Abstract

We present an image-based autofocusing system applied in nonlinear microscopy and spectroscopy with a wide range of excitation wavelengths. The core of the developed autofocusing system consists of an adapted two-step procedure maximizing an image score with six different image scorings algorithms implemented to cover different types of focusing scenarios in automated regime for broad wavelength region. The developed approach is combined with an automated multi-axis alignment procedure. We demonstrate the key abilities of the autofocusing procedure on different types of structures: single nanoparticles, nanowires and complex 3D nanostructures. Based on these experiments, we determine the optimal autofocusing algorithms for different types of structures and applications.

© 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

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References

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2019 (3)

L. Abdeladim, K. S. Matho, S. Clavreul, P. Mahou, J. M. Sintes, X. Solinas, I. Arganda-Carreras, S. G. Turney, J. W. Lichtman, A. Chessel, A. P. Bemelmans, K. Loulier, W. Supatto, J. Livet, and E. Beaurepaire, “Multicolor multiscale brain imaging with chromatic multiphoton serial microscopy,” Nat. Commun. 10(1), 1–14 (2019).
[PubMed]

F. Timpu, J. Sendra, C. Renaut, L. Lang, M. Timofeeva, M. T. Buscaglia, V. Buscaglia, and R. Grange, “Lithium Niobate Nanocubes as Linear and Nonlinear Ultraviolet Mie Resonators,” ACS Photonics 6(2), 545–552 (2019).
[Crossref]

C. Renaut, L. Lang, K. Frizyuk, M. Timofeeva, F. E. Komissarenko, I. S. Mukhin, D. Smirnova, F. Timpu, M. Petrov, Y. Kivshar, and R. Grange, “Reshaping the Second-Order Polar Response of Hybrid Metal-Dielectric Nanodimers,” Nano Lett. 19(2), 877–884 (2019).
[Crossref] [PubMed]

2018 (2)

R. Li, X. Wang, Y. Zhou, H. Zong, M. Chen, and M. Sun, “Advances in nonlinear optical microscopy for biophotonics,” J. Nanophotonics 12(03), 033007 (2018).
[Crossref]

A. Prylepa, C. Reitböck, M. Cobet, A. Jesacher, X. Jin, R. Adelung, M. Schatzl-Linder, G. Luckeneder, K. H. Stellnberger, T. Steck, J. Faderl, T. Stehrer, and D. Stifter, “Material characterisation with methods of nonlinear optics,” J. Phys. D Appl. Phys. 51(4), 043001 (2018).
[Crossref]

2017 (4)

K. Y. Yang, J. Butet, C. Yan, G. D. Bernasconi, and O. J. F. Martin, “Enhancement Mechanisms of the Second Harmonic Generation from Double Resonant Aluminum Nanostructures,” ACS Photonics 4(6), 1522–1530 (2017).
[Crossref]

K. R. Campbell and P. J. Campagnola, “Wavelength-Dependent Second Harmonic Generation Circular Dichroism for Differentiation of Col I and Col III Isoforms in Stromal Models of Ovarian Cancer Based on Intrinsic Chirality Differences,” J. Phys. Chem. B 121(8), 1749–1757 (2017).
[Crossref] [PubMed]

S. S. Kruk, R. Camacho-Morales, L. Xu, M. Rahmani, D. A. Smirnova, L. Wang, H. H. Tan, C. Jagadish, D. N. Neshev, and Y. S. Kivshar, “Nonlinear optical magnetism revealed by second-harmonic generation in nanoantennas,” Nano Lett. 17(6), 3914–3918 (2017).
[Crossref] [PubMed]

Y. Zhang, H. Wang, Y. Wu, M. Tamamitsu, and A. Ozcan, “Edge sparsity criterion for robust holographic autofocusing,” Opt. Lett. 42(19), 3824–3827 (2017).
[Crossref] [PubMed]

2016 (4)

L. Mancini, D. Hernández-Maldonado, W. Lefebvre, J. Houard, I. Blum, F. Vurpillot, J. Eymery, C. Durand, M. Tchernycheva, and L. Rigutti, “Multi-microscopy study of the influence of stacking faults and three-dimensional In distribution on the optical properties of m-plane InGaN quantum wells grown on microwire sidewalls,” Appl. Phys. Lett. 108(4), 042102 (2016).
[Crossref]

M. Timofeeva, A. Bouravleuv, G. Cirlin, I. Shtrom, I. Soshnikov, M. Reig Escalé, A. Sergeyev, and R. Grange, “Polar Second-Harmonic Imaging to Resolve Pure and Mixed Crystal Phases along GaAs Nanowires,” Nano Lett. 16(10), 6290–6297 (2016).
[Crossref] [PubMed]

J. Sun, Y. J. Gu, D. Y. Lei, S. P. Lau, W. T. Wong, K. Y. Wong, and H. L. W. Chan, “Mechanistic Understanding of Excitation-Correlated Nonlinear Optical Properties in MoS2 Nanosheets and Nanodots: The Role of Exciton Resonance,” ACS Photonics 3(12), 2434–2444 (2016).
[Crossref]

M. Timofeeva, A. Bouravleuv, G. Cirlin, I. Shtrom, I. Soshnikov, M. Reig Escalé, A. Sergeyev, and R. Grange, “Polar Second-Harmonic Imaging to Resolve Pure and Mixed Crystal Phases along GaAs Nanowires,” Nano Lett. 16(10), 6290–6297 (2016).
[Crossref] [PubMed]

2013 (1)

L. Huang and J.-X. Cheng, “Nonlinear Optical Microscopy of Single Nanostructures,” Annu. Rev. Mater. Res. 43(1), 213–236 (2013).
[Crossref]

2012 (1)

R. Grange, G. Brönstrup, M. Kiometzis, A. Sergeyev, J. Richter, C. Leiterer, W. Fritzsche, C. Gutsche, A. Lysov, W. Prost, F. J. Tegude, T. Pertsch, A. Tünnermann, and S. Christiansen, “Far-field imaging for direct visualization of light interferences in GaAs nanowires,” Nano Lett. 12(10), 5412–5417 (2012).
[Crossref] [PubMed]

2011 (2)

R. Koester, J. S. Hwang, D. Salomon, X. Chen, C. Bougerol, J. P. Barnes, D. S. Dang, L. Rigutti, A. de Luna Bugallo, G. Jacopin, M. Tchernycheva, C. Durand, and J. Eymery, “M-Plane Core-Shell InGaN/GaN Multiple-Quantum-Wells on GaN Wires for Electroluminescent Devices,” Nano Lett. 11(11), 4839–4845 (2011).
[Crossref] [PubMed]

S. Brasselet, “Polarization-resolved nonlinear microscopy: application to structural molecular and biological imaging,” Adv. Opt. Photonics 3(3), 205–271 (2011).
[Crossref]

2008 (1)

S. Palomba and L. Novotny, “Nonlinear excitation of surface plasmon polaritons by four-wave mixing,” Phys. Rev. Lett. 101(5), 056802 (2008).
[Crossref] [PubMed]

2006 (1)

S. Kühn, U. Håkanson, L. Rogobete, and V. Sandoghdar, “Enhancement of single-molecule fluorescence using a gold nanoparticle as an optical nanoantenna,” Phys. Rev. Lett. 97(1), 017402 (2006).
[Crossref] [PubMed]

2005 (1)

F. Helmchen and W. Denk, “Deep tissue two-photon microscopy,” Nat. Methods 2(12), 932–940 (2005).
[Crossref] [PubMed]

2004 (2)

D. Krause, C. W. Teplin, and C. T. Rogers, “Optical surface second harmonic measurements of Isotropic thin-film metals: Gold, silver, copper, aluminum, and tantalum,” J. Appl. Phys. 96(7), 3626–3634 (2004).
[Crossref]

Y. Sun, S. Duthaler, and B. J. Nelson, “Autofocusing in computer microscopy: selecting the optimal focus algorithm,” Microsc. Res. Tech. 65(3), 139–149 (2004).
[Crossref] [PubMed]

2003 (2)

P. J. Campagnola and L. M. Loew, “Second-harmonic imaging microscopy for visualizing biomolecular arrays in cells, tissues and organisms,” Nat. Biotechnol. 21(11), 1356–1360 (2003).
[Crossref] [PubMed]

W. R. Zipfel, R. M. Williams, and W. W. Webb, “Nonlinear magic: Multiphoton microscopy in the biosciences,” Nat. Biotechnol. 21(11), 1369–1377 (2003).
[Crossref] [PubMed]

2000 (1)

K. König, “Multiphoton microscopy in Life Sciences,” J. Microsc. 200(2), 83–104 (2000).
[Crossref] [PubMed]

1998 (1)

1993 (1)

T. Yeo, S. Ong, Jayasooriah, and R. Sinniah, “Autofocusing for tissue microscopy,” Image Vis. Comput. 11(10), 629–639 (1993).
[Crossref]

1991 (2)

L. Firestone, K. Cook, K. Culp, N. Talsania, and K. Preston, “Comparison of autofocus methods for automated microscopy,” Cytometry 12(3), 195–206 (1991).
[Crossref] [PubMed]

R. A. Myers, N. Mukherjee, and S. R. J. Brueck, “Large second-order nonlinearity in poled fused silica,” Opt. Lett. 16(22), 1732–1734 (1991).
[Crossref] [PubMed]

1987 (1)

D. Vollath, “Automatic focusing by correlative methods,” J. Microsc. 147(3), 279–288 (1987).
[Crossref]

1985 (1)

F. C. A. Groen, I. T. Young, and G. Ligthart, “A comparison of different focus functions for use in autofocus algorithms,” Cytometry 6(2), 81–91 (1985).
[Crossref] [PubMed]

1981 (1)

D. Fröhlich, “Aspects of Nonlinear Spectroscopy,” Festkörperprobleme 21, 363–381 (1981).
[Crossref]

1976 (1)

J. F. Brenner, B. S. Dew, J. B. Horton, T. King, P. W. Neurath, and W. D. Selles, “An Automated Microscope for Cytologic Research,” J. Histochem. Cytochem. 24(1), 100–111 (1976).
[Crossref] [PubMed]

Abdeladim, L.

L. Abdeladim, K. S. Matho, S. Clavreul, P. Mahou, J. M. Sintes, X. Solinas, I. Arganda-Carreras, S. G. Turney, J. W. Lichtman, A. Chessel, A. P. Bemelmans, K. Loulier, W. Supatto, J. Livet, and E. Beaurepaire, “Multicolor multiscale brain imaging with chromatic multiphoton serial microscopy,” Nat. Commun. 10(1), 1–14 (2019).
[PubMed]

Adelung, R.

A. Prylepa, C. Reitböck, M. Cobet, A. Jesacher, X. Jin, R. Adelung, M. Schatzl-Linder, G. Luckeneder, K. H. Stellnberger, T. Steck, J. Faderl, T. Stehrer, and D. Stifter, “Material characterisation with methods of nonlinear optics,” J. Phys. D Appl. Phys. 51(4), 043001 (2018).
[Crossref]

Arganda-Carreras, I.

L. Abdeladim, K. S. Matho, S. Clavreul, P. Mahou, J. M. Sintes, X. Solinas, I. Arganda-Carreras, S. G. Turney, J. W. Lichtman, A. Chessel, A. P. Bemelmans, K. Loulier, W. Supatto, J. Livet, and E. Beaurepaire, “Multicolor multiscale brain imaging with chromatic multiphoton serial microscopy,” Nat. Commun. 10(1), 1–14 (2019).
[PubMed]

Barnes, J. P.

R. Koester, J. S. Hwang, D. Salomon, X. Chen, C. Bougerol, J. P. Barnes, D. S. Dang, L. Rigutti, A. de Luna Bugallo, G. Jacopin, M. Tchernycheva, C. Durand, and J. Eymery, “M-Plane Core-Shell InGaN/GaN Multiple-Quantum-Wells on GaN Wires for Electroluminescent Devices,” Nano Lett. 11(11), 4839–4845 (2011).
[Crossref] [PubMed]

Beaurepaire, E.

L. Abdeladim, K. S. Matho, S. Clavreul, P. Mahou, J. M. Sintes, X. Solinas, I. Arganda-Carreras, S. G. Turney, J. W. Lichtman, A. Chessel, A. P. Bemelmans, K. Loulier, W. Supatto, J. Livet, and E. Beaurepaire, “Multicolor multiscale brain imaging with chromatic multiphoton serial microscopy,” Nat. Commun. 10(1), 1–14 (2019).
[PubMed]

Bemelmans, A. P.

L. Abdeladim, K. S. Matho, S. Clavreul, P. Mahou, J. M. Sintes, X. Solinas, I. Arganda-Carreras, S. G. Turney, J. W. Lichtman, A. Chessel, A. P. Bemelmans, K. Loulier, W. Supatto, J. Livet, and E. Beaurepaire, “Multicolor multiscale brain imaging with chromatic multiphoton serial microscopy,” Nat. Commun. 10(1), 1–14 (2019).
[PubMed]

Bernasconi, G. D.

K. Y. Yang, J. Butet, C. Yan, G. D. Bernasconi, and O. J. F. Martin, “Enhancement Mechanisms of the Second Harmonic Generation from Double Resonant Aluminum Nanostructures,” ACS Photonics 4(6), 1522–1530 (2017).
[Crossref]

Blum, I.

L. Mancini, D. Hernández-Maldonado, W. Lefebvre, J. Houard, I. Blum, F. Vurpillot, J. Eymery, C. Durand, M. Tchernycheva, and L. Rigutti, “Multi-microscopy study of the influence of stacking faults and three-dimensional In distribution on the optical properties of m-plane InGaN quantum wells grown on microwire sidewalls,” Appl. Phys. Lett. 108(4), 042102 (2016).
[Crossref]

Bougerol, C.

R. Koester, J. S. Hwang, D. Salomon, X. Chen, C. Bougerol, J. P. Barnes, D. S. Dang, L. Rigutti, A. de Luna Bugallo, G. Jacopin, M. Tchernycheva, C. Durand, and J. Eymery, “M-Plane Core-Shell InGaN/GaN Multiple-Quantum-Wells on GaN Wires for Electroluminescent Devices,” Nano Lett. 11(11), 4839–4845 (2011).
[Crossref] [PubMed]

Bouravleuv, A.

M. Timofeeva, A. Bouravleuv, G. Cirlin, I. Shtrom, I. Soshnikov, M. Reig Escalé, A. Sergeyev, and R. Grange, “Polar Second-Harmonic Imaging to Resolve Pure and Mixed Crystal Phases along GaAs Nanowires,” Nano Lett. 16(10), 6290–6297 (2016).
[Crossref] [PubMed]

M. Timofeeva, A. Bouravleuv, G. Cirlin, I. Shtrom, I. Soshnikov, M. Reig Escalé, A. Sergeyev, and R. Grange, “Polar Second-Harmonic Imaging to Resolve Pure and Mixed Crystal Phases along GaAs Nanowires,” Nano Lett. 16(10), 6290–6297 (2016).
[Crossref] [PubMed]

Brakenhoff, G.

Brasselet, S.

S. Brasselet, “Polarization-resolved nonlinear microscopy: application to structural molecular and biological imaging,” Adv. Opt. Photonics 3(3), 205–271 (2011).
[Crossref]

Brenner, J. F.

J. F. Brenner, B. S. Dew, J. B. Horton, T. King, P. W. Neurath, and W. D. Selles, “An Automated Microscope for Cytologic Research,” J. Histochem. Cytochem. 24(1), 100–111 (1976).
[Crossref] [PubMed]

Brönstrup, G.

R. Grange, G. Brönstrup, M. Kiometzis, A. Sergeyev, J. Richter, C. Leiterer, W. Fritzsche, C. Gutsche, A. Lysov, W. Prost, F. J. Tegude, T. Pertsch, A. Tünnermann, and S. Christiansen, “Far-field imaging for direct visualization of light interferences in GaAs nanowires,” Nano Lett. 12(10), 5412–5417 (2012).
[Crossref] [PubMed]

Brueck, S. R. J.

Buscaglia, M. T.

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L. Abdeladim, K. S. Matho, S. Clavreul, P. Mahou, J. M. Sintes, X. Solinas, I. Arganda-Carreras, S. G. Turney, J. W. Lichtman, A. Chessel, A. P. Bemelmans, K. Loulier, W. Supatto, J. Livet, and E. Beaurepaire, “Multicolor multiscale brain imaging with chromatic multiphoton serial microscopy,” Nat. Commun. 10(1), 1–14 (2019).
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A. Prylepa, C. Reitböck, M. Cobet, A. Jesacher, X. Jin, R. Adelung, M. Schatzl-Linder, G. Luckeneder, K. H. Stellnberger, T. Steck, J. Faderl, T. Stehrer, and D. Stifter, “Material characterisation with methods of nonlinear optics,” J. Phys. D Appl. Phys. 51(4), 043001 (2018).
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R. Grange, G. Brönstrup, M. Kiometzis, A. Sergeyev, J. Richter, C. Leiterer, W. Fritzsche, C. Gutsche, A. Lysov, W. Prost, F. J. Tegude, T. Pertsch, A. Tünnermann, and S. Christiansen, “Far-field imaging for direct visualization of light interferences in GaAs nanowires,” Nano Lett. 12(10), 5412–5417 (2012).
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L. Abdeladim, K. S. Matho, S. Clavreul, P. Mahou, J. M. Sintes, X. Solinas, I. Arganda-Carreras, S. G. Turney, J. W. Lichtman, A. Chessel, A. P. Bemelmans, K. Loulier, W. Supatto, J. Livet, and E. Beaurepaire, “Multicolor multiscale brain imaging with chromatic multiphoton serial microscopy,” Nat. Commun. 10(1), 1–14 (2019).
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K. Y. Yang, J. Butet, C. Yan, G. D. Bernasconi, and O. J. F. Martin, “Enhancement Mechanisms of the Second Harmonic Generation from Double Resonant Aluminum Nanostructures,” ACS Photonics 4(6), 1522–1530 (2017).
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Mukherjee, N.

Mukhin, I. S.

C. Renaut, L. Lang, K. Frizyuk, M. Timofeeva, F. E. Komissarenko, I. S. Mukhin, D. Smirnova, F. Timpu, M. Petrov, Y. Kivshar, and R. Grange, “Reshaping the Second-Order Polar Response of Hybrid Metal-Dielectric Nanodimers,” Nano Lett. 19(2), 877–884 (2019).
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Myers, R. A.

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S. S. Kruk, R. Camacho-Morales, L. Xu, M. Rahmani, D. A. Smirnova, L. Wang, H. H. Tan, C. Jagadish, D. N. Neshev, and Y. S. Kivshar, “Nonlinear optical magnetism revealed by second-harmonic generation in nanoantennas,” Nano Lett. 17(6), 3914–3918 (2017).
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J. F. Brenner, B. S. Dew, J. B. Horton, T. King, P. W. Neurath, and W. D. Selles, “An Automated Microscope for Cytologic Research,” J. Histochem. Cytochem. 24(1), 100–111 (1976).
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C. Renaut, L. Lang, K. Frizyuk, M. Timofeeva, F. E. Komissarenko, I. S. Mukhin, D. Smirnova, F. Timpu, M. Petrov, Y. Kivshar, and R. Grange, “Reshaping the Second-Order Polar Response of Hybrid Metal-Dielectric Nanodimers,” Nano Lett. 19(2), 877–884 (2019).
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L. Firestone, K. Cook, K. Culp, N. Talsania, and K. Preston, “Comparison of autofocus methods for automated microscopy,” Cytometry 12(3), 195–206 (1991).
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R. Grange, G. Brönstrup, M. Kiometzis, A. Sergeyev, J. Richter, C. Leiterer, W. Fritzsche, C. Gutsche, A. Lysov, W. Prost, F. J. Tegude, T. Pertsch, A. Tünnermann, and S. Christiansen, “Far-field imaging for direct visualization of light interferences in GaAs nanowires,” Nano Lett. 12(10), 5412–5417 (2012).
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A. Prylepa, C. Reitböck, M. Cobet, A. Jesacher, X. Jin, R. Adelung, M. Schatzl-Linder, G. Luckeneder, K. H. Stellnberger, T. Steck, J. Faderl, T. Stehrer, and D. Stifter, “Material characterisation with methods of nonlinear optics,” J. Phys. D Appl. Phys. 51(4), 043001 (2018).
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M. Timofeeva, A. Bouravleuv, G. Cirlin, I. Shtrom, I. Soshnikov, M. Reig Escalé, A. Sergeyev, and R. Grange, “Polar Second-Harmonic Imaging to Resolve Pure and Mixed Crystal Phases along GaAs Nanowires,” Nano Lett. 16(10), 6290–6297 (2016).
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A. Prylepa, C. Reitböck, M. Cobet, A. Jesacher, X. Jin, R. Adelung, M. Schatzl-Linder, G. Luckeneder, K. H. Stellnberger, T. Steck, J. Faderl, T. Stehrer, and D. Stifter, “Material characterisation with methods of nonlinear optics,” J. Phys. D Appl. Phys. 51(4), 043001 (2018).
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F. Timpu, J. Sendra, C. Renaut, L. Lang, M. Timofeeva, M. T. Buscaglia, V. Buscaglia, and R. Grange, “Lithium Niobate Nanocubes as Linear and Nonlinear Ultraviolet Mie Resonators,” ACS Photonics 6(2), 545–552 (2019).
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Richter, J.

R. Grange, G. Brönstrup, M. Kiometzis, A. Sergeyev, J. Richter, C. Leiterer, W. Fritzsche, C. Gutsche, A. Lysov, W. Prost, F. J. Tegude, T. Pertsch, A. Tünnermann, and S. Christiansen, “Far-field imaging for direct visualization of light interferences in GaAs nanowires,” Nano Lett. 12(10), 5412–5417 (2012).
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Rigutti, L.

L. Mancini, D. Hernández-Maldonado, W. Lefebvre, J. Houard, I. Blum, F. Vurpillot, J. Eymery, C. Durand, M. Tchernycheva, and L. Rigutti, “Multi-microscopy study of the influence of stacking faults and three-dimensional In distribution on the optical properties of m-plane InGaN quantum wells grown on microwire sidewalls,” Appl. Phys. Lett. 108(4), 042102 (2016).
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Rogers, C. T.

D. Krause, C. W. Teplin, and C. T. Rogers, “Optical surface second harmonic measurements of Isotropic thin-film metals: Gold, silver, copper, aluminum, and tantalum,” J. Appl. Phys. 96(7), 3626–3634 (2004).
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A. Prylepa, C. Reitböck, M. Cobet, A. Jesacher, X. Jin, R. Adelung, M. Schatzl-Linder, G. Luckeneder, K. H. Stellnberger, T. Steck, J. Faderl, T. Stehrer, and D. Stifter, “Material characterisation with methods of nonlinear optics,” J. Phys. D Appl. Phys. 51(4), 043001 (2018).
[Crossref]

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J. F. Brenner, B. S. Dew, J. B. Horton, T. King, P. W. Neurath, and W. D. Selles, “An Automated Microscope for Cytologic Research,” J. Histochem. Cytochem. 24(1), 100–111 (1976).
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Sendra, J.

F. Timpu, J. Sendra, C. Renaut, L. Lang, M. Timofeeva, M. T. Buscaglia, V. Buscaglia, and R. Grange, “Lithium Niobate Nanocubes as Linear and Nonlinear Ultraviolet Mie Resonators,” ACS Photonics 6(2), 545–552 (2019).
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M. Timofeeva, A. Bouravleuv, G. Cirlin, I. Shtrom, I. Soshnikov, M. Reig Escalé, A. Sergeyev, and R. Grange, “Polar Second-Harmonic Imaging to Resolve Pure and Mixed Crystal Phases along GaAs Nanowires,” Nano Lett. 16(10), 6290–6297 (2016).
[Crossref] [PubMed]

M. Timofeeva, A. Bouravleuv, G. Cirlin, I. Shtrom, I. Soshnikov, M. Reig Escalé, A. Sergeyev, and R. Grange, “Polar Second-Harmonic Imaging to Resolve Pure and Mixed Crystal Phases along GaAs Nanowires,” Nano Lett. 16(10), 6290–6297 (2016).
[Crossref] [PubMed]

R. Grange, G. Brönstrup, M. Kiometzis, A. Sergeyev, J. Richter, C. Leiterer, W. Fritzsche, C. Gutsche, A. Lysov, W. Prost, F. J. Tegude, T. Pertsch, A. Tünnermann, and S. Christiansen, “Far-field imaging for direct visualization of light interferences in GaAs nanowires,” Nano Lett. 12(10), 5412–5417 (2012).
[Crossref] [PubMed]

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M. Timofeeva, A. Bouravleuv, G. Cirlin, I. Shtrom, I. Soshnikov, M. Reig Escalé, A. Sergeyev, and R. Grange, “Polar Second-Harmonic Imaging to Resolve Pure and Mixed Crystal Phases along GaAs Nanowires,” Nano Lett. 16(10), 6290–6297 (2016).
[Crossref] [PubMed]

M. Timofeeva, A. Bouravleuv, G. Cirlin, I. Shtrom, I. Soshnikov, M. Reig Escalé, A. Sergeyev, and R. Grange, “Polar Second-Harmonic Imaging to Resolve Pure and Mixed Crystal Phases along GaAs Nanowires,” Nano Lett. 16(10), 6290–6297 (2016).
[Crossref] [PubMed]

Sinniah, R.

T. Yeo, S. Ong, Jayasooriah, and R. Sinniah, “Autofocusing for tissue microscopy,” Image Vis. Comput. 11(10), 629–639 (1993).
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L. Abdeladim, K. S. Matho, S. Clavreul, P. Mahou, J. M. Sintes, X. Solinas, I. Arganda-Carreras, S. G. Turney, J. W. Lichtman, A. Chessel, A. P. Bemelmans, K. Loulier, W. Supatto, J. Livet, and E. Beaurepaire, “Multicolor multiscale brain imaging with chromatic multiphoton serial microscopy,” Nat. Commun. 10(1), 1–14 (2019).
[PubMed]

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C. Renaut, L. Lang, K. Frizyuk, M. Timofeeva, F. E. Komissarenko, I. S. Mukhin, D. Smirnova, F. Timpu, M. Petrov, Y. Kivshar, and R. Grange, “Reshaping the Second-Order Polar Response of Hybrid Metal-Dielectric Nanodimers,” Nano Lett. 19(2), 877–884 (2019).
[Crossref] [PubMed]

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S. S. Kruk, R. Camacho-Morales, L. Xu, M. Rahmani, D. A. Smirnova, L. Wang, H. H. Tan, C. Jagadish, D. N. Neshev, and Y. S. Kivshar, “Nonlinear optical magnetism revealed by second-harmonic generation in nanoantennas,” Nano Lett. 17(6), 3914–3918 (2017).
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L. Abdeladim, K. S. Matho, S. Clavreul, P. Mahou, J. M. Sintes, X. Solinas, I. Arganda-Carreras, S. G. Turney, J. W. Lichtman, A. Chessel, A. P. Bemelmans, K. Loulier, W. Supatto, J. Livet, and E. Beaurepaire, “Multicolor multiscale brain imaging with chromatic multiphoton serial microscopy,” Nat. Commun. 10(1), 1–14 (2019).
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M. Timofeeva, A. Bouravleuv, G. Cirlin, I. Shtrom, I. Soshnikov, M. Reig Escalé, A. Sergeyev, and R. Grange, “Polar Second-Harmonic Imaging to Resolve Pure and Mixed Crystal Phases along GaAs Nanowires,” Nano Lett. 16(10), 6290–6297 (2016).
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M. Timofeeva, A. Bouravleuv, G. Cirlin, I. Shtrom, I. Soshnikov, M. Reig Escalé, A. Sergeyev, and R. Grange, “Polar Second-Harmonic Imaging to Resolve Pure and Mixed Crystal Phases along GaAs Nanowires,” Nano Lett. 16(10), 6290–6297 (2016).
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Squier, J.

Steck, T.

A. Prylepa, C. Reitböck, M. Cobet, A. Jesacher, X. Jin, R. Adelung, M. Schatzl-Linder, G. Luckeneder, K. H. Stellnberger, T. Steck, J. Faderl, T. Stehrer, and D. Stifter, “Material characterisation with methods of nonlinear optics,” J. Phys. D Appl. Phys. 51(4), 043001 (2018).
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A. Prylepa, C. Reitböck, M. Cobet, A. Jesacher, X. Jin, R. Adelung, M. Schatzl-Linder, G. Luckeneder, K. H. Stellnberger, T. Steck, J. Faderl, T. Stehrer, and D. Stifter, “Material characterisation with methods of nonlinear optics,” J. Phys. D Appl. Phys. 51(4), 043001 (2018).
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A. Prylepa, C. Reitböck, M. Cobet, A. Jesacher, X. Jin, R. Adelung, M. Schatzl-Linder, G. Luckeneder, K. H. Stellnberger, T. Steck, J. Faderl, T. Stehrer, and D. Stifter, “Material characterisation with methods of nonlinear optics,” J. Phys. D Appl. Phys. 51(4), 043001 (2018).
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Stifter, D.

A. Prylepa, C. Reitböck, M. Cobet, A. Jesacher, X. Jin, R. Adelung, M. Schatzl-Linder, G. Luckeneder, K. H. Stellnberger, T. Steck, J. Faderl, T. Stehrer, and D. Stifter, “Material characterisation with methods of nonlinear optics,” J. Phys. D Appl. Phys. 51(4), 043001 (2018).
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Y. Sun, S. Duthaler, and B. J. Nelson, “Autofocusing in computer microscopy: selecting the optimal focus algorithm,” Microsc. Res. Tech. 65(3), 139–149 (2004).
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Supatto, W.

L. Abdeladim, K. S. Matho, S. Clavreul, P. Mahou, J. M. Sintes, X. Solinas, I. Arganda-Carreras, S. G. Turney, J. W. Lichtman, A. Chessel, A. P. Bemelmans, K. Loulier, W. Supatto, J. Livet, and E. Beaurepaire, “Multicolor multiscale brain imaging with chromatic multiphoton serial microscopy,” Nat. Commun. 10(1), 1–14 (2019).
[PubMed]

Talsania, N.

L. Firestone, K. Cook, K. Culp, N. Talsania, and K. Preston, “Comparison of autofocus methods for automated microscopy,” Cytometry 12(3), 195–206 (1991).
[Crossref] [PubMed]

Tamamitsu, M.

Tan, H. H.

S. S. Kruk, R. Camacho-Morales, L. Xu, M. Rahmani, D. A. Smirnova, L. Wang, H. H. Tan, C. Jagadish, D. N. Neshev, and Y. S. Kivshar, “Nonlinear optical magnetism revealed by second-harmonic generation in nanoantennas,” Nano Lett. 17(6), 3914–3918 (2017).
[Crossref] [PubMed]

Tchernycheva, M.

L. Mancini, D. Hernández-Maldonado, W. Lefebvre, J. Houard, I. Blum, F. Vurpillot, J. Eymery, C. Durand, M. Tchernycheva, and L. Rigutti, “Multi-microscopy study of the influence of stacking faults and three-dimensional In distribution on the optical properties of m-plane InGaN quantum wells grown on microwire sidewalls,” Appl. Phys. Lett. 108(4), 042102 (2016).
[Crossref]

R. Koester, J. S. Hwang, D. Salomon, X. Chen, C. Bougerol, J. P. Barnes, D. S. Dang, L. Rigutti, A. de Luna Bugallo, G. Jacopin, M. Tchernycheva, C. Durand, and J. Eymery, “M-Plane Core-Shell InGaN/GaN Multiple-Quantum-Wells on GaN Wires for Electroluminescent Devices,” Nano Lett. 11(11), 4839–4845 (2011).
[Crossref] [PubMed]

Tegude, F. J.

R. Grange, G. Brönstrup, M. Kiometzis, A. Sergeyev, J. Richter, C. Leiterer, W. Fritzsche, C. Gutsche, A. Lysov, W. Prost, F. J. Tegude, T. Pertsch, A. Tünnermann, and S. Christiansen, “Far-field imaging for direct visualization of light interferences in GaAs nanowires,” Nano Lett. 12(10), 5412–5417 (2012).
[Crossref] [PubMed]

Teplin, C. W.

D. Krause, C. W. Teplin, and C. T. Rogers, “Optical surface second harmonic measurements of Isotropic thin-film metals: Gold, silver, copper, aluminum, and tantalum,” J. Appl. Phys. 96(7), 3626–3634 (2004).
[Crossref]

Timofeeva, M.

F. Timpu, J. Sendra, C. Renaut, L. Lang, M. Timofeeva, M. T. Buscaglia, V. Buscaglia, and R. Grange, “Lithium Niobate Nanocubes as Linear and Nonlinear Ultraviolet Mie Resonators,” ACS Photonics 6(2), 545–552 (2019).
[Crossref]

C. Renaut, L. Lang, K. Frizyuk, M. Timofeeva, F. E. Komissarenko, I. S. Mukhin, D. Smirnova, F. Timpu, M. Petrov, Y. Kivshar, and R. Grange, “Reshaping the Second-Order Polar Response of Hybrid Metal-Dielectric Nanodimers,” Nano Lett. 19(2), 877–884 (2019).
[Crossref] [PubMed]

M. Timofeeva, A. Bouravleuv, G. Cirlin, I. Shtrom, I. Soshnikov, M. Reig Escalé, A. Sergeyev, and R. Grange, “Polar Second-Harmonic Imaging to Resolve Pure and Mixed Crystal Phases along GaAs Nanowires,” Nano Lett. 16(10), 6290–6297 (2016).
[Crossref] [PubMed]

M. Timofeeva, A. Bouravleuv, G. Cirlin, I. Shtrom, I. Soshnikov, M. Reig Escalé, A. Sergeyev, and R. Grange, “Polar Second-Harmonic Imaging to Resolve Pure and Mixed Crystal Phases along GaAs Nanowires,” Nano Lett. 16(10), 6290–6297 (2016).
[Crossref] [PubMed]

Timpu, F.

C. Renaut, L. Lang, K. Frizyuk, M. Timofeeva, F. E. Komissarenko, I. S. Mukhin, D. Smirnova, F. Timpu, M. Petrov, Y. Kivshar, and R. Grange, “Reshaping the Second-Order Polar Response of Hybrid Metal-Dielectric Nanodimers,” Nano Lett. 19(2), 877–884 (2019).
[Crossref] [PubMed]

F. Timpu, J. Sendra, C. Renaut, L. Lang, M. Timofeeva, M. T. Buscaglia, V. Buscaglia, and R. Grange, “Lithium Niobate Nanocubes as Linear and Nonlinear Ultraviolet Mie Resonators,” ACS Photonics 6(2), 545–552 (2019).
[Crossref]

Tünnermann, A.

R. Grange, G. Brönstrup, M. Kiometzis, A. Sergeyev, J. Richter, C. Leiterer, W. Fritzsche, C. Gutsche, A. Lysov, W. Prost, F. J. Tegude, T. Pertsch, A. Tünnermann, and S. Christiansen, “Far-field imaging for direct visualization of light interferences in GaAs nanowires,” Nano Lett. 12(10), 5412–5417 (2012).
[Crossref] [PubMed]

Turney, S. G.

L. Abdeladim, K. S. Matho, S. Clavreul, P. Mahou, J. M. Sintes, X. Solinas, I. Arganda-Carreras, S. G. Turney, J. W. Lichtman, A. Chessel, A. P. Bemelmans, K. Loulier, W. Supatto, J. Livet, and E. Beaurepaire, “Multicolor multiscale brain imaging with chromatic multiphoton serial microscopy,” Nat. Commun. 10(1), 1–14 (2019).
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D. Vollath, “Automatic focusing by correlative methods,” J. Microsc. 147(3), 279–288 (1987).
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L. Mancini, D. Hernández-Maldonado, W. Lefebvre, J. Houard, I. Blum, F. Vurpillot, J. Eymery, C. Durand, M. Tchernycheva, and L. Rigutti, “Multi-microscopy study of the influence of stacking faults and three-dimensional In distribution on the optical properties of m-plane InGaN quantum wells grown on microwire sidewalls,” Appl. Phys. Lett. 108(4), 042102 (2016).
[Crossref]

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Figures (9)

Fig. 1
Fig. 1 Schematic of the nonlinear optical microscope a) in transmission and b) in reflection. To switch from transmission to reflection, a beam splitter and a mirror are added. The focusing and collection is then performed with the same objective.
Fig. 2
Fig. 2 Illustration of the autofocusing procedure a) Images of the laser beam at three different wavelengths (700, 800 and 900 nm) for various distances between the excitation and collection objectives. The corresponding normalized focus score was given by the maximum pixel intensity of the captured image and shown for 700 nm. b) The normalized focus score curves are shown for the wavelength range 700 to 900 nm with 10 nm wavelength sweep step. The maximum in each curve indicates the focused position and shifts during a wavelength sweep. c) For an automated measurement procedure, the wavelength sweep step is followed by an autofocusing step. The different positions being evaluated during the autofocusing procedure are shown with purple dots.
Fig. 3
Fig. 3 Schematic representation of the autofocusing strategy. If the Brenner Gradient or the Image Power algorithms are selected, the maximum threshold θ is first calculated from several images around the starting point. The coarse focusing step is divided in several loops, focus score values are measured with defined coarse step intervals, n consecutive values are averaged to reduce fluctuations (n points average) and three of these averages are compared to find the region of interest (three points comparison). In the fine focusing step, this region of interest is evaluated with finer step intervals and in the end, the stage is moved to the position with the maximum focus score.
Fig. 4
Fig. 4 Schematic representation of the autofocusing strategy. a) During the coarse focusing step (star shaped markers), the global maximum is searched using the hill-climbing strategy. A wrong search direction (red points) is identified by checking for three consecutively lower focus scores. During the fine focusing step (square points), the region of interest around the identified global maximum is scanned to find the focused position. b) Averaging over n points during the coarse focusing step to smooth out the focus score curve, which ensures the global maximum (labeled “Corrected”) is found instead of a local one (labeled “Early”).
Fig. 5
Fig. 5 Schematic of the multi-axis focus procedure. In each step, the position of the indicated axis is optimized using the autofocusing routine. The position of each stage is cyclically optimized until the change of position is smaller than a given tolerance.
Fig. 6
Fig. 6 Wavelength sweep with multi-axis autofocusing performed every 10 nm a)-d) from 780 to 1080 nm (red) and from 1080 to 780 nm (blue) for a BTO nanoparticle and e)-f) from 1040 to 1590 nm (orange) and from 1590 to 1040 nm (green) for a woodpile structure. Position recorded for the translational stages for the BTO nanoparticle for the a) excitation objective, b) the collection objective, and c)-d) the sample in x- and y-direction. Position recorded for e) the excitation and f) the collection objective for the woodpile structure.
Fig. 7
Fig. 7 Images and focus score curves calculated with different focus measure functions for the nanowire images around the focused position under a) bright light, b) under laser spot and c) under laser with SHG signal being captured. In the first situation, only the Brenner Gradient and the Variance & Edge filter algorithms were well suited for the autofocusing system. In the second one, only the Brenner Gradient algorithm could return the two focused positions. In the last situation, all algorithms are suitable for autofocusing. The colored vertical lines and frames indicate the true focused positions and the corresponding images. The difference between the true focused position and the one returned by the algorithm is indicated by an error arrow and a shaded region.
Fig. 8
Fig. 8 The SHG images around the true focused position and the focus score curves calculated with different focus measure functions for a) a BTO nanoparticle in transmission. All the algorithms are suited to autofocus the signal. b) SHG images for an Al0.2Ga0.8As layer in reflection mode. The Variance and Image Power algorithms return a different position than the other methods, which appears to be incorrect upon visual inspection. The green vertical lines and frames indicate the focused positions and corresponding images. The difference between the true focused position and the one returned by the algorithm is indicated by an error arrow and a shaded region.
Fig. 9
Fig. 9 The SHG images of a woodpile photonic crystal structure around the true focused position and the focus score curves calculated with different focus measure functions. a) Either the excitation objective or b) the collection objective was moved. All algorithms were suited in both cases, yet it was more difficult to evaluate the best focused position in a). The green vertical lines and frames indicate the focused positions and corresponding images.

Tables (2)

Tables Icon

Table 1 Description of the six implemented algorithms. H and W are the height and width of the image, i(x,y) is the intensity at a given pixel, μ is the mean intensity of the image and B is the measured background obtained by averaging the pixel intensity of the border pixels of the image. They The algorithms can be categorized as statistical, derivative-based or intuitive algorithms.

Tables Icon

Table 2 Axes that are involved in the focusing procedure depending on the dimensionality (class) of the sample. In reflection mode, the collection and excitation are performed by the same objective. The axes x and y represent the position of the sample, z1 and z2 represent positions of excitation and collection objectives correspondently.

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