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Applying Space-Variant Point Spread Function to Three-Dimensional Reconstruction of Fluorescence Microscopic Images

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Abstract

Three-dimensional (3D) reconstruction of fluorescence microscopic images is a challenging topic in the image processing, because the imaging system is very complex, and the point spread function (PSF) continuously varies along the optical axis. Generally, the more exact the PSF is, the higher the reconstruction accuracy is. An image reconstruction method is proposed for fluorescence microscopic sample based on space-variant PSF (SV-PSF) which is generated by cubic spline theory in this paper. Firstly, key PSFs are estimated by blind deconvolution algorithm at several depths of fluorescence microscopic image stack along the optical axis. Then, other PSFs are interpolated using cubic spline theory. Finally, a 3D microscopic specimen model is reconstructed by this group of SV-PSFs. The experimental results show that the proposed method is obviously superior to the method in which space-invariant (SI) PSF is used to reconstruct the simulated and real fluorescence microscopic images.

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REFERENCES

  1. Dey, N., Blanc-Féraud, L., Zimmer, C., Roux, P., Kam, Z., Olivo-Marin, J.C., and Zerubia, J., 3D Microscopy Deconvolution Using Richardson–Lucy Algorithm with Total Variation Regularization, Research Report, RR-5272, INRIA, 2004.

  2. Dey, N., Blanc-Féraud, L., Zimmer, C., Kam, Z., Olivo-Marin, J.C., and Zerubia, J., A deconvolution method for confocal microscopy with total variation regularization, IEEE International Symposium on Biomedical Imaging, Arlington, VA, 2004, pp. 1223–1226.

  3. Chacko, N. and Liebling, M., Fast spatially variant deconvolution for optical microscopy via iterative shrinkage thresholding, IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Florence, 2014, pp. 2838–2842.

  4. Hadj, S.B., Blanc-Féraud, L., and Aubert, G., Space Variant Blind Image Restoration, Research Report, RR-8073, INRIA, 2012.

  5. Jia, S., Vaughan, J.C., and Zhuang, X.W., Isotropic three-dimensional super-resolution imaging with a self-bending point spread function, Nat. Photonics, 2014, vol. 8, no. 2, pp. 302–306.

    Article  Google Scholar 

  6. Ghosh, S. and Preza, C., Space-variant image formation for 3D fluorescence microscopy using a computationally efficient block-based model, IEEE International Symposium on Biomedical Imaging, New York, 2015, pp. 789–792.

  7. Li, J.Z., Xue, F., and Blu, T., Accurate 3D PSF estimation from a wide-field microscopy image, IEEE International Symposium on Biomedical Imaging, Washington, D.C., 2018, pp. 501–504.

  8. Hadj, S.B., Blanc-Féraud, L., Aubert, G., and Englerl, G., Blind restoration of confocal microscopy images in presence of a depth-variant blur and poisson noise, IEEE International Conference on Acoustics, Speech and Signal Processing, 2013, Vancouver, pp. 915–919.

  9. Bardsley, J., Jefferies, S., Nagy, J., and Plemmons, R., A computational method for the restoration of images with an unknown, spatially-varying blur, Opt. Express, 2006, vol. 14, no. 5, pp. 1767–1782.

    Article  Google Scholar 

  10. Preza, C. and Conchello, J.A., Depth-variant maximum-likelihood restoration for three-dimensional fluorescence microscopy, J. Opt. Soc. Am. A, 2004, vol. 21, no. 9, pp. 1593–1601.

    Article  Google Scholar 

  11. Biggs, D.S.C. and Andrews, M., Acceleration of iterative image restoration algorithms, Appl. Opt., 1997, vol. 36, no. 8, pp. 1766–1775.

    Article  Google Scholar 

  12. Lucy, L.B., An iterative technique for rectification of observed distributions, Astron. J., 1974, vol. 79, no. 6, pp. 745–765.

    Article  Google Scholar 

  13. Preza, C., Miller, M.I., Thomas, L.J., and McNally, J.G., Regularized linear method for reconstruction of three-dimensional microscopic objects from optical sections, J. Opt. Soc. Amer. A, 1992, vol. 9, no. 2, pp. 219–228.

    Article  Google Scholar 

  14. Verveer, P.J. and Jovin, T.M., Efficient super resolution restoration algorithms using maximum a posteriori estimations with application to fluorescence microscopy, J. Opt. Soc. Amer. A, 1997, vol. 14, no. 8, pp. 1696–1706.

    Article  Google Scholar 

  15. Holmes, T.J., Blind deconvolution of quantum-limited incoherent imagery: Maximum-likelihood approach, J. Opt. Soc. Amer. A, 1992, vol. 9, no. 7, pp. 1052–1061.

    Article  Google Scholar 

  16. Dey, N., Blanc-Féraud, L., Zimmer, C., Roux, P., Kam, Z., Olivo-Marin, J.C., and Zerubia, J., Richardson—Lucy algorithm with total variation regularization for 3D confocal microscope deconvolution, Microsc. Res. Tech., 2006, vol. 69, no. 4, pp. 260–266.

    Article  Google Scholar 

  17. Zhang, B., Zerubia, J., and Olivo-Marin, J.C., Gaussian approximations of fluorescence microscope point-spread function models, Appl. Opt., 2007, vol. 46, no. 10, pp. 1819–1829.

    Article  Google Scholar 

  18. Wang, Z., Bovik, A.C., Sheikh, H.R., and Simoncelli, E.P., Image quality assessment: From error visibility to structural similarity, IEEE Trans. Image Process., 2004, vol. 13, no. 4, pp. 600–612.

    Article  Google Scholar 

  19. Wang, Y., He, X., and Wang, H., The depth-variant image restoration based on Hopfield neural network, The 3rd International Conference on Natural Computation, Haikou, 2007, pp. 363–366.

  20. The Lecture on Microscopic Image Processing and the Network on Ultrahigh Resolution Microscopy, 2012. http://www.microimage.com.cn/article/2012/0927/article_2840.html

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Yu Wang, Chen, X., Jiang, H. et al. Applying Space-Variant Point Spread Function to Three-Dimensional Reconstruction of Fluorescence Microscopic Images. Aut. Control Comp. Sci. 53, 194–201 (2019). https://doi.org/10.3103/S0146411619020111

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  • DOI: https://doi.org/10.3103/S0146411619020111

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