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Applied Optics

Applied Optics

APPLICATIONS-CENTERED RESEARCH IN OPTICS

  • Editor: Joseph N. Mait
  • Vol. 48, Iss. 22 — Aug. 1, 2009
  • pp: 4437–4448

Blind deconvolution for thin-layered confocal imaging

Praveen Pankajakshan, Bo Zhang, Laure Blanc-Féraud, Zvi Kam, Jean-Christophe Olivo-Marin, and Josiane Zerubia  »View Author Affiliations


Applied Optics, Vol. 48, Issue 22, pp. 4437-4448 (2009)
http://dx.doi.org/10.1364/AO.48.004437


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Abstract

We propose an alternate minimization algorithm for estimating the point-spread function (PSF) of a confocal laser scanning microscope and the specimen fluorescence distribution. A three-dimensional separable Gaussian model is used to restrict the PSF solution space and a constraint on the specimen is used so as to favor the stabilization and convergence of the algorithm. The results obtained from the simulation show that the PSF can be estimated to a high degree of accuracy, and those on real data show better deconvolution as compared to a full theoretical PSF model.

© 2009 Optical Society of America

OCIS Codes
(100.3190) Image processing : Inverse problems
(180.1790) Microscopy : Confocal microscopy
(100.1455) Image processing : Blind deconvolution

ToC Category:
Image Processing

History
Original Manuscript: January 9, 2009
Revised Manuscript: May 14, 2009
Manuscript Accepted: May 15, 2009
Published: July 27, 2009

Virtual Issues
Vol. 4, Iss. 10 Virtual Journal for Biomedical Optics

Citation
Praveen Pankajakshan, Bo Zhang, Laure Blanc-Féraud, Zvi Kam, Jean-Christophe Olivo-Marin, and Josiane Zerubia, "Blind deconvolution for thin-layered confocal imaging," Appl. Opt. 48, 4437-4448 (2009)
http://www.opticsinfobase.org/ao/abstract.cfm?URI=ao-48-22-4437


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References

  1. J.B.Pawley, ed., Handbook of Biological Confocal Microscopy, 3rd ed. (Springer, 2006).
  2. M. Born and E. Wolf, Principles of Optics (Cambridge U. Press, 1999).
  3. D. A. Agard, “Optical sectioning microscopy: cellular architecture in three dimensions,” Annu. Rev. Biophys. Bioeng. 13, 191-219 (1984). [CrossRef]
  4. R. Hudson, J. N. Aarsvold, C.-T. Chen, J. Chen, P. Davies, T. Disz, I. Foster, M. Griem, M. K. Kwong, and B. Lin, “Optical microscopy system for 3D dynamic imaging,” Proc. SPIE 2655, 187-198 (1996). [CrossRef]
  5. B. Zhang, J. Zerubia, and J. C. Olivo-Marin., “Gaussian approximations of fluorescence microscope point-spread function models,” Appl. Opt. 46, 1819-1829 (2007). [CrossRef]
  6. J. G. McNally, C. Preza, J.-Á. Conchello, and L. J. Thomas, Jr., “Artifacts in computational optical-sectioning microscopy,” J. Opt. Soc. Am. A 11, 1056-1067 (1994). [CrossRef]
  7. J. W. Shaevitz and D. A. Fletcher, “Enhanced three-dimensional deconvolution microscopy using a measured depth-varying point-spread function,” J. Opt. Soc. Am. A 24, 2622-2627 (2007). [CrossRef]
  8. P. J. Shaw and D. J. Rawlins, “The point-spread function of a confocal microscope: its measurement and use in deconvolution of 3-D data,” J. Microsc. 163, 151-165 (1991).
  9. P. J. Shaw, “Deconvolution in 3-D optical microscopy,” Histochem. J. 26, 687-694 (1994). [CrossRef]
  10. A. Dieterlen, M. Debailleul, A. De Meyer, B. Simon, V. Georges, B. Colicchio, O. Haeberle, and V. Lauer, “Recent advances in 3-D fluorescence microscopy: tomography as a source of information,” Proc. SPIE 7008, 70080S1 (2008).
  11. P. A. Stokseth, “Properties of a defocused optical system,” J. Opt. Soc. Am. A 59, 1314-1321 (1969). [CrossRef]
  12. S. F. Gibson and F. Lanni, “Diffraction by a circular aperture as a model for three-dimensional optical microscopy,” J. Opt. Soc. Am. A A6, 1357-1367 (1989). [CrossRef]
  13. O. V. Michailovich and D. R. Adam, “Deconvolution of medical images from microscopic to whole body images,” in Blind Image Deconvolution: Theory and Applications, P. Campisi and K. Egiazarian, eds. (CRC, 2007), pp. 169-237.
  14. T. J. Holmes, “Blind deconvolution of quantum-limited incoherent imagery: maximum-likelihood approach,” J. Opt. Soc. Am. A 9, 1052-1061 (1992). [CrossRef]
  15. J. Markham and J.-A. Conchello, “Parametric blind deconvolution: a robust method for the simultaneous estimation of image and blur,” J. Opt. Soc. Am. A 16, 2377-2391 (1999). [CrossRef]
  16. E. F. Y. Hom, F. Marchis, T. K. Lee, S. Haase, D. A. Agard, and J. W. Sedat, “AIDA: an adaptive image deconvolution algorithm with application to multi-frame and three-dimensional data,” J. Opt. Soc. Am. A 24, 1580-1600 (2007). [CrossRef]
  17. L. Mandel, “Sub-Poissonian photon statistics in resonance fluorescence,” Opt. Lett. 4, 205-207 (1979). [CrossRef]
  18. D. A. Agard, Y. Hiraoka, P. Shaw, and J. W. Sedat, “Fluorescence microscopy in three dimensions,” Methods Cell Biol. 30, 353-377 (1989). [CrossRef]
  19. G. B. Avinash, “Data-driven, simultaneous blur and image restoration in 3-D fluorescence microscopy,” J. Microsc. 183, 145-157 (1996). [CrossRef]
  20. P. Pankajakshan, L. Blanc-Féraud, Z. Kam, and J. Zerubia, “Point-spread function retrieval in fluorescence microscopy,” in Proceedings of IEEE International Symposium on Biomedical Imaging (IEEE, 2009).
  21. B. M. Hanser, M. G. Gustafsson, D. A. Agard, and J. W. Sedat, “Phase retrieval for high-numerical-aperture optical systems,” Opt. Lett. 28, 801-803 (2003). [CrossRef]
  22. C. J. R. Sheppard and C. J. Cogswell, “Three-dimensional image formation in confocal microscopy,” J. Microsc. 159, 179-194 (1990).
  23. A. Erhardt, G. Zinser, D. Komitowski, and J. Bille, “Reconstructing 3-D light-microscopic images by digital image processing,” Appl. Opt. 24, 194-200 (1985). [CrossRef]
  24. W. A. Carrington, K. E. Fogarty, and F. S. Fay, 3D Fluorescence Imaging of Single Cells Using Image Restoration (Wiley-Liss, 1990), pp. 53-72.
  25. C. Preza, M. I. Miller, L. J. Thomas, Jr., and J. G. McNally, “Regularized linear method for reconstruction of three-dimensional microscopic objects from optical sections,” J. Opt. Soc. Am. A 9, 219-228 (1992). [CrossRef]
  26. T. Tommasi, A. Diaspro, and B. Bianco, “3-D reconstruction in optical microscopy by a frequency-domain approach,” Signal Process. 32, 357-366 (1993). [CrossRef]
  27. T. J. Holmes, “Maximum-likelihood image restoration adapted for noncoherent optical imaging,” J. Opt. Soc. Am. A 5, 666-673 (1988). [CrossRef]
  28. N. Dey, L. Blanc-Féraud, C. Zimmer, Z. Kam, P. Roux, J. C. Olivo-Marin, and J. Zerubia, “Richardson-Lucy algorithm with total variation regularization for 3D confocal microscope deconvolution,” Microsc. Res. Tech. 69, 260-266(2006). [CrossRef]
  29. P. Pankajakshan, B. Zhang, L. Blanc-Féraud, Z. Kam, J. C. Olivo-Marin, and J. Zerubia, “Parametric blind deconvolution for confocal laser scanning microscopy (CLSM)-proof of concept,” Research Report 6493 (INRIA Sophia-Antipolis, March 2008).
  30. G. M. P. Van Kempen, L. J. Van Vliet, P. J. Verveer, and H. T. M. Van Der Voort, “A quantitative comparison of image restoration methods for confocal microscopy,” J. Microsc. 185, 354-365 (1997). [CrossRef]
  31. A. Dieterlen, C. Xu, O. Haeberle, N. Hueber, R. Malfara, B. Colicchio, and S. Jacquey, “Identification and restoration in 3D fluorescence microscopy,” Proc. SPIE 5477, 105-113(2004). [CrossRef]
  32. G. Demoment, “Image reconstruction and restoration: overview of common estimation structures and problems,” IEEE Trans. Acoust. Speech Signal Process. 37, 2024-2036 (1989). [CrossRef]
  33. A. N. Tikhonov and V. A. Arsenin, Solution of Ill-posed Problems (Winston, 1977).
  34. K. Miller, “Least squares methods for ill-posed problems with a prescribed bound,” SIAM J. Math. Anal. 1, 52-74(1970). [CrossRef]
  35. L. I. Rudin, S. Osher, and E. Fatemi, “Nonlinear total variation based noise removal algorithms,” Phys. D 60, 259-268(1992). [CrossRef]
  36. N. Dey, L. Blanc-Féraud, C. Zimmer, P. Roux, Z. Kam, and J. C. Olivo-Marin, “3D microscopy deconvolution using Richardson-Lucy algorithm with total variation regularization,” Research Report 5272(INRIA, July 2004).
  37. L. B. Lucy, “An iterative technique for the rectification of observed distributions,” Astron. J. 79, 745-754(1974). [CrossRef]
  38. W. H. Richardson, “Bayesian-based iterative method of image restoration,” J. Opt. Soc. Am. A 62, 55-59 (1972). [CrossRef]
  39. A. P. Dempster, N. M. Laird, and D. B. Rubin, “Maximum likelihood from incomplete data via the EM algorithm,” J. R. Stat. Soc. Ser. B. Methodol. 39, 1-38 (1977).
  40. M. Jiang and G. Wang, “Development of blind image deconvolution and its applications,” J. X-Ray Sci. Technol. 11, 13-19(2003).
  41. T. F. Chan and C.-K. Wong, “Total variation blind deconvolution,” IEEE Trans. Image Process. 7, 370-375 (1998). [CrossRef]
  42. L. Bar, N. A. Sochen, and N. Kiryati, “Variational pairing of image segmentation and blind restoration,” in Proceedings of Eighth European Conference on Computer Vision, T. Pajdla and J. Matas, eds., Vol. 3022 of Lecture Notes in Computer Science (Springer, 2004), pp. 166-177.
  43. A. Santos and I. T. Young, “Model-based resolution: applying the theory in quantitative microscopy,” Appl. Opt. 39, 2948-2958 (2000). [CrossRef]
  44. K. E. Atkinson, An Introduction to Numerical Analysis, 2nd ed. (Wiley1989).
  45. A. Jalobeanu, L. Blanc-Féraud, and J. Zerubia, “Hyperparameter estimation for satellite image restoration using a MCMC maximum likelihood method,” Pattern Recog. 35, 341-352 (2002). [CrossRef]
  46. A. Mohammad-Djafari, “A full Bayesian approach for inverse problems,” in Maximum Entropy and Bayesian Methods, Vol. 79 of Fundamental Theories of Physics, K. Hanson and R. N. Silver, eds. (Kluwer Academic, 1996), pp. 135-143.
  47. P. Pankajakshan, B. Zhang, L. Blanc-Féraud, Z. Kam, J. C. Olivo-Marin, and J. Zerubia, “Parametric blind deconvolution for confocal laser scanning microscopy,” in Proceedings of IEEE International Conference of Engineering in Medicine and Biology Society (IEEE, 2007), pp. 6531-6534.
  48. M. de Moraes Marim, B. Zhang, J.-C. Olivo-Marin, and C. Zimmer, “Improving single particle localization with an empirically calibrated Gaussian kernel,” in Proceedings of IEEE International Symposium on Biomedical Imaging (IEEE, 2008), pp. 1003-1006.
  49. P. Pankajakshan, B. Zhang, L. Blanc-Féraud, Z. Kam, J. C. Olivo-Marin, and J. Zerubia, “Blind deconvolution for diffraction-limited fluorescence microscopy,” in Proceedings of IEEE International Symposium on Biomedical Imaging (IEEE, 2008), pp. 740-743.

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