Abstract

High focusing accuracy in microscopes could improve the imaging quality to reduce the error rate in DNA sequencing. We propose a new feedback method to improve the focusing condition to a very high accuracy. A reference laser reflected by the sample is detected by two or more sensors around the confocal point. After acquiring the signals from the out-of-focus positions, online data processing is implemented to provide feedbacks for real-time focus-plane locking on the sample surface. This method provides an accuracy better than 1/10 of the objective depth-of-focus. To balance optical aberrations, a specific optical feedback system should be designed, with athermal design considerations to adapt DNA sequencing work to temperature fluctuations.

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

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References

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2016 (3)

2014 (1)

2013 (3)

C. S. Liu, Y. C. Lin, and P. H. Hu, “Design and characterization of precise laser-based autofocusing microscope with reduced geometrical fluctuations,” Microsyst. Technol. 19(11), 1717–1724 (2013).
[Crossref]

F. Haque, J. Li, H. C. Wu, X. J. Liang, and P. Guo, “Solid-state and biological nanopore for real-time sensing of single chemical and sequencing of DNA,” Nano Today 8(1), 56–74 (2013).
[Crossref] [PubMed]

R. Nishi, Y. Moriyama, K. Yoshida, N. Kajimura, H. Mogaki, M. Ozawa, and S. Isakozawa, “An autofocus method using quasi-Gaussian fitting of image sharpness in ultra-high-voltage electron microscopy,” Microscopy (Oxf.) 62(5), 515–519 (2013).
[Crossref] [PubMed]

2012 (1)

2009 (1)

W. Y. Hsu, C. S. Lee, P. J. Chen, N. T. Chen, F. Z. Chen, Z. R. Yu, C. H. Kuo, and C. H. Hwang, “Development of the fast astigmatic auto-focus microscope system,” Meas. Sci. Technol. 20(4), 045902 (2009).
[Crossref]

2008 (1)

M. C. Wendl and R. K. Wilson, “Aspects of coverage in medical DNA sequencing,” BMC Bioinformatics 9(12), 239 (2008).
[Crossref] [PubMed]

2007 (3)

K. H. Kim, S. Y. Lee, S. Kim, S. H. Lee, and S. G. Jeong, “A new DNA chip detection mechanism using optical pick-up actuators,” Microsyst. Technol. 13(8), 1359–1369 (2007).
[Crossref]

P. Latreille, S. Norton, B. S. Goldman, J. Henkhaus, N. Miller, B. Barbazuk, H. B. Bode, C. Darby, Z. Du, S. Forst, S. Gaudriault, B. Goodner, H. Goodrich-Blair, and S. Slater, “Optical mapping as a routine tool for bacterial genome sequence finishing,” BMC Genomics 8(6), 321 (2007).
[Crossref] [PubMed]

C. Gierl, T. Kondo, H. Voos, W. Kongprawechon, and S. Phoojaruenchanachai, “Image processing algorithms for an auto focus system for slit lamp microscopy,” Advanced Concepts for Intelligent Vision Systems. Proc. Springer 4678, 909–919 (2007).

2000 (1)

S. J. Lassiter, W. Stryjewski, B. L. Legendre, R. Erdmann, M. Wahl, J. Wurm, R. Peterson, L. Middendorf, and S. A. Soper, “Time-resolved fluorescence imaging of slab gels for lifetime base-calling in DNA sequencing applications,” Anal. Chem. 72(21), 5373–5382 (2000).
[Crossref] [PubMed]

1995 (1)

L. F. McKeogh, J. P. Sharpe, and K. M. Johnson, “A low-cost automatic translation and autofocusing system for a microscope,” Meas. Sci. Technol. 6(5), 583–587 (1995).
[Crossref]

1989 (1)

E. Viegas-Pequignot, B. Dutrillaux, H. Magdelenat, and M. Coppey-Moisan, “Mapping of single-copy DNA sequences on human chromosomes by in situ hybridization with biotinylated probes: Enhancement of detection sensitivity by intensified-fluorescence digital-imaging microscopy,” Proc. Natl. Acad. Sci. U.S.A. 86(2), 582–586 (1989).
[Crossref] [PubMed]

1976 (1)

Aksimentiev, A.

S. Bhattacharya, J. Yoo, and A. Aksimentiev, “Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore,” ACS Nano 10(4), 4644–4651 (2016).
[Crossref] [PubMed]

Barbazuk, B.

P. Latreille, S. Norton, B. S. Goldman, J. Henkhaus, N. Miller, B. Barbazuk, H. B. Bode, C. Darby, Z. Du, S. Forst, S. Gaudriault, B. Goodner, H. Goodrich-Blair, and S. Slater, “Optical mapping as a routine tool for bacterial genome sequence finishing,” BMC Genomics 8(6), 321 (2007).
[Crossref] [PubMed]

Bhattacharya, S.

S. Bhattacharya, J. Yoo, and A. Aksimentiev, “Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore,” ACS Nano 10(4), 4644–4651 (2016).
[Crossref] [PubMed]

Bode, H. B.

P. Latreille, S. Norton, B. S. Goldman, J. Henkhaus, N. Miller, B. Barbazuk, H. B. Bode, C. Darby, Z. Du, S. Forst, S. Gaudriault, B. Goodner, H. Goodrich-Blair, and S. Slater, “Optical mapping as a routine tool for bacterial genome sequence finishing,” BMC Genomics 8(6), 321 (2007).
[Crossref] [PubMed]

Chen, F. Z.

W. Y. Hsu, C. S. Lee, P. J. Chen, N. T. Chen, F. Z. Chen, Z. R. Yu, C. H. Kuo, and C. H. Hwang, “Development of the fast astigmatic auto-focus microscope system,” Meas. Sci. Technol. 20(4), 045902 (2009).
[Crossref]

Chen, N. T.

W. Y. Hsu, C. S. Lee, P. J. Chen, N. T. Chen, F. Z. Chen, Z. R. Yu, C. H. Kuo, and C. H. Hwang, “Development of the fast astigmatic auto-focus microscope system,” Meas. Sci. Technol. 20(4), 045902 (2009).
[Crossref]

Chen, P. J.

W. Y. Hsu, C. S. Lee, P. J. Chen, N. T. Chen, F. Z. Chen, Z. R. Yu, C. H. Kuo, and C. H. Hwang, “Development of the fast astigmatic auto-focus microscope system,” Meas. Sci. Technol. 20(4), 045902 (2009).
[Crossref]

Coppey-Moisan, M.

E. Viegas-Pequignot, B. Dutrillaux, H. Magdelenat, and M. Coppey-Moisan, “Mapping of single-copy DNA sequences on human chromosomes by in situ hybridization with biotinylated probes: Enhancement of detection sensitivity by intensified-fluorescence digital-imaging microscopy,” Proc. Natl. Acad. Sci. U.S.A. 86(2), 582–586 (1989).
[Crossref] [PubMed]

Darby, C.

P. Latreille, S. Norton, B. S. Goldman, J. Henkhaus, N. Miller, B. Barbazuk, H. B. Bode, C. Darby, Z. Du, S. Forst, S. Gaudriault, B. Goodner, H. Goodrich-Blair, and S. Slater, “Optical mapping as a routine tool for bacterial genome sequence finishing,” BMC Genomics 8(6), 321 (2007).
[Crossref] [PubMed]

Du, Z.

P. Latreille, S. Norton, B. S. Goldman, J. Henkhaus, N. Miller, B. Barbazuk, H. B. Bode, C. Darby, Z. Du, S. Forst, S. Gaudriault, B. Goodner, H. Goodrich-Blair, and S. Slater, “Optical mapping as a routine tool for bacterial genome sequence finishing,” BMC Genomics 8(6), 321 (2007).
[Crossref] [PubMed]

Dutrillaux, B.

E. Viegas-Pequignot, B. Dutrillaux, H. Magdelenat, and M. Coppey-Moisan, “Mapping of single-copy DNA sequences on human chromosomes by in situ hybridization with biotinylated probes: Enhancement of detection sensitivity by intensified-fluorescence digital-imaging microscopy,” Proc. Natl. Acad. Sci. U.S.A. 86(2), 582–586 (1989).
[Crossref] [PubMed]

Erdmann, R.

S. J. Lassiter, W. Stryjewski, B. L. Legendre, R. Erdmann, M. Wahl, J. Wurm, R. Peterson, L. Middendorf, and S. A. Soper, “Time-resolved fluorescence imaging of slab gels for lifetime base-calling in DNA sequencing applications,” Anal. Chem. 72(21), 5373–5382 (2000).
[Crossref] [PubMed]

Forst, S.

P. Latreille, S. Norton, B. S. Goldman, J. Henkhaus, N. Miller, B. Barbazuk, H. B. Bode, C. Darby, Z. Du, S. Forst, S. Gaudriault, B. Goodner, H. Goodrich-Blair, and S. Slater, “Optical mapping as a routine tool for bacterial genome sequence finishing,” BMC Genomics 8(6), 321 (2007).
[Crossref] [PubMed]

Gaudriault, S.

P. Latreille, S. Norton, B. S. Goldman, J. Henkhaus, N. Miller, B. Barbazuk, H. B. Bode, C. Darby, Z. Du, S. Forst, S. Gaudriault, B. Goodner, H. Goodrich-Blair, and S. Slater, “Optical mapping as a routine tool for bacterial genome sequence finishing,” BMC Genomics 8(6), 321 (2007).
[Crossref] [PubMed]

Gierl, C.

C. Gierl, T. Kondo, H. Voos, W. Kongprawechon, and S. Phoojaruenchanachai, “Image processing algorithms for an auto focus system for slit lamp microscopy,” Advanced Concepts for Intelligent Vision Systems. Proc. Springer 4678, 909–919 (2007).

Goldman, B. S.

P. Latreille, S. Norton, B. S. Goldman, J. Henkhaus, N. Miller, B. Barbazuk, H. B. Bode, C. Darby, Z. Du, S. Forst, S. Gaudriault, B. Goodner, H. Goodrich-Blair, and S. Slater, “Optical mapping as a routine tool for bacterial genome sequence finishing,” BMC Genomics 8(6), 321 (2007).
[Crossref] [PubMed]

Goodner, B.

P. Latreille, S. Norton, B. S. Goldman, J. Henkhaus, N. Miller, B. Barbazuk, H. B. Bode, C. Darby, Z. Du, S. Forst, S. Gaudriault, B. Goodner, H. Goodrich-Blair, and S. Slater, “Optical mapping as a routine tool for bacterial genome sequence finishing,” BMC Genomics 8(6), 321 (2007).
[Crossref] [PubMed]

Goodrich-Blair, H.

P. Latreille, S. Norton, B. S. Goldman, J. Henkhaus, N. Miller, B. Barbazuk, H. B. Bode, C. Darby, Z. Du, S. Forst, S. Gaudriault, B. Goodner, H. Goodrich-Blair, and S. Slater, “Optical mapping as a routine tool for bacterial genome sequence finishing,” BMC Genomics 8(6), 321 (2007).
[Crossref] [PubMed]

Guo, P.

F. Haque, J. Li, H. C. Wu, X. J. Liang, and P. Guo, “Solid-state and biological nanopore for real-time sensing of single chemical and sequencing of DNA,” Nano Today 8(1), 56–74 (2013).
[Crossref] [PubMed]

Haque, F.

F. Haque, J. Li, H. C. Wu, X. J. Liang, and P. Guo, “Solid-state and biological nanopore for real-time sensing of single chemical and sequencing of DNA,” Nano Today 8(1), 56–74 (2013).
[Crossref] [PubMed]

Henkhaus, J.

P. Latreille, S. Norton, B. S. Goldman, J. Henkhaus, N. Miller, B. Barbazuk, H. B. Bode, C. Darby, Z. Du, S. Forst, S. Gaudriault, B. Goodner, H. Goodrich-Blair, and S. Slater, “Optical mapping as a routine tool for bacterial genome sequence finishing,” BMC Genomics 8(6), 321 (2007).
[Crossref] [PubMed]

Hsu, W. Y.

W. Y. Hsu, C. S. Lee, P. J. Chen, N. T. Chen, F. Z. Chen, Z. R. Yu, C. H. Kuo, and C. H. Hwang, “Development of the fast astigmatic auto-focus microscope system,” Meas. Sci. Technol. 20(4), 045902 (2009).
[Crossref]

Hu, P. H.

C. S. Liu, Y. C. Lin, and P. H. Hu, “Design and characterization of precise laser-based autofocusing microscope with reduced geometrical fluctuations,” Microsyst. Technol. 19(11), 1717–1724 (2013).
[Crossref]

Hwang, C. H.

W. Y. Hsu, C. S. Lee, P. J. Chen, N. T. Chen, F. Z. Chen, Z. R. Yu, C. H. Kuo, and C. H. Hwang, “Development of the fast astigmatic auto-focus microscope system,” Meas. Sci. Technol. 20(4), 045902 (2009).
[Crossref]

Isakozawa, S.

R. Nishi, Y. Moriyama, K. Yoshida, N. Kajimura, H. Mogaki, M. Ozawa, and S. Isakozawa, “An autofocus method using quasi-Gaussian fitting of image sharpness in ultra-high-voltage electron microscopy,” Microscopy (Oxf.) 62(5), 515–519 (2013).
[Crossref] [PubMed]

Jeong, S. G.

K. H. Kim, S. Y. Lee, S. Kim, S. H. Lee, and S. G. Jeong, “A new DNA chip detection mechanism using optical pick-up actuators,” Microsyst. Technol. 13(8), 1359–1369 (2007).
[Crossref]

Jiang, H.

Johnson, K. M.

L. F. McKeogh, J. P. Sharpe, and K. M. Johnson, “A low-cost automatic translation and autofocusing system for a microscope,” Meas. Sci. Technol. 6(5), 583–587 (1995).
[Crossref]

Kajimura, N.

R. Nishi, Y. Moriyama, K. Yoshida, N. Kajimura, H. Mogaki, M. Ozawa, and S. Isakozawa, “An autofocus method using quasi-Gaussian fitting of image sharpness in ultra-high-voltage electron microscopy,” Microscopy (Oxf.) 62(5), 515–519 (2013).
[Crossref] [PubMed]

Kim, K. H.

K. H. Kim, S. Y. Lee, S. Kim, S. H. Lee, and S. G. Jeong, “A new DNA chip detection mechanism using optical pick-up actuators,” Microsyst. Technol. 13(8), 1359–1369 (2007).
[Crossref]

Kim, S.

K. H. Kim, S. Y. Lee, S. Kim, S. H. Lee, and S. G. Jeong, “A new DNA chip detection mechanism using optical pick-up actuators,” Microsyst. Technol. 13(8), 1359–1369 (2007).
[Crossref]

Kondo, T.

C. Gierl, T. Kondo, H. Voos, W. Kongprawechon, and S. Phoojaruenchanachai, “Image processing algorithms for an auto focus system for slit lamp microscopy,” Advanced Concepts for Intelligent Vision Systems. Proc. Springer 4678, 909–919 (2007).

Kongprawechon, W.

C. Gierl, T. Kondo, H. Voos, W. Kongprawechon, and S. Phoojaruenchanachai, “Image processing algorithms for an auto focus system for slit lamp microscopy,” Advanced Concepts for Intelligent Vision Systems. Proc. Springer 4678, 909–919 (2007).

Kuo, C. H.

W. Y. Hsu, C. S. Lee, P. J. Chen, N. T. Chen, F. Z. Chen, Z. R. Yu, C. H. Kuo, and C. H. Hwang, “Development of the fast astigmatic auto-focus microscope system,” Meas. Sci. Technol. 20(4), 045902 (2009).
[Crossref]

Lassiter, S. J.

S. J. Lassiter, W. Stryjewski, B. L. Legendre, R. Erdmann, M. Wahl, J. Wurm, R. Peterson, L. Middendorf, and S. A. Soper, “Time-resolved fluorescence imaging of slab gels for lifetime base-calling in DNA sequencing applications,” Anal. Chem. 72(21), 5373–5382 (2000).
[Crossref] [PubMed]

Latreille, P.

P. Latreille, S. Norton, B. S. Goldman, J. Henkhaus, N. Miller, B. Barbazuk, H. B. Bode, C. Darby, Z. Du, S. Forst, S. Gaudriault, B. Goodner, H. Goodrich-Blair, and S. Slater, “Optical mapping as a routine tool for bacterial genome sequence finishing,” BMC Genomics 8(6), 321 (2007).
[Crossref] [PubMed]

Lee, C. S.

W. Y. Hsu, C. S. Lee, P. J. Chen, N. T. Chen, F. Z. Chen, Z. R. Yu, C. H. Kuo, and C. H. Hwang, “Development of the fast astigmatic auto-focus microscope system,” Meas. Sci. Technol. 20(4), 045902 (2009).
[Crossref]

Lee, S. H.

K. H. Kim, S. Y. Lee, S. Kim, S. H. Lee, and S. G. Jeong, “A new DNA chip detection mechanism using optical pick-up actuators,” Microsyst. Technol. 13(8), 1359–1369 (2007).
[Crossref]

Lee, S. Y.

K. H. Kim, S. Y. Lee, S. Kim, S. H. Lee, and S. G. Jeong, “A new DNA chip detection mechanism using optical pick-up actuators,” Microsyst. Technol. 13(8), 1359–1369 (2007).
[Crossref]

Legendre, B. L.

S. J. Lassiter, W. Stryjewski, B. L. Legendre, R. Erdmann, M. Wahl, J. Wurm, R. Peterson, L. Middendorf, and S. A. Soper, “Time-resolved fluorescence imaging of slab gels for lifetime base-calling in DNA sequencing applications,” Anal. Chem. 72(21), 5373–5382 (2000).
[Crossref] [PubMed]

Li, J.

F. Haque, J. Li, H. C. Wu, X. J. Liang, and P. Guo, “Solid-state and biological nanopore for real-time sensing of single chemical and sequencing of DNA,” Nano Today 8(1), 56–74 (2013).
[Crossref] [PubMed]

Li, Z.

Liang, X. J.

F. Haque, J. Li, H. C. Wu, X. J. Liang, and P. Guo, “Solid-state and biological nanopore for real-time sensing of single chemical and sequencing of DNA,” Nano Today 8(1), 56–74 (2013).
[Crossref] [PubMed]

Lin, Y. C.

C. S. Liu, Y. C. Lin, and P. H. Hu, “Design and characterization of precise laser-based autofocusing microscope with reduced geometrical fluctuations,” Microsyst. Technol. 19(11), 1717–1724 (2013).
[Crossref]

Liu, C. S.

C. S. Liu, Y. C. Lin, and P. H. Hu, “Design and characterization of precise laser-based autofocusing microscope with reduced geometrical fluctuations,” Microsyst. Technol. 19(11), 1717–1724 (2013).
[Crossref]

Magdelenat, H.

E. Viegas-Pequignot, B. Dutrillaux, H. Magdelenat, and M. Coppey-Moisan, “Mapping of single-copy DNA sequences on human chromosomes by in situ hybridization with biotinylated probes: Enhancement of detection sensitivity by intensified-fluorescence digital-imaging microscopy,” Proc. Natl. Acad. Sci. U.S.A. 86(2), 582–586 (1989).
[Crossref] [PubMed]

McKeogh, L. F.

L. F. McKeogh, J. P. Sharpe, and K. M. Johnson, “A low-cost automatic translation and autofocusing system for a microscope,” Meas. Sci. Technol. 6(5), 583–587 (1995).
[Crossref]

Middendorf, L.

S. J. Lassiter, W. Stryjewski, B. L. Legendre, R. Erdmann, M. Wahl, J. Wurm, R. Peterson, L. Middendorf, and S. A. Soper, “Time-resolved fluorescence imaging of slab gels for lifetime base-calling in DNA sequencing applications,” Anal. Chem. 72(21), 5373–5382 (2000).
[Crossref] [PubMed]

Miller, N.

P. Latreille, S. Norton, B. S. Goldman, J. Henkhaus, N. Miller, B. Barbazuk, H. B. Bode, C. Darby, Z. Du, S. Forst, S. Gaudriault, B. Goodner, H. Goodrich-Blair, and S. Slater, “Optical mapping as a routine tool for bacterial genome sequence finishing,” BMC Genomics 8(6), 321 (2007).
[Crossref] [PubMed]

Mogaki, H.

R. Nishi, Y. Moriyama, K. Yoshida, N. Kajimura, H. Mogaki, M. Ozawa, and S. Isakozawa, “An autofocus method using quasi-Gaussian fitting of image sharpness in ultra-high-voltage electron microscopy,” Microscopy (Oxf.) 62(5), 515–519 (2013).
[Crossref] [PubMed]

Moriyama, Y.

R. Nishi, Y. Moriyama, K. Yoshida, N. Kajimura, H. Mogaki, M. Ozawa, and S. Isakozawa, “An autofocus method using quasi-Gaussian fitting of image sharpness in ultra-high-voltage electron microscopy,” Microscopy (Oxf.) 62(5), 515–519 (2013).
[Crossref] [PubMed]

Nishi, R.

R. Nishi, Y. Moriyama, K. Yoshida, N. Kajimura, H. Mogaki, M. Ozawa, and S. Isakozawa, “An autofocus method using quasi-Gaussian fitting of image sharpness in ultra-high-voltage electron microscopy,” Microscopy (Oxf.) 62(5), 515–519 (2013).
[Crossref] [PubMed]

Noll, R. J.

Norton, S.

P. Latreille, S. Norton, B. S. Goldman, J. Henkhaus, N. Miller, B. Barbazuk, H. B. Bode, C. Darby, Z. Du, S. Forst, S. Gaudriault, B. Goodner, H. Goodrich-Blair, and S. Slater, “Optical mapping as a routine tool for bacterial genome sequence finishing,” BMC Genomics 8(6), 321 (2007).
[Crossref] [PubMed]

Ozawa, M.

R. Nishi, Y. Moriyama, K. Yoshida, N. Kajimura, H. Mogaki, M. Ozawa, and S. Isakozawa, “An autofocus method using quasi-Gaussian fitting of image sharpness in ultra-high-voltage electron microscopy,” Microscopy (Oxf.) 62(5), 515–519 (2013).
[Crossref] [PubMed]

Peterson, R.

S. J. Lassiter, W. Stryjewski, B. L. Legendre, R. Erdmann, M. Wahl, J. Wurm, R. Peterson, L. Middendorf, and S. A. Soper, “Time-resolved fluorescence imaging of slab gels for lifetime base-calling in DNA sequencing applications,” Anal. Chem. 72(21), 5373–5382 (2000).
[Crossref] [PubMed]

Phoojaruenchanachai, S.

C. Gierl, T. Kondo, H. Voos, W. Kongprawechon, and S. Phoojaruenchanachai, “Image processing algorithms for an auto focus system for slit lamp microscopy,” Advanced Concepts for Intelligent Vision Systems. Proc. Springer 4678, 909–919 (2007).

Qiu, L.

Sharpe, J. P.

L. F. McKeogh, J. P. Sharpe, and K. M. Johnson, “A low-cost automatic translation and autofocusing system for a microscope,” Meas. Sci. Technol. 6(5), 583–587 (1995).
[Crossref]

Shen, Y.

Slater, S.

P. Latreille, S. Norton, B. S. Goldman, J. Henkhaus, N. Miller, B. Barbazuk, H. B. Bode, C. Darby, Z. Du, S. Forst, S. Gaudriault, B. Goodner, H. Goodrich-Blair, and S. Slater, “Optical mapping as a routine tool for bacterial genome sequence finishing,” BMC Genomics 8(6), 321 (2007).
[Crossref] [PubMed]

Soper, S. A.

S. J. Lassiter, W. Stryjewski, B. L. Legendre, R. Erdmann, M. Wahl, J. Wurm, R. Peterson, L. Middendorf, and S. A. Soper, “Time-resolved fluorescence imaging of slab gels for lifetime base-calling in DNA sequencing applications,” Anal. Chem. 72(21), 5373–5382 (2000).
[Crossref] [PubMed]

Stryjewski, W.

S. J. Lassiter, W. Stryjewski, B. L. Legendre, R. Erdmann, M. Wahl, J. Wurm, R. Peterson, L. Middendorf, and S. A. Soper, “Time-resolved fluorescence imaging of slab gels for lifetime base-calling in DNA sequencing applications,” Anal. Chem. 72(21), 5373–5382 (2000).
[Crossref] [PubMed]

Viegas-Pequignot, E.

E. Viegas-Pequignot, B. Dutrillaux, H. Magdelenat, and M. Coppey-Moisan, “Mapping of single-copy DNA sequences on human chromosomes by in situ hybridization with biotinylated probes: Enhancement of detection sensitivity by intensified-fluorescence digital-imaging microscopy,” Proc. Natl. Acad. Sci. U.S.A. 86(2), 582–586 (1989).
[Crossref] [PubMed]

Voos, H.

C. Gierl, T. Kondo, H. Voos, W. Kongprawechon, and S. Phoojaruenchanachai, “Image processing algorithms for an auto focus system for slit lamp microscopy,” Advanced Concepts for Intelligent Vision Systems. Proc. Springer 4678, 909–919 (2007).

Wahl, M.

S. J. Lassiter, W. Stryjewski, B. L. Legendre, R. Erdmann, M. Wahl, J. Wurm, R. Peterson, L. Middendorf, and S. A. Soper, “Time-resolved fluorescence imaging of slab gels for lifetime base-calling in DNA sequencing applications,” Anal. Chem. 72(21), 5373–5382 (2000).
[Crossref] [PubMed]

Wendl, M. C.

M. C. Wendl and R. K. Wilson, “Aspects of coverage in medical DNA sequencing,” BMC Bioinformatics 9(12), 239 (2008).
[Crossref] [PubMed]

Wilson, R. K.

M. C. Wendl and R. K. Wilson, “Aspects of coverage in medical DNA sequencing,” BMC Bioinformatics 9(12), 239 (2008).
[Crossref] [PubMed]

Wu, H.

Wu, H. C.

F. Haque, J. Li, H. C. Wu, X. J. Liang, and P. Guo, “Solid-state and biological nanopore for real-time sensing of single chemical and sequencing of DNA,” Nano Today 8(1), 56–74 (2013).
[Crossref] [PubMed]

Wurm, J.

S. J. Lassiter, W. Stryjewski, B. L. Legendre, R. Erdmann, M. Wahl, J. Wurm, R. Peterson, L. Middendorf, and S. A. Soper, “Time-resolved fluorescence imaging of slab gels for lifetime base-calling in DNA sequencing applications,” Anal. Chem. 72(21), 5373–5382 (2000).
[Crossref] [PubMed]

Yang, J.

Yang, S.

Yoo, J.

S. Bhattacharya, J. Yoo, and A. Aksimentiev, “Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore,” ACS Nano 10(4), 4644–4651 (2016).
[Crossref] [PubMed]

Yoshida, K.

R. Nishi, Y. Moriyama, K. Yoshida, N. Kajimura, H. Mogaki, M. Ozawa, and S. Isakozawa, “An autofocus method using quasi-Gaussian fitting of image sharpness in ultra-high-voltage electron microscopy,” Microscopy (Oxf.) 62(5), 515–519 (2013).
[Crossref] [PubMed]

Yu, Z. R.

W. Y. Hsu, C. S. Lee, P. J. Chen, N. T. Chen, F. Z. Chen, Z. R. Yu, C. H. Kuo, and C. H. Hwang, “Development of the fast astigmatic auto-focus microscope system,” Meas. Sci. Technol. 20(4), 045902 (2009).
[Crossref]

Zhao, Q.

Zhao, W.

ACS Nano (1)

S. Bhattacharya, J. Yoo, and A. Aksimentiev, “Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore,” ACS Nano 10(4), 4644–4651 (2016).
[Crossref] [PubMed]

Advanced Concepts for Intelligent Vision Systems. Proc. Springer (1)

C. Gierl, T. Kondo, H. Voos, W. Kongprawechon, and S. Phoojaruenchanachai, “Image processing algorithms for an auto focus system for slit lamp microscopy,” Advanced Concepts for Intelligent Vision Systems. Proc. Springer 4678, 909–919 (2007).

Anal. Chem. (1)

S. J. Lassiter, W. Stryjewski, B. L. Legendre, R. Erdmann, M. Wahl, J. Wurm, R. Peterson, L. Middendorf, and S. A. Soper, “Time-resolved fluorescence imaging of slab gels for lifetime base-calling in DNA sequencing applications,” Anal. Chem. 72(21), 5373–5382 (2000).
[Crossref] [PubMed]

Appl. Opt. (1)

BMC Bioinformatics (1)

M. C. Wendl and R. K. Wilson, “Aspects of coverage in medical DNA sequencing,” BMC Bioinformatics 9(12), 239 (2008).
[Crossref] [PubMed]

BMC Genomics (1)

P. Latreille, S. Norton, B. S. Goldman, J. Henkhaus, N. Miller, B. Barbazuk, H. B. Bode, C. Darby, Z. Du, S. Forst, S. Gaudriault, B. Goodner, H. Goodrich-Blair, and S. Slater, “Optical mapping as a routine tool for bacterial genome sequence finishing,” BMC Genomics 8(6), 321 (2007).
[Crossref] [PubMed]

J. Opt. Soc. Am. (1)

Meas. Sci. Technol. (2)

W. Y. Hsu, C. S. Lee, P. J. Chen, N. T. Chen, F. Z. Chen, Z. R. Yu, C. H. Kuo, and C. H. Hwang, “Development of the fast astigmatic auto-focus microscope system,” Meas. Sci. Technol. 20(4), 045902 (2009).
[Crossref]

L. F. McKeogh, J. P. Sharpe, and K. M. Johnson, “A low-cost automatic translation and autofocusing system for a microscope,” Meas. Sci. Technol. 6(5), 583–587 (1995).
[Crossref]

Microscopy (Oxf.) (1)

R. Nishi, Y. Moriyama, K. Yoshida, N. Kajimura, H. Mogaki, M. Ozawa, and S. Isakozawa, “An autofocus method using quasi-Gaussian fitting of image sharpness in ultra-high-voltage electron microscopy,” Microscopy (Oxf.) 62(5), 515–519 (2013).
[Crossref] [PubMed]

Microsyst. Technol. (2)

K. H. Kim, S. Y. Lee, S. Kim, S. H. Lee, and S. G. Jeong, “A new DNA chip detection mechanism using optical pick-up actuators,” Microsyst. Technol. 13(8), 1359–1369 (2007).
[Crossref]

C. S. Liu, Y. C. Lin, and P. H. Hu, “Design and characterization of precise laser-based autofocusing microscope with reduced geometrical fluctuations,” Microsyst. Technol. 19(11), 1717–1724 (2013).
[Crossref]

Nano Today (1)

F. Haque, J. Li, H. C. Wu, X. J. Liang, and P. Guo, “Solid-state and biological nanopore for real-time sensing of single chemical and sequencing of DNA,” Nano Today 8(1), 56–74 (2013).
[Crossref] [PubMed]

Opt. Express (2)

Opt. Lett. (1)

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

E. Viegas-Pequignot, B. Dutrillaux, H. Magdelenat, and M. Coppey-Moisan, “Mapping of single-copy DNA sequences on human chromosomes by in situ hybridization with biotinylated probes: Enhancement of detection sensitivity by intensified-fluorescence digital-imaging microscopy,” Proc. Natl. Acad. Sci. U.S.A. 86(2), 582–586 (1989).
[Crossref] [PubMed]

Other (1)

CODE V Lens System Setup Reference Manual, Version11(1), 580–581 (2017) (Synopsys, Inc.).

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Figures (11)

Fig. 1
Fig. 1 Microscope with the laser differential confocal autofocus system. BS is the beam splitter, PD is the photodiode, d is the offset distance of the PDs with pinhole from the focus of the collimating lens, z is the defocus distance of the silicon wafer from the focus plane of the microscope objective, and SMF Laser is the laser with single-mode-fiber output.
Fig. 2
Fig. 2 Differential confocal autofocus sensitivity and monotonic region with different uc.
Fig. 3
Fig. 3 Layout of the multi-position laser differential confocal autofocus method.
Fig. 4
Fig. 4 Normalized detected signals of the multi-position photodiodes.
Fig. 5
Fig. 5 Multi-position laser differential confocal signal curves.
Fig. 6
Fig. 6 Rapid decrease in differential confocal autofocus sensitivity with the increase in aberration, (a) spherical aberration (Z9), (b) coma (Z8), and (c) astigmatism (Z5).
Fig. 7
Fig. 7 Block diagram of the autofocus microscope operation.
Fig. 8
Fig. 8 Variation in the focal point position of the collimating lens with temperature.
Fig. 9
Fig. 9 Layout of the collimating lens.
Fig. 10
Fig. 10 Offset change with temperature variation.
Fig. 11
Fig. 11 Departure of the differential confocal signal from zero with temperature variation.

Tables (1)

Tables Icon

Table 1 Required Parameters and Autofocus Parameters for Microscope Objective

Equations (6)

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I( u o , u c )= I 1 - I 2 = [ sin( u o /2 u c /4 ) u o /2 u c /4 ] 2 [ sin( u o /2 + u c /4 ) u o /2 + u c /4 ] 2
u o = π 2λ D 2 f o 2 z
u c = π 2λ D 2 f c 2 d
r p 2λ π( D/ f c ) .
σ= 2λ 0.54πSNR ( D/ f o ) 2 .
I( u o , u c )={ [ sin( u o /2 3 u c /4 ) u o /2 3 u c /4 ] 2 [ sin( u o /2 - u c /4 ) u o /2 - u c /4 ] 2 8.16< u o <2.72 [ sin( u o /2 u c /4 ) u o /2 u c /4 ] 2 [ sin( u o /2 + u c /4 ) u o /2 + u c /4 ] 2 2.72 u o 2.72. [ sin( u o /2 + u c /4 ) u o /2 + u c /4 ] 2 [ sin( u o /2 + 3 u c /4 ) u o /2 + 3 u c /4 ] 2 2.72< u o <8.16

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