A comparison of image restoration approaches applied to three- dimensional confocal and wide-field fluorescence microscopy

Journal of Microscopy

Volumn 193, Issue 1, 1999, Pages 50-61

  Verveer, P J ^a   Gemkow, M J ^a   Jovin, T M ^a  

^a MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

Author keywords

Confocal microscopy; Deconvolution; Fluoresence; Image restoration; Three dimensional microscopy; Wide field microscopy

Indexed keywords

FLUORESCENCE IMAGING; FLUORESCENCE MICROSCOPY; GAUSSIAN NOISE (ELECTRONIC); MAXIMUM LIKELIHOOD ESTIMATION; MEAN SQUARE ERROR; RESTORATION;

CLASSIFIEDS; DECONVOLUTIONS; FIELD DATA; FLUORESENCE; NOISE MODELS; POISSON MODEL; REGULARISATION; THREE-DIMENSIONAL MICROSCOPY; WIDE-FIELD; WIDE-FIELD MICROSCOPIES;

IMAGE RECONSTRUCTION;

ALGORITHM; ANIMAL CELL; ARTICLE; BAYES THEOREM; CONFOCAL LASER MICROSCOPY; DROSOPHILA MELANOGASTER; EMBRYO; FLUORESCENCE MICROSCOPY; IMAGE RECONSTRUCTION; LASER MICROSCOPE; MAXIMUM LIKELIHOOD METHOD; NOISE; NONHUMAN; PRIORITY JOURNAL; STATISTICAL MODEL;

ANIMALIA; DROSOPHILA MELANOGASTER; MELANOGASTER;

EID: 0032944772     PISSN: 00222720     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2818.1999.00421.x     Document Type: Article

References (58)

1. Agard, D.A. (1984) Optical sectioning microscopy: cellular architecture in three dimensions. Annu. Rev. Biophys. Bioeng. 13, 191-219.
2. Agard, D.A., Hiraoka, Y., Shaw, P. & Sedat, J.W. (1989) Fluorescence microscopy in three dimensions. Meth. Cell. Biol. 30, 353-377.
3. Agard, D.A. & Sedat, J.W. (1983) Three-dimensional architecture of a polytene nucleus. Nature, 302, 676-681.
4. Avinash, G.B. (1996) Data-driven, simultaneous blur and image restoration in 3-D fluorescence microscopy. J. Microsc. 183, 145-157.
5. Bard, Y. (1974) Nonlinear Parameter Estimation. Academic Press, New York.
6. Bertero, M. & Boccacci, P. (1995) Regularization methods in image restoration: an application to HST images. Int. J. Imaging Syst. Technol. 6, 376-386.
7. Biemond, J., Lagendijk, R.L. & Merserau, R.M. (1990) Iterative methods for image deblurring. Proc. IEEE, 78, 856-883.
8. Carrington, W.A. (1990) Image restoration in 3D microscopy with limited data. Bioimaging and Two-Dimensional Spectroscopy (ed. by L. C. Smith), Vol. 1205 of Proc. SPIE, pp. 72-83.
9. Carrington, W.A., Lynch, R.M., Moore, E.D.W., Isenberg, G., Fogarty, K.E. & Fay, F.S. (1995) Superresolution three-dimensional images of fluorescence in cells with minimal light exposure. Science, 268, 1483-1487.
10. Conchello, J.-A. & Hansen, E.W. (1989) Three-dimensional reconstruction of noisy confocal scanning microscope images. New Methods in Microscopy and Low Light Imaging (ed. by J.E. Wampler), vol. 1161 of Proc. SPIE, pp. 279-285.
11. Conchello, J.-A. & Hansen, E.W. (1990) Enhanced 3-D reconstruction from confocal scanning microscope images. I: Deterministic and maximum likelihood reconstructions. Appl. Opt. 29, 3795-3804.
12. Conchello, J.A. & McNally, J.G. (1996) Fast regularization technique for expectation maximization algorithm for computational sectioning microscopy. Three-Dimensional Microscopy: Image Acquisition and Processing (ed. by C. J. Cogswell, G. Kino and T. Wilson), vol. 2655 of Proc. SPIEE. pp. 199-208.
13. Csiszár, I. (1991) Why least squares and maximum entropy? An axiomatic approach to inference for linear inverse problems. Ann. Statist. 19, 2032-2066.
14. Dempster, A.P., Laird, N.M. & Rubin, D.B. (1977) Maximum likelihood from incomplete data via the EM algorithm. J.R. Statist. Soc. B, 39, 1-38.
15. Galatsanos, N.P., Katsaggelos, A.K. (1992) Methods for choosing the regularization parameter and estimating the noise variance in image restoration and their relation. IEEE Trans. Image Proc. 1, 322-336.
16. Gemkow, M.J., Buchenau, P. & Arndt-Jovin, D.J. (1996) FISH in whole-mount Drosophila embryos. RNA: activation of a transcriptional locus, DNA: gene architecture and expression. Bioimaging, 4, 107-120.
17. Good, I.J. (1971) Nonparametric roughness penalties for probability densities. Biometrika, 58, 255-277.
18. Harris, J.L. (1964) Diffraction and resolving power. J. Opt. Soc. Am. 54, 931-936.
19. Hell, S.W., Schrader, M. & van der Voort, H.T.M. (1997) Far-field fluorescence microscopy with three-dimensional resolution in the 100-nm range. J. Microsc. 187, 1-7.
20. Holmes, T.J. (1988) Maximum-likelihood image restoration adapted for noncoherent optical imaging. J. Opt. Soc. Am. A, 5, 666-673.
21. Holmes, T.J. (1989) Expectation-maximization restoration of hand-limited truncated point-process intensities with application in microscopy. J. Opt. Soc. Am. A, 6, 1006-1014.
22. Holmes, T.J. (1992) Blind deconvolution of quantum-limited incoherent imagery: maximum-likelihood approach. J. Opt. Soc. Am. A, 9, 1052-1061.
23. Holmes, T.J., Bhattacharyya, S., Cooper, J.A., Hanzel, D., Krishnamurthi, V., Lin, W.-C., Roysam, B., Szarowski, D.H. & Turner, J.N. (1995) Light microscopic images reconstructed by maximum likelihood deconvolution. Handbook of Biological Confocal Microscopy 2nd edn. (ed. by J. B. Pawley), pp. 389-402. Plenum Press, New York.
24. Holmes, T.J. & Liu, Y.-H. (1989) Richardson-Lucy/maximum likelihood image restoration algorithm, for fluorescence microscopy: further testing. Appl. Opt. 28, 4930-4938.
25. Holmes, T.J. & Liu, Y.-H. (1991) Acceleration of maximum-likelihood image restoration for fluorescence microscopy and other noncoherent imagery. J. Opt. Soc. Am. A, 8, 893-907.
26. Jain, A.K. (1989) Fundamentals of Digital Image Processing. Prentice Hall, Englewood Cliffs, NJ.
27. Joshi, S. & Miller, M.I. (1993) Maximum a posteriori estimation with Good's roughness for three-dimensional optical-sectioning microscopy. J. Opt. Soc. Am. A, 10, 1078-1085.
28. Jovin, T.M. & Arndt-Jovin, D.J. (1989) Luminescence digital imaging microscopy. Annu. Rev. Biophys. Chem. 18, 271-308.
29. Kano, H., van der Voort, H.T.M., Schrader, M., van Kempen, G.M.P. & Hell, S.W. (1996) Avalanche photodiode detection with object scanning and image restoration provides 2-4 fold resolution increase in two-photon fluorescence microscopy. Bioimaging, 4, 187-197.
30. van Kempen, G.M.P., van Vliet, L.J., Verveer, P.J. & van der Voort, H.T.M. (1997) A quantitative comparison of image restoration methods for confocal microscopy. J. Microsc. 185, 354-365.
31. Krishnamurthi, V., Liu, Y.-H., Bhattacharyya, S., Turner, J.N. & Holmes, T.J. (1995) Blind deconvolution of fluorescence micrographs by maximum-likelihood estimation. Appl. Opt. 34, 6633-6647.
32. Lagendijk, R.L. (1990) Iterative identification and restoration of images. PhD thesis, Delft Technical University, Delft, The Netherlands.
33. Landweber, L. (1951) An iteration formula for Fredholm integral equations of the first kind. Am. J. Math. 4, 189-199.
34. Markham, J. & Conchello, J.-A. (1997) Tradeoffs in regularized maximum-likelihood image restoration. Three-Dimensional Microscopy: Image Acquisition and Processing IV (ed. by C. J. Cogswell, J.-A. Conchello and T. Wilson). Proc. SPIE, 2984, 136-145.
35. McNally, J.G., Markham, J. & Conchello, J.-A. (1998) Comparing methods for 3D microscopy. Three-Dimensional Microscopy: Image Acquisition and Processing V (ed. by C. J. Cogswell, J.-A. Conchello & T. Wilson), Proc. SPIE, in press.
36. Miller, M.I. & Roysam, B. (1991 ) Bayesian image reconstruction for emission tomography: implementation of the EM algorithm and Good's roughness prior on massively parallel processors. Proc. Natl. Acad. Sci. USA, 88, 3223-3227.
37. Press, W.H., Teukolsky, S.A. & Vetterling, W.T. (1992) Numerical Recipes in C. Cambridge University Press, Cambridge.
38. Schrader, M., Hell, S.W. & van der Voort, H.T.M. (1996) Potential of confocal microscope to resolve in the 50-100 nm range. Appl. Phys. Lett. 69, 3644-3646.
39. Sementilli, P.J., Hunt, B.R. & Nadar, M.S. (1993) Analysis of the limit to superresolution in incoherent imaging. J. Opt. Soc. Am. A, 10, 2265-2276.
40. Shaw, P. (1995) Comparison of wide-field/deconvolution and confocal microscopy for 3D imaging. Handbook of Biological Confocal Microscopy. 2nd edn (ed. by J. B. Pawley), pp. 373-387. Plenum Press, New York.
41. Sheppard, C.J.R. (1986a) The spatial frequency cut-off in three-dimensional imaging. Optik. 72, 131-133.
42. Sheppard, C.J.R. (1986b) The spatial frequency cut-off in three-dimensional imaging II. Optik, 74, 128-129.
43. Sheppard, C.J.R. (1989) Axial resolution of confocal fluorescence microscopy. J. Microsc. 154, 237-241.
44. Sheppard, C.J.R. & Gu, M. (1992) The significance of 3-D transfer functions in confocal scanning microscopy. J. Microsc. 165, 377-390.
45. Skilling, J. (1989) Classic maximum entropy. Maximum Entropy and Bayesian Methods (ed. by J. Skilling), pp. 45-52. Kluwer Academic, Dordrecht.
46. Skilling, J. (1998) Probabilistic data analysis: an introductory guide. J. Microsc. 190, 28-36.
47. Snyder, D.L. & Hammoud, A.M. (1993) Image recovery from data acquired with a charge-coupled-device camera. J. Opt. Soc. Am. A, 10, 1014-1023.
48. Snyder, D.L., Schulz, T.J. & O'Sullivan, J.A. (1992) Deblurring subject to non-negativity constraints. IEEE Trans. Signal Proc. 40, 1143-1150.
49. Stefanou, S.S. & Hansen, E.W. (1994) Maximum likelihood reconstruction of 3D confocal data sets. Three-Dimensional Microscopy (ed. by C. J. Cogswell and K. Carlsson), Proc. SPIE, 2184, 182-187.
50. Sullivan, B.J. & Katsaggelos, A.K. (1990) New termination rule for linear iterative image restoration algorithms. Opt. Eng. 29, 471-477.
51. Toraldo di Francia, G. (1969) Degrees of freedom of an image. J. Opt. Soc. Am. 59, 799-804.
52. VanCittert, P.H. (1931) Zum Einfluss der Spaltbreit auf die Intensitätsverteilung in Spektrallinien II. Z. Physik, 69, 298-308.
53. Verveer, P.J. & Jovin, T.M. (1997a) Acceleration of the ICTM image restoration algorithm. J. Microsc. 188, 191-195.
54. Verveer, P.J. & Jovin, T.M. (1997b) Efficient superresolution restoration algorithms using maximum a posteriori estimations with application to fluorescence microscopy. J. Opt. Soc. Am. A, 14, 1696-1706.
55. Verveer, P.J. & Jovin, T.M. (1998) Efficient image restoration based on Good's roughness penalty with application to fluorescence microscopy. J. Opt. Sor. Am. A, 15, 1077-1083.
56. van der Voort, H.T.M. & Brakenhoff, G.J. (1990) 3-D image formation in a high-aperture fluorescence confocal microscope: a numerical analysis. J. Microsc. 158, 43-54.
57. van der Voort, H.T.M. & Strasters, K.C. (1995) Restoration of confocal images for quantitative image analysis. J. Microsc. 178, 165-181.
58. Wilson, T. (1989) Optical sectioning in confocal fluorescent microscopes. J. Microsc. 154, 143-156.