Compressed Blind Deconvolution and Denoising for Complementary Beam Subtraction Light-Sheet Fluorescence Microscopy

Objective: The side-lobes of a Bessel beam (BB) create a severe out-of-focus background in scanning light-sheet fluorescence microscopy, thereby extremely limiting the axial resolution. The complementary beam subtraction (CBS) method can significantly reduce the out-of-focus background by double scanning a BB and its complementary beam. However, the blurring and noise caused by the system instability during the double scanning and subtraction operations degrade the image quality significantly. Therefore, we propose a compressed blind deconvolution and denoising (CBDD) method that solves this problem. Methods: We use a unified formulation that comprehensively takes advantage of multiple compressed sensing reconstructions and blind sparse representation. Results: The simulations and experiments were performed using the microbeads and model organisms to verify the effectiveness of the proposed method. Compared with the CBS light-sheet method, the proposed CBDD algorithm achieved the gain improvement in the axial and lateral resolution of about 1.81 and 2.22 times, respectively, while the average signal-to-noise ratio (SNR) was increased by about 3 dB. Conclusion: Accordingly, the proposed method can suppress the noise level, enhance the SNR, and recover the degraded resolution simultaneously. Significance: The obtained results demonstrate the proposed CBDD algorithm is well suited to improve the imaging performance of the CBS light-sheet fluorescence microscopy.

[1]  Ernst H. K. Stelzer,et al.  Light sheet-based fluorescence microscopy (LSFM) for the quantitative imaging of cells and tissues , 2015, Cell and Tissue Research.

[2]  Jordi Andilla,et al.  Light-sheet microscopy: a tutorial , 2018 .

[3]  Rob Fergus,et al.  Blind deconvolution using a normalized sparsity measure , 2011, CVPR 2011.

[4]  Nidal Kamel,et al.  Image SNR estimation using the autoregressive modeling , 2010, 2010 International Conference on Intelligent and Advanced Systems.

[5]  Aggelos K. Katsaggelos,et al.  Compressive Blind Image Deconvolution , 2013, IEEE Transactions on Image Processing.

[6]  Eero P. Simoncelli,et al.  Image quality assessment: from error visibility to structural similarity , 2004, IEEE Transactions on Image Processing.

[7]  Ernst H. K. Stelzer,et al.  Improving your four-dimensional image: traveling through a decade of light-sheet-based fluorescence microscopy research , 2017, Nature Protocols.

[8]  William T. Freeman,et al.  Removing camera shake from a single photograph , 2006, SIGGRAPH 2006.

[9]  Junfeng Yang,et al.  Alternating Direction Algorithms for 1-Problems in Compressive Sensing , 2009, SIAM J. Sci. Comput..

[10]  A. Petropulu,et al.  Higher order spectra based deconvolution of ultrasound images , 1995, IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control.

[11]  William Meiniel,et al.  Image denoising by adaptive Compressed Sensing reconstructions and fusions , 2015, SPIE Optical Engineering + Applications.

[12]  Frédo Durand,et al.  Understanding and evaluating blind deconvolution algorithms , 2009, CVPR.

[13]  P. Eilers,et al.  Sparse deconvolution of high-density super-resolution images , 2016, Scientific Reports.

[14]  Christoph J. Engelbrecht,et al.  Resolution enhancement in a light-sheet-based microscope (SPIM). , 2006, Optics letters.

[15]  K. Egiazarian,et al.  Blind image deconvolution , 2007 .

[16]  Lionel Moisan,et al.  Posterior Expectation of the Total Variation Model: Properties and Experiments , 2013, SIAM J. Imaging Sci..

[17]  Elsa D. Angelini,et al.  An Unbiased Risk Estimator for Image Denoising in the Presence of Mixed Poisson–Gaussian Noise , 2014, IEEE Transactions on Image Processing.

[18]  Josiane Zerubia,et al.  Blind deconvolution for thin-layered confocal imaging. , 2009, Applied optics.

[19]  Emmanuel J. Candès,et al.  NESTA: A Fast and Accurate First-Order Method for Sparse Recovery , 2009, SIAM J. Imaging Sci..

[20]  Huiqian Du,et al.  Minmax-concave total variation denoising , 2018, Signal Image Video Process..

[21]  H. Leitte,et al.  Rules and Self-Organizing Properties of Post-embryonic Plant Organ Cell Division Patterns , 2016, Current Biology.

[22]  Baoli Yao,et al.  Axial resolution enhancement of light‐sheet microscopy by double scanning of Bessel beam and its complementary beam , 2018, Journal of biophotonics.

[23]  Liang Gao,et al.  3D live fluorescence imaging of cellular dynamics using Bessel beam plane illumination microscopy , 2014, Nature Protocols.

[24]  Qionghai Dai,et al.  Blind deconvolution subject to sparse representation for fluorescence microscopy , 2013 .

[25]  Bo Zhang,et al.  Blind deconvolution for diffraction-limited fluorescence microscopy , 2008, 2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro.

[26]  F. Gran,et al.  P2B-12 Minimum Variance Beamforming for High Frame-Rate Ultrasound Imaging , 2007, 2007 IEEE Ultrasonics Symposium Proceedings.

[27]  Adrian Basarab,et al.  Compressive Deconvolution in Medical Ultrasound Imaging , 2015, IEEE Transactions on Medical Imaging.

[28]  Zongfu Jiang,et al.  Application of the vector ε and ρ extrapolation methods in the acceleration of the Richardson–Lucy algorithm , 2010 .

[29]  Peyman Milanfar,et al.  A Tour of Modern Image Filtering: New Insights and Methods, Both Practical and Theoretical , 2013, IEEE Signal Processing Magazine.

[30]  Patricia Ladret,et al.  The blur effect: perception and estimation with a new no-reference perceptual blur metric , 2007, Electronic Imaging.

[31]  J. Zerubia,et al.  Parametric Blind Deconvolution for Confocal Laser Scanning Microscopy , 2007, 2007 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

[32]  Philipp J. Keller,et al.  Towards comprehensive cell lineage reconstructions in complex organisms using light‐sheet microscopy , 2013, Development, growth & differentiation.

[33]  M. Marim A Compressed Sensing Framework for Biological Microscopy , 2011 .

[34]  Jeremy Freeman,et al.  Light-sheet imaging for systems neuroscience , 2014, Nature Methods.

[35]  Junbo Duan,et al.  Increasing Axial Resolution of Ultrasonic Imaging With a Joint Sparse Representation Model. , 2016, IEEE transactions on ultrasonics, ferroelectrics, and frequency control.

[36]  Brendt Wohlberg,et al.  AN ℓ1-TV algorithm for deconvolution with salt and pepper noise , 2009, 2009 IEEE International Conference on Acoustics, Speech and Signal Processing.

[37]  Philipp J. Keller,et al.  Reconstruction of Zebrafish Early Embryonic Development by Scanned Light Sheet Microscopy , 2008, Science.

[38]  J. Zerubia,et al.  Gaussian approximations of fluorescence microscope point-spread function models. , 2007, Applied optics.

[39]  R. DeVore,et al.  A Simple Proof of the Restricted Isometry Property for Random Matrices , 2008 .

[40]  Iben Kraglund Minimum Variance Beamforming for High Frame-Rate Ultrasound Imaging , 2009 .

[41]  F. Del Bene,et al.  Optical Sectioning Deep Inside Live Embryos by Selective Plane Illumination Microscopy , 2004, Science.

[42]  Josiane Zerubia,et al.  Richardson–Lucy algorithm with total variation regularization for 3D confocal microscope deconvolution , 2006, Microscopy research and technique.