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      Bayesian-based deconvolution fluorescence microscopy using dynamically updated nonstationary expectation estimates

      a , 1 , 1 , 1

      Scientific Reports

      Nature Publishing Group

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          Abstract

          Fluorescence microscopy is widely used for the study of biological specimens. Deconvolution can significantly improve the resolution and contrast of images produced using fluorescence microscopy; in particular, Bayesian-based methods have become very popular in deconvolution fluorescence microscopy. An ongoing challenge with Bayesian-based methods is in dealing with the presence of noise in low SNR imaging conditions. In this study, we present a Bayesian-based method for performing deconvolution using dynamically updated nonstationary expectation estimates that can improve the fluorescence microscopy image quality in the presence of noise, without explicit use of spatial regularization.

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          Most cited references 15

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          Efficient Bayesian-based multiview deconvolution.

          Light-sheet fluorescence microscopy is able to image large specimens with high resolution by capturing the samples from multiple angles. Multiview deconvolution can substantially improve the resolution and contrast of the images, but its application has been limited owing to the large size of the data sets. Here we present a Bayesian-based derivation of multiview deconvolution that drastically improves the convergence time, and we provide a fast implementation using graphics hardware.
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            Methods for choosing the regularization parameter and estimating the noise variance in image restoration and their relation.

            The application of regularization to ill-conditioned problems necessitates the choice of a regularization parameter which trades fidelity to the data with smoothness of the solution. The value of the regularization parameter depends on the variance of the noise in the data. The problem of choosing the regularization parameter and estimating the noise variance in image restoration is examined. An error analysis based on an objective mean-square-error (MSE) criterion is used to motivate regularization. Two approaches for choosing the regularization parameter and estimating the noise variance are proposed. The proposed and existing methods are compared and their relationship to linear minimum-mean-square-error filtering is examined. Experiments are presented that verify the theoretical results.
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              Richardson-Lucy algorithm with total variation regularization for 3D confocal microscope deconvolution.

              Confocal laser scanning microscopy is a powerful and popular technique for 3D imaging of biological specimens. Although confocal microscopy images are much sharper than standard epifluorescence ones, they are still degraded by residual out-of-focus light and by Poisson noise due to photon-limited detection. Several deconvolution methods have been proposed to reduce these degradations, including the Richardson-Lucy iterative algorithm, which computes maximum likelihood estimation adapted to Poisson statistics. As this algorithm tends to amplify noise, regularization constraints based on some prior knowledge on the data have to be applied to stabilize the solution. Here, we propose to combine the Richardson-Lucy algorithm with a regularization constraint based on Total Variation, which suppresses unstable oscillations while preserving object edges. We show on simulated and real images that this constraint improves the deconvolution results as compared with the unregularized Richardson-Lucy algorithm, both visually and quantitatively. Copyright (c) 2006 Wiley-Liss, Inc.
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                Author and article information

                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group
                2045-2322
                08 June 2015
                2015
                : 5
                Affiliations
                [1 ]Department of Systems Design Engineering, University of Waterloo , Ontario, Canada, N2L 3G1
                Author notes
                Article
                srep10849
                10.1038/srep10849
                4459105
                26054051
                Copyright © 2015, Macmillan Publishers Limited

                This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

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