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Applied Optics

Applied Optics

APPLICATIONS-CENTERED RESEARCH IN OPTICS

  • Editor: Joseph N. Mait
  • Vol. 53, Iss. 20 — Jul. 10, 2014
  • pp: 4509–4518

Autofocus using adaptive prediction approximation combined search for the fluorescence microscope in second-generation DNA sequencing system

Hancong Xu, Jinfeng Liu, Yang Li, Yan Yin, Chenxu Zhu, and Hua Lu  »View Author Affiliations


Applied Optics, Vol. 53, Issue 20, pp. 4509-4518 (2014)
http://dx.doi.org/10.1364/AO.53.004509


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Abstract

Autofocus is an important technique for high-speed image acquisition in the second-generation DNA sequencing system, and this paper studies the passive focus algorithm for the system, which consists of two parts: focus measurement (FM) and focus search (FS). Based on the properties of DNA chips’ images, we choose the normalized variance as the FM algorithm and develop a new robust FS named adaptive prediction approximation combined search (APACS). APACS utilizes golden section search (GSS) to approximate the focus position and engages the curve-fitting search (CFS) to predict the position simultaneously in every step of GSS. When the difference between consecutive predictions meets the set precision, the search finishes. Otherwise, it ends as GSS. In APACS, we also propose an estimation method, named the combination of centroid estimation and overdetermined equations estimation by least squares solution, to calculate the initial vector for the nonlinear equations in APACS prediction, which reduces the iterations and accelerates the search. The simulation and measured results demonstrate that APACS not only maintains the stability but also reduces the focus time compared with GSS and CFS, which indicates APACS is a robust and fast FS for the fluorescence microscope in a sequencing system.

© 2014 Optical Society of America

OCIS Codes
(170.2520) Medical optics and biotechnology : Fluorescence microscopy
(170.3880) Medical optics and biotechnology : Medical and biological imaging
(170.3890) Medical optics and biotechnology : Medical optics instrumentation

ToC Category:
Medical Optics and Biotechnology

History
Original Manuscript: March 7, 2014
Revised Manuscript: May 20, 2014
Manuscript Accepted: May 24, 2014
Published: July 9, 2014

Citation
Hancong Xu, Jinfeng Liu, Yang Li, Yan Yin, Chenxu Zhu, and Hua Lu, "Autofocus using adaptive prediction approximation combined search for the fluorescence microscope in second-generation DNA sequencing system," Appl. Opt. 53, 4509-4518 (2014)
http://www.opticsinfobase.org/ao/abstract.cfm?URI=ao-53-20-4509


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References

  1. L. Shih, “Autofocus survey: a comparison of algorithms,” Proc. SPIE 6502, 65020B (2007). [CrossRef]
  2. Y. Sun, S. Duthaler, and B. J. Nelson, “Autofocusing in computer microscopy: selecting the optimal focus algorithm,” Microsc. Res. Tech. 65, 139–149 (2004). [CrossRef]
  3. J. F. Schlag, A. C. Sanderson, C. P. Neuman, and F. C. Wimberly, Implementation of Automatic Focusing Algorithms for a Computer Vision System with Camera Control (Citeseer, 1983).
  4. N. Kehtarnavaz and H. J. Oh, “Development and real-time implementation of a rule-based auto-focus algorithm,” Real-Time Imaging 9, 197–203 (2003). [CrossRef]
  5. C.-Y. Chen, R.-C. Hwang, and Y.-J. Chen, “A passive auto-focus camera control system,” Appl. Soft Comput. 10, 296–303 (2010). [CrossRef]
  6. H.-L. Shen, Z.-H. Zheng, W. Wang, X. Du, S.-J. Shao, and J. H. Xin, “Autofocus for multispectral camera using focus symmetry,” Appl. Opt. 51, 2616–2623 (2012). [CrossRef]
  7. M. Gamadia, V. Peddigari, N. Kehtarnavaz, S.-Y. Lee, and G. Cook, “Real-time implementation of autofocus on the TI DSC processor,” Proc. SPIE 5297, 10–18 (2004). [CrossRef]
  8. R. Redondo, G. Bueno, J. C. Valdiviezo, R. Nava, G. Cristobal, O. Deniz, M. Garcia-Rojo, J. Salido, M. del Milagro Fernandez, J. Vidal, and B. Escalante-Ramirez, “Autofocus evaluation for brightfield microscopy pathology,” J. Biomed. Opt. 17, 036008 (2012). [CrossRef]
  9. O. Osibote, R. Dendere, S. Krishnan, and T. Douglas, “Automated focusing in bright-field microscopy for tuberculosis detection,” J. Microsc. 240, 155–163 (2010). [CrossRef]
  10. F. C. Groen, I. T. Young, and G. Ligthart, “A comparison of different focus functions for use in autofocus algorithms,” Cytometry 6, 81–91 (1985). [CrossRef]
  11. J. M. Tenenbaum, “Accommodation in computer vision,” Ph.D. thesis (Stanford University, 1970).
  12. T. Yeo, S. Ong, and R. Sinniah, “Autofocusing for tissue microscopy,” in Image and Vision Computing (1993), pp. 629–639.
  13. M. A. Bueno-Ibarra and L. Acho, “Fast autofocus algorithm for automated microscopes,” Opt. Eng. 44, 063601 (2005). [CrossRef]
  14. J. H. Price and D. A. Gough, “Comparison of phase-contrast and fluorescence digital autofocus for scanning microscopy,” Cytometry 16, 283–297 (1994). [CrossRef]
  15. D. Vollath, “Automatic focusing by correlative methods,” J. Microsc. 147, 279–288 (1987). [CrossRef]
  16. A. Santos, C. Ortiz de Solorzano, J. J. Vaquero, J. Pena, N. Malpica, and F. Del Pozo, “Evaluation of autofocus functions in molecular cytogenetic analysis,” J. Microsc. 188, 264–272 (1997). [CrossRef]
  17. Y. Sun, S. Duthaler, and B. J. Nelson, “Autofocusing algorithm selection in computer microscopy,” in 2005 IEEE/RSJ International Conference on Intelligent Robots and Systems (IEEE, 2005), pp. 70–76.
  18. Y. Yao, B. Abidi, N. Doggaz, and M. Abidi, “Evaluation of sharpness measures and search algorithms for the auto focusing of high-magnification images,” in Defense and Security Symposium (International Society for Optics and Photonics, 2006), p. 62460G.
  19. M. Rahman and N. Kehtarnavaz, “Real-time face-priority auto focus for digital and cell-phone cameras,” IEEE Trans. Consum. Electron. 54, 1506–1513 (2008). [CrossRef]
  20. J. He, R. Zhou, and Z. Hong, “Modified fast climbing search auto-focus algorithm with adaptive step size searching technique for digital camera,” IEEE Trans. Consum. Electron. 49, 257–262 (2003). [CrossRef]
  21. K. Ooi, K. Izumi, M. Nozaki, and I. Takeda, “An advanced autofocus system for video camera using quasi condition reasoning,” IEEE Trans. Consum. Electron. 36, 526–530 (1990). [CrossRef]
  22. R. A. Jarvis, “Focus optimization criteria for computer image processing,” Microscope 24, 163–180 (1976).
  23. E. P. Krotkov, Active Computer Vision by Cooperative Focus and Stereo (Springer-Verlag, 1989).
  24. J. Baina and J. Dublet, “Automatic focus and iris control for video cameras,” in Fifth International Conference on Image Processing and its Applications (IET, 1995), pp. 232–235.
  25. M. Subbarao and J.-K. Tyan, “Selecting the optimal focus measure for autofocusing and depth-from-focus,” IEEE Trans. Pattern Anal. Mach. Intell. 20, 864–870 (1998). [CrossRef]
  26. E. Krotkov, “Focusing,” Int. J. Comput. Vis. 1, 223–237 (1956).
  27. D. L. Marks, A. L. Oldenburg, J. J. Reynolds, and S. A. Boppart, “Autofocus algorithm for dispersion correction in optical coherence tomography,” Appl. Opt. 42, 3038–3046 (2003). [CrossRef]
  28. Q. Wu, F. Merchant, and K. Castleman, Microscope Image Processing (Elsevier, 2010).
  29. S. Yazdanfar, K. B. Kenny, K. Tasimi, A. D. Corwin, E. L. Dixon, and R. J. Filkins, “Simple and robust image-based autofocusing for digital microscopy,” Opt. Express 16, 8670–8677 (2008). [CrossRef]
  30. H. Anton, Elementary Linear Algebra (Wiley, 2010).

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