. Bolius, A. Bensimon, M. Fillies, P. Domaing, Y. M. Rozanov, H. Leonhardt, and M. C. Cardoso, “4D Visualization of replication foci in mammalian cells corresponding to individual replicons,” Nat. Commun. 7, 11231 (2016).
[Crossref] [PubMed]

Mandula, O.

L. M. Hirvonen, K. Wicker, O. Mandula, and R. Heintzmann, “Structured illumination microscopy of a living cell,” Eur. Biophys. J. 38(6), 807–812 (2009).
[Crossref] [PubMed]

Margolin, W.

V. W. Rowlett and W. Margolin, “3D-SIM super-resolution of FtsZ and its membrane tethers in Escherichia coli cells,” Biophys. J. 107(8), L17–L20 (2014).
[Crossref] [PubMed]

Markaki, Y.

V. O. Chagin, C. S. Casas-Delucchi, M. Reinhart, L. Schermelleh, Y. Markaki, A. Maiser, J. J. Bolius, A. Bensimon, M. Fillies, P. Domaing, Y. M. Rozanov, H. Leonhardt, and M. C. Cardoso, “4D Visualization of replication foci in mammalian cells corresponding to individual replicons,” Nat. Commun. 7, 11231 (2016).
[Crossref] [PubMed]

Martinez-Corral, M.

Martínez-Corral, M.

Martínez-Cuenca, R.

McCourt, P.

V. C. Cogger, G. P. McNerney, T. Nyunt, L. D. DeLeve, P. McCourt, B. Smedsrød, D. G. Le Couteur, and T. R. Huser, “Three-dimensional structured illumination microscopy of liver sinusoidal endothelial cell fenestrations,” J. Struct. Biol. 171(3), 382–388 (2010).
[Crossref] [PubMed]

McNerney, G. P.

V. C. Cogger, G. P. McNerney, T. Nyunt, L. D. DeLeve, P. McCourt, B. Smedsrød, D. G. Le Couteur, and T. R. Huser, “Three-dimensional structured illumination microscopy of liver sinusoidal endothelial cell fenestrations,” J. Struct. Biol. 171(3), 382–388 (2010).
[Crossref] [PubMed]

Neil, M. A. A.

A. C. N. Brown, S. Oddos, I. M. Dobbie, J. M. Alakoskela, R. M. Parton, P. Eissmann, M. A. A. Neil, C. Dunsby, P. M. W. French, I. Davis, and D. M. Davis, “Remodelling of cortical actin where lytic granules dock at Natural Killer cell immune synapses revealed by super-resolution microscopy,” PLoS Biol. 9(9), e1001152 (2011).
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M. A. A. Neil, R. Juskaitis, and T. Wilson, “Method of obtaining optical sectioning by using structured light in a conventional microscope,” Opt. Lett. 22(24), 1905–1907 (1997).
[Crossref] [PubMed]

Nigg, E. A.

K. F. Sonnen, L. Schermelleh, H. Leonhardt, and E. A. Nigg, “3D-structured illumination microscopy provides novel insight into architecture of human centrosomes,” Biol. Open 1(10), 965–976 (2012).
[Crossref] [PubMed]

Nyunt, T.

V. C. Cogger, G. P. McNerney, T. Nyunt, L. D. DeLeve, P. McCourt, B. Smedsrød, D. G. Le Couteur, and T. R. Huser, “Three-dimensional structured illumination microscopy of liver sinusoidal endothelial cell fenestrations,” J. Struct. Biol. 171(3), 382–388 (2010).
[Crossref] [PubMed]

Oddos, S.

A. C. N. Brown, S. Oddos, I. M. Dobbie, J. M. Alakoskela, R. M. Parton, P. Eissmann, M. A. A. Neil, C. Dunsby, P. M. W. French, I. Davis, and D. M. Davis, “Remodelling of cortical actin where lytic granules dock at Natural Killer cell immune synapses revealed by super-resolution microscopy,” PLoS Biol. 9(9), e1001152 (2011).
[Crossref] [PubMed]

Oh, T. K.

Olivo-Marin, J. C.

F. Orieux, V. Loriette, J. C. Olivo-Marin, E. Sepulveda, and A. Fragola, “Fast myopic 2D-SIM super resolution microscopy with joint modulation pattern estimation,” Inverse Probl. 33(12), 1–22 (2017).
[Crossref]

P. Vermeulen, H. Zhan, F. Orieux, J. C. Olivo-Marin, Z. Lenkei, V. Loriette, and A. Fragola, “Out-of-focus background subtraction for fast structured illumination super-resolution microscopy of optically thick samples,” J. Microsc. 259(3), 257–268 (2015).
[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]

Oparka, K. J.

J. Tilsner, O. Linnik, M. Louveaux, I. M. Roberts, S. N. Chapman, and K. J. Oparka, “Replication and trafficking of a plant virus are coupled at the entrances of plasmodesmata,” J. Cell Biol. 201(7), 981–995 (2013).
[Crossref] [PubMed]

Orieux, F.

F. Orieux, V. Loriette, J. C. Olivo-Marin, E. Sepulveda, and A. Fragola, “Fast myopic 2D-SIM super resolution microscopy with joint modulation pattern estimation,” Inverse Probl. 33(12), 1–22 (2017).
[Crossref]

P. Vermeulen, H. Zhan, F. Orieux, J. C. Olivo-Marin, Z. Lenkei, V. Loriette, and A. Fragola, “Out-of-focus background subtraction for fast structured illumination super-resolution microscopy of optically thick samples,” J. Microsc. 259(3), 257–268 (2015).
[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]

Paek, E. G.

Parton, R. M.

A. C. N. Brown, S. Oddos, I. M. Dobbie, J. M. Alakoskela, R. M. Parton, P. Eissmann, M. A. A. Neil, C. Dunsby, P. M. W. French, I. Davis, and D. M. Davis, “Remodelling of cortical actin where lytic granules dock at Natural Killer cell immune synapses revealed by super-resolution microscopy,” PLoS Biol. 9(9), e1001152 (2011).
[Crossref] [PubMed]

Patwary, N.

N. Patwary, A. Doblas, and C. Preza, “Image restoration approach to address reduced modulation contrast in structured illumination microscopy,” Biomed. Opt. Express 9(4), 1630–1647 (2018).
[Crossref] [PubMed]

H. Shabani, N. Patwary, A. Doblas, G. Saavedra, and C. Preza, “Comparison of two structured illumination techniques based on different 3D illumination patterns,” Proc. SPIE 10070, 1007013 (2017).
[Crossref]

Piolot, T.

J. Boulanger, N. Pustelnik, L. Condat, L. Sengmanivong, and T. Piolot, “Nonsmooth convex optimization for structured illumination microscopy image reconstruction,” Inverse Probl. 34(9), 095004 (2018).
[Crossref] [PubMed]

Preza, C.

H. Shabani, A. Doblas, G. Saavedra, and C. Preza, “Preprocessing method to correct illumination pattern in sinusoidal-based structured illumination microscopy,” Proc. SPIE 10499, 104991Z (2018).
[Crossref]

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, 1049903 (2018).
[Crossref]

H. Shabani, A. Doblas, G. Saavedra, E. Sanchez-Ortiga, and C. Preza, “Improvement of two-dimensional structured illumination microscopy with an incoherent illumination pattern of tunable frequency,” Appl. Opt. 57(7), B92–B101 (2018).
[Crossref] [PubMed]

N. Patwary, A. Doblas, and C. Preza, “Image restoration approach to address reduced modulation contrast in structured illumination microscopy,” Biomed. Opt. Express 9(4), 1630–1647 (2018).
[Crossref] [PubMed]

H. Shabani, N. Patwary, A. Doblas, G. Saavedra, and C. Preza, “Comparison of two structured illumination techniques based on different 3D illumination patterns,” Proc. SPIE 10070, 1007013 (2017).
[Crossref]

A. Doblas and C. Preza, “Incoherent-based tunable frequency structured illumination microscopy,” in IS Conference of 2017 OSA Technical Digest Series (Optical Society of America) (2017), paper ITh4.

Pustelnik, N.

J. Boulanger, N. Pustelnik, L. Condat, L. Sengmanivong, and T. Piolot, “Nonsmooth convex optimization for structured illumination microscopy image reconstruction,” Inverse Probl. 34(9), 095004 (2018).
[Crossref] [PubMed]

Rego, E. H.

R. Fiolka, L. Shao, E. H. Rego, M. W. Davidson, and M. G. L. Gustafsson, “Time-lapse two-color 3D imaging of live cells with doubled resolution using structured illumination,” Proc. Natl. Acad. Sci. U.S.A. 109(14), 5311–5315 (2012).
[Crossref] [PubMed]

Reinhart, M.

V. O. Chagin, C. S. Casas-Delucchi, M. Reinhart, L. Schermelleh, Y. Markaki, A. Maiser, J. J. Bolius, A. Bensimon, M. Fillies, P. Domaing, Y. M. Rozanov, H. Leonhardt, and M. C. Cardoso, “4D Visualization of replication foci in mammalian cells corresponding to individual replicons,” Nat. Commun. 7, 11231 (2016).
[Crossref] [PubMed]

Roberts, I. M.

J. Tilsner, O. Linnik, M. Louveaux, I. M. Roberts, S. N. Chapman, and K. J. Oparka, “Replication and trafficking of a plant virus are coupled at the entrances of plasmodesmata,” J. Cell Biol. 201(7), 981–995 (2013).
[Crossref] [PubMed]

Rowlett, V. W.

V. W. Rowlett and W. Margolin, “3D-SIM super-resolution of FtsZ and its membrane tethers in Escherichia coli cells,” Biophys. J. 107(8), L17–L20 (2014).
[Crossref] [PubMed]

Rozanov, Y. M.

V. O. Chagin, C. S. Casas-Delucchi, M. Reinhart, L. Schermelleh, Y. Markaki, A. Maiser, J. J. Bolius, A. Bensimon, M. Fillies, P. Domaing, Y. M. Rozanov, H. Leonhardt, and M. C. Cardoso, “4D Visualization of replication foci in mammalian cells corresponding to individual replicons,” Nat. Commun. 7, 11231 (2016).
[Crossref] [PubMed]

Saavedra, G.

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, 1049903 (2018).
[Crossref]

H. Shabani, A. Doblas, G. Saavedra, and C. Preza, “Preprocessing method to correct illumination pattern in sinusoidal-based structured illumination microscopy,” Proc. SPIE 10499, 104991Z (2018).
[Crossref]

H. Shabani, A. Doblas, G. Saavedra, E. Sanchez-Ortiga, and C. Preza, “Improvement of two-dimensional structured illumination microscopy with an incoherent illumination pattern of tunable frequency,” Appl. Opt. 57(7), B92–B101 (2018).
[Crossref] [PubMed]

H. Shabani, N. Patwary, A. Doblas, G. Saavedra, and C. Preza, “Comparison of two structured illumination techniques based on different 3D illumination patterns,” Proc. SPIE 10070, 1007013 (2017).
[Crossref]

A. Doblas, G. Saavedra, M. Martinez-Corral, J. C. Barreiro, E. Sanchez-Ortiga, and A. Llavador, “Axial resonance of periodic patterns by using a Fresnel biprism,” J. Opt. Soc. Am. A 30(1), 140–148 (2013).
[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]

M. Martínez-Corral and G. Saavedra, “The Resolution Challenge in 3D Optical Microscopy,” Prog. Opt. 53, 1–67 (2009).
[Crossref]

Sanchez-Ortiga, E.

Sánchez-Ortiga, E.

Schermelleh, L.

V. O. Chagin, C. S. Casas-Delucchi, M. Reinhart, L. Schermelleh, Y. Markaki, A. Maiser, J. J. Bolius, A. Bensimon, M. Fillies, P. Domaing, Y. M. Rozanov, H. Leonhardt, and M. C. Cardoso, “4D Visualization of replication foci in mammalian cells corresponding to individual replicons,” Nat. Commun. 7, 11231 (2016).
[Crossref] [PubMed]

C. Lesterlin, G. Ball, L. Schermelleh, and D. J. Sherratt, “RecA bundles mediate homology pairing between distant sisters during DNA break repair,” Nature 506(7487), 249–253 (2014).
[Crossref] [PubMed]

K. F. Sonnen, L. Schermelleh, H. Leonhardt, and E. A. Nigg, “3D-structured illumination microscopy provides novel insight into architecture of human centrosomes,” Biol. Open 1(10), 965–976 (2012).
[Crossref] [PubMed]

Sedat, J. W.

M. G. L. Gustafsson, L. Shao, P. M. Carlton, C. J. R. 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]

Sengmanivong, L.

J. Boulanger, N. Pustelnik, L. Condat, L. Sengmanivong, and T. Piolot, “Nonsmooth convex optimization for structured illumination microscopy image reconstruction,” Inverse Probl. 34(9), 095004 (2018).
[Crossref] [PubMed]

Sepulveda, E.

F. Orieux, V. Loriette, J. C. Olivo-Marin, E. Sepulveda, and A. Fragola, “Fast myopic 2D-SIM super resolution microscopy with joint modulation pattern estimation,” Inverse Probl. 33(12), 1–22 (2017).
[Crossref]

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]

Shabani, H.

H. Shabani, A. Doblas, G. Saavedra, and C. Preza, “Preprocessing method to correct illumination pattern in sinusoidal-based structured illumination microscopy,” Proc. SPIE 10499, 104991Z (2018).
[Crossref]

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, 1049903 (2018).
[Crossref]

H. Shabani, A. Doblas, G. Saavedra, E. Sanchez-Ortiga, and C. Preza, “Improvement of two-dimensional structured illumination microscopy with an incoherent illumination pattern of tunable frequency,” Appl. Opt. 57(7), B92–B101 (2018).
[Crossref] [PubMed]

H. Shabani, N. Patwary, A. Doblas, G. Saavedra, and C. Preza, “Comparison of two structured illumination techniques based on different 3D illumination patterns,” Proc. SPIE 10070, 1007013 (2017).
[Crossref]

Shan, C.

A. Lal, C. Shan, K. Zhao, W. Liu, X. Huang, W. Zong, L. Chen, and P. Xi, “A Frequency Domain SIM Reconstruction Algorithm Using Reduced Number of Images,” IEEE Trans. Image Process. 27(9), 4555–4570 (2018).
[Crossref] [PubMed]

Shao, L.

R. Fiolka, L. Shao, E. H. Rego, M. W. Davidson, and M. G. L. Gustafsson, “Time-lapse two-color 3D imaging of live cells with doubled resolution using structured illumination,” Proc. Natl. Acad. Sci. U.S.A. 109(14), 5311–5315 (2012).
[Crossref] [PubMed]

M. G. L. Gustafsson, L. Shao, P. M. Carlton, C. J. R. 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]

Sherratt, D. J.

C. Lesterlin, G. Ball, L. Schermelleh, and D. J. Sherratt, “RecA bundles mediate homology pairing between distant sisters during DNA break repair,” Nature 506(7487), 249–253 (2014).
[Crossref] [PubMed]

Shroff, S. A.

Smedh, M.

C. Karras, M. Smedh, R. Förster, H. Deschout, J. Fernandez-Rodriguez, and R. Heintzmann, “Successful optimization of reconstruction parameters in structured illumination microscopy - a practical guide,” bioRxiv 402115, 1–13 (2018).

Smedsrød, B.

V. C. Cogger, G. P. McNerney, T. Nyunt, L. D. DeLeve, P. McCourt, B. Smedsrød, D. G. Le Couteur, and T. R. Huser, “Three-dimensional structured illumination microscopy of liver sinusoidal endothelial cell fenestrations,” J. Struct. Biol. 171(3), 382–388 (2010).
[Crossref] [PubMed]

Sonnen, K. F.

K. F. Sonnen, L. Schermelleh, H. Leonhardt, and E. A. Nigg, “3D-structured illumination microscopy provides novel insight into architecture of human centrosomes,” Biol. Open 1(10), 965–976 (2012).
[Crossref] [PubMed]

Suo, J.

Tilsner, J.

J. Tilsner, O. Linnik, M. Louveaux, I. M. Roberts, S. N. Chapman, and K. J. Oparka, “Replication and trafficking of a plant virus are coupled at the entrances of plasmodesmata,” J. Cell Biol. 201(7), 981–995 (2013).
[Crossref] [PubMed]

Vermeulen, P.

P. Vermeulen, H. Zhan, F. Orieux, J. C. Olivo-Marin, Z. Lenkei, V. Loriette, and A. Fragola, “Out-of-focus background subtraction for fast structured illumination super-resolution microscopy of optically thick samples,” J. Microsc. 259(3), 257–268 (2015).
[Crossref] [PubMed]

Vicidomini, G.

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

Wang, C. J. R.

C. J. R. Wang, P. M. Carlton, I. N. Golubovskaya, and W. Z. Cande, “Interlock formation and coiling of meiotic chromosome axes during synapsis,” Genetics 183(3), 905–915 (2009).
[Crossref] [PubMed]

M. G. L. Gustafsson, L. Shao, P. M. Carlton, C. J. R. 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]

Wicker, K.

L. M. Hirvonen, K. Wicker, O. Mandula, and R. Heintzmann, “Structured illumination microscopy of a living cell,” Eur. Biophys. J. 38(6), 807–812 (2009).
[Crossref] [PubMed]

Williams, D. R.

Wilson, T.

Winoto, L.

P. Kner, B. B. Chhun, E. R. Griffis, L. Winoto, and M. G. L. Gustafsson, “Super-resolution video microscopy of live cells by structured illumination,” Nat. Methods 6(5), 339–342 (2009).
[Crossref] [PubMed]

Xi, P.

A. Lal, C. Shan, K. Zhao, W. Liu, X. Huang, W. Zong, L. Chen, and P. Xi, “A Frequency Domain SIM Reconstruction Algorithm Using Reduced Number of Images,” IEEE Trans. Image Process. 27(9), 4555–4570 (2018).
[Crossref] [PubMed]

Zhan, H.

P. Vermeulen, H. Zhan, F. Orieux, J. C. Olivo-Marin, Z. Lenkei, V. Loriette, and A. Fragola, “Out-of-focus background subtraction for fast structured illumination super-resolution microscopy of optically thick samples,” J. Microsc. 259(3), 257–268 (2015).
[Crossref] [PubMed]

Zhao, K.

A. Lal, C. Shan, K. Zhao, W. Liu, X. Huang, W. Zong, L. Chen, and P. Xi, “A Frequency Domain SIM Reconstruction Algorithm Using Reduced Number of Images,” IEEE Trans. Image Process. 27(9), 4555–4570 (2018).
[Crossref] [PubMed]

Zheng, G.

Zong, W.

A. Lal, C. Shan, K. Zhao, W. Liu, X. Huang, W. Zong, L. Chen, and P. Xi, “A Frequency Domain SIM Reconstruction Algorithm Using Reduced Number of Images,” IEEE Trans. Image Process. 27(9), 4555–4570 (2018).
[Crossref] [PubMed]

Appl. Opt. (1)

Biol. Open (1)

K. F. Sonnen, L. Schermelleh, H. Leonhardt, and E. A. Nigg, “3D-structured illumination microscopy provides novel insight into architecture of human centrosomes,” Biol. Open 1(10), 965–976 (2012).
[Crossref] [PubMed]

Biomed. Opt. Express (2)

Biophys. J. (2)

M. G. L. Gustafsson, L. Shao, P. M. Carlton, C. J. R. 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]

V. W. Rowlett and W. Margolin, “3D-SIM super-resolution of FtsZ and its membrane tethers in Escherichia coli cells,” Biophys. J. 107(8), L17–L20 (2014).
[Crossref] [PubMed]

bioRxiv (1)

C. Karras, M. Smedh, R. Förster, H. Deschout, J. Fernandez-Rodriguez, and R. Heintzmann, “Successful optimization of reconstruction parameters in structured illumination microscopy - a practical guide,” bioRxiv 402115, 1–13 (2018).

Eur. Biophys. J. (1)

L. M. Hirvonen, K. Wicker, O. Mandula, and R. Heintzmann, “Structured illumination microscopy of a living cell,” Eur. Biophys. J. 38(6), 807–812 (2009).
[Crossref] [PubMed]

Genetics (1)

C. J. R. Wang, P. M. Carlton, I. N. Golubovskaya, and W. Z. Cande, “Interlock formation and coiling of meiotic chromosome axes during synapsis,” Genetics 183(3), 905–915 (2009).
[Crossref] [PubMed]

IEEE Trans. Image Process. (2)

A. Lal, C. Shan, K. Zhao, W. Liu, X. Huang, W. Zong, L. Chen, and P. Xi, “A Frequency Domain SIM Reconstruction Algorithm Using Reduced Number of Images,” IEEE Trans. Image Process. 27(9), 4555–4570 (2018).
[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]

Inverse Probl. (3)

J. Boulanger, N. Pustelnik, L. Condat, L. Sengmanivong, and T. Piolot, “Nonsmooth convex optimization for structured illumination microscopy image reconstruction,” Inverse Probl. 34(9), 095004 (2018).
[Crossref] [PubMed]

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

F. Orieux, V. Loriette, J. C. Olivo-Marin, E. Sepulveda, and A. Fragola, “Fast myopic 2D-SIM super resolution microscopy with joint modulation pattern estimation,” Inverse Probl. 33(12), 1–22 (2017).
[Crossref]

J. Cell Biol. (1)

J. Tilsner, O. Linnik, M. Louveaux, I. M. Roberts, S. N. Chapman, and K. J. Oparka, “Replication and trafficking of a plant virus are coupled at the entrances of plasmodesmata,” J. Cell Biol. 201(7), 981–995 (2013).
[Crossref] [PubMed]

J. Microsc. (1)

P. Vermeulen, H. Zhan, F. Orieux, J. C. Olivo-Marin, Z. Lenkei, V. Loriette, and A. Fragola, “Out-of-focus background subtraction for fast structured illumination super-resolution microscopy of optically thick samples,” J. Microsc. 259(3), 257–268 (2015).
[Crossref] [PubMed]

J. Opt. Soc. Am. A (2)

J. Struct. Biol. (1)

V. C. Cogger, G. P. McNerney, T. Nyunt, L. D. DeLeve, P. McCourt, B. Smedsrød, D. G. Le Couteur, and T. R. Huser, “Three-dimensional structured illumination microscopy of liver sinusoidal endothelial cell fenestrations,” J. Struct. Biol. 171(3), 382–388 (2010).
[Crossref] [PubMed]

Micron (1)

R. Heintzmann, “Saturated patterned excitation microscopy with two-dimensional excitation patterns,” Micron 34(6-7), 283–291 (2003).
[Crossref] [PubMed]

Nat. Commun. (1)

V. O. Chagin, C. S. Casas-Delucchi, M. Reinhart, L. Schermelleh, Y. Markaki, A. Maiser, J. J. Bolius, A. Bensimon, M. Fillies, P. Domaing, Y. M. Rozanov, H. Leonhardt, and M. C. Cardoso, “4D Visualization of replication foci in mammalian cells corresponding to individual replicons,” Nat. Commun. 7, 11231 (2016).
[Crossref] [PubMed]

Nat. Methods (1)

P. Kner, B. B. Chhun, E. R. Griffis, L. Winoto, and M. G. L. Gustafsson, “Super-resolution video microscopy of live cells by structured illumination,” Nat. Methods 6(5), 339–342 (2009).
[Crossref] [PubMed]

Nature (1)

C. Lesterlin, G. Ball, L. Schermelleh, and D. J. Sherratt, “RecA bundles mediate homology pairing between distant sisters during DNA break repair,” Nature 506(7487), 249–253 (2014).
[Crossref] [PubMed]

Opt. Express (1)

Opt. Lett. (2)

PLoS Biol. (1)

A. C. N. Brown, S. Oddos, I. M. Dobbie, J. M. Alakoskela, R. M. Parton, P. Eissmann, M. A. A. Neil, C. Dunsby, P. M. W. French, I. Davis, and D. M. Davis, “Remodelling of cortical actin where lytic granules dock at Natural Killer cell immune synapses revealed by super-resolution microscopy,” PLoS Biol. 9(9), e1001152 (2011).
[Crossref] [PubMed]

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

R. Fiolka, L. Shao, E. H. Rego, M. W. Davidson, and M. G. L. Gustafsson, “Time-lapse two-color 3D imaging of live cells with doubled resolution using structured illumination,” Proc. Natl. Acad. Sci. U.S.A. 109(14), 5311–5315 (2012).
[Crossref] [PubMed]

Proc. SPIE (3)

H. Shabani, A. Doblas, G. Saavedra, and C. Preza, “Preprocessing method to correct illumination pattern in sinusoidal-based structured illumination microscopy,” Proc. SPIE 10499, 104991Z (2018).
[Crossref]

H. Shabani, N. Patwary, A. Doblas, G. Saavedra, and C. Preza, “Comparison of two structured illumination techniques based on different 3D illumination patterns,” Proc. SPIE 10070, 1007013 (2017).
[Crossref]

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, 1049903 (2018).
[Crossref]

Prog. Opt. (1)

M. Martínez-Corral and G. Saavedra, “The Resolution Challenge in 3D Optical Microscopy,” Prog. Opt. 53, 1–67 (2009).
[Crossref]

Other (4)

E. Hecht, Optics (Pearson, 2016).

L. H. Schaefer and D. Schuster, “Method and device for reconstructing images,” U.S. Patent No. 8,041,142 (2011).

J. W. Goodman, Introduction to Fourier Optics (McGraw-Hill, 1996).

A. Doblas and C. Preza, “Incoherent-based tunable frequency structured illumination microscopy,” in IS Conference of 2017 OSA Technical Digest Series (Optical Society of America) (2017), paper ITh4.

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Figures (11)

Fig. 1
Fig. 1 Tunable-frequency 3D-SIM system based on a Fresnel biprism illuminated by a set of equidistant incoherent slits (N). (a) Illustration of the system. (b) 3D SI pattern with periodic visibility variation [Eq. (2)] created by the system in the sample space (zobj). High-contrast fringes are located at a set of discrete axial planes. The 3D pattern exhibits a periodic axial contrast and its characteristics are controlled by three system parameters: N, x0 and η. (c) Illustration demonstrating that improper imaging of the slits in the back focal-plane of the objective lens can lead to clipping of the slits and consequently, to a reduction in the contrast of the fringes. zill refers to axial coordinate located after L1 lens
Fig. 2
Fig. 2 Experimental and numerical xz-section images of the 3D SI pattern generated using a different number of slits N. The lateral modulation frequency (um) for both numerical and experimental results is ~0.8 uc for uc = 1.9 µm−1. The axial modulation frequency of the 3D SI pattern is wm = 0.0156 um.
Fig. 3
Fig. 3 Numerical and experimental xz-section images of the 3D SI pattern generated using a different lateral modulation frequency (um). The axial modulation frequency of the 3D SI pattern is wm = 0.0156 um. The cutoff frequency of the system is uc = 1.9 µm−1. The number of slits used was N = 9. For the experimental data we report the mean and the standard deviation of the measured axial extent of the fringes computed from 12 axial profiles through the maxima of four different resonant planes.
Fig. 4
Fig. 4 Evaluation of the experimental 3D-SIM system (N = 9 slits) through comparison of experimental and numerical [Eq. (3)] 3D forward images of a fluorescent uniform layer (Case 1) and a 6-µm spherical shell (Case 2). Case 1: xy and xz views of the numerical (a) and experimental (b) 3D image; normalized lateral (c) and axial (d) intensity profile through the center (marked by the red arrows) of the xy and xz sections in (a) and (b), respectively. The experimental lateral profile was obtained from the average of 6 central rows while the axial profile was obtained from the average of 16 axial profiles through the maxima. Intensity profiles were obtained after background subtraction followed by normalization. Case 2: xy and xz views of the numerical (e) and experimental (f) 3D image; lateral (g, h) and axial (i) intensity profiles obtained from the center (marked by the red arrows) of the xy and xz sections in (e) and (f), respectively. The cutoff frequency uc = 1.9 µm−1. Lateral and axial modulation frequencies: um = 0.85 µm−1 and wm = 0.0135 µm−1 for Case 1; and um = 1.33 µm−1 and wm = 0.021 µm−1 for Case 2.
Fig. 5
Fig. 5 Meridional section (uw) of the 3D synthetic MTF (absolute value of the synthetic OTF) for: (a) our 3D-SIM system with N = 9 slits; and (b) the conventional three-wave 3D-SIM system [1]. In both systems, we have considered the maximum lateral SR capability (um = 0.8uc). Our synthetic OTF is composed of the 3 terms in Eq. (7). The pink and white dashed lines mark the compact support of the widefield and the 3D-SIM synthetic OTFs, respectively. The pink arrows highlight the extension of the lateral and axial cut-off frequencies achieved in both 3D-SIM synthetic OTFs.
Fig. 6
Fig. 6 Qualitative and quantitative evaluation of the proposed 3D-SIM system performance using simulated data. Lateral view (top row), axial view (middle row) and zoomed view of the cropped square marked with a pink line in the top left image (bottom row) of the 3D: (a) true object; (b) reconstructed image from three-wave interference 3D SIM; (c) reconstructed image from our 3D-SIM system; (d) reconstructed 3D image with proposed 2D processing method. Lateral (e) and axial (f) views of normalized intensity profiles. For both 3D-SIM systems, the lateral modulation frequency was set at um = 0.8uc = 4.35 μm−1.
Fig. 7
Fig. 7 Achieved OS capability verified with experimental images of an axially-thin fluorescent layer: xz-sections of the raw (a and d) and restored SIM image (b and c) from the tunable 3D-SIM (um = 0.8uc) and the ApoTome-SIM (um = 0.14uc) systems. Because ApoTome processing does not consider the widefield component, which is equivalent to the D ^ 0 (·)component [Eq. (8)], we neglected this term when computing the restored image in the case of our system (b) for a fair comparison. In panels (a) and (d), the pink arrows indicate the axial extent of the SI pattern, quantified by the value shown on each image. The pink arrows in panels (b) and (c) quantify the FWHM of the integrated intensity, obtained by averaging the intensity values along its lateral coordinate for each restored image.
Fig. 8
Fig. 8 Achieved SR verified in experimental images of the fluorescent USAF target: (a) Reconstructed SIM image for um = 0.8uc and (b) Synthetic deconvolved widefield image. (c) and (d) Normalized intensity profiles through the center of the vertical elements 10-2 and 10-6, marked by the dashed rectangles in (a) and (b), from both images.
Fig. 9
Fig. 9 Experimental raw images of a titled fluorescent USAF target at three different axial positions (zi). Note that the fringes are visible only in the region of the FoV where the target is in-focus, marked by the pink double arrow in the zoomed versions of the areas marked by the yellow rectangles in the images shown on the left.
Fig. 10
Fig. 10 Experimental verification of simultaneous OS and SR achieved with our tunable 3D-SIM system by imaging a tilted fluorescent USAF target. xy-sections images obtained at three different axial locations of the target: (a) Synthetic raw widefield images; (b) Reconstructed SIM images from our systems using 2D processing (Sect. 2.4); (c) Reconstructed ApoTome-SIM images using the Zeiss ZEN.2 software. The corresponding magenta rectangles in (a) and (b) highlight the reduction of out-of-focus light achieved in the tunable 3D-SIM system image (b) compared to the conventional widefield image (a). The rectangles highlight different regions of the FoV in which in-focus information is not expected in each axial location of the tilted target. The yellow arrows indicate the lateral extent of the FoV reconstructed in the final image. The images in each case (a), (b) and (c) are displayed using a separate color scale. However, the group of three images in (a), (b), and (c), respectively, are displayed using a global minimum and maximum intensity mapped to the same color scale to show relative intensities in different axial planes. Lens: 20× /0.5 NA dry lens; Emission wavelength: 515 nm. Lateral modulation frequency: um = 0.8uc = 1.552 µm−1 for the tunable 3D-SIM system and um = 0.14uc = 0.27 µm−1 for the commercial ApoTome-SIM system.
Fig. 11
Fig. 11 Verification of the lateral SR capability in the experimental image of the tilted fluorescent USAF target: (a) zoomed version of the groups 10 and 11 in the reconstructed SIM image obtained at the axial location z2 in Fig. 10(b). (b) Normalized intensity profiles through the center of the vertical elements 10-4 and 10-5, marked by light blue and red dashed rectangles, along the horizontal direction.

Equations (8)

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

e( x ill , z ill ;η, x 0 ,N )1+V'( z ill ;η, x 0 ,N )cos[ 2π a(η) λ f L1 x ill ],
V'( z ill ;η, x 0 ,N )= sin( 2πNw ' m ( η, x 0 ) z ill ) Nsin( 2πw ' m ( η, x 0 ) z ill ) ,
g( x,z )=o( x,z ) 3 | h( x,z ) | 2 + { cos( 2π u m ( η )x+ϕ )×o( x,z ) } 3 { | h( x,z ) | 2 ×V( z;η, x 0 ,N ) },
V( z;η, x 0 ,N )= sin( 2πN w m ( η; x 0 )z ) Nsin( 2π w m ( η; x 0 )z ) ,
G( u,w )= D 0 (u,w)+ e iϕ 2 D +1 (u,w)+ e iϕ 2 D 1 (u,w),
D n (u,w)=O(un u m ,v,w) H n (u,w), n=0,±1,
H n (u,w)={ H(u,w) n=0 FT{ | h( x,z ) | 2 V( z;η, x 0 ,N ) } n=±1 .
D ^ n (u,w)= D n (u,w) H n * (u,w) n' | H n' (u+n' u m n u m ,v,w) | 2 + β 2 A(un u m ,v,w), n=0,±1

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