Literature DB >> 24106307

High-resolution restoration of 3D structures from widefield images with extreme low signal-to-noise-ratio.

Muthuvel Arigovindan1, Jennifer C Fung, Daniel Elnatan, Vito Mennella, Yee-Hung Mark Chan, Michael Pollard, Eric Branlund, John W Sedat, David A Agard.   

Abstract

Four-dimensional fluorescence microscopy--which records 3D image information as a function of time--provides an unbiased way of tracking dynamic behavior of subcellular components in living samples and capturing key events in complex macromolecular processes. Unfortunately, the combination of phototoxicity and photobleaching can severely limit the density or duration of sampling, thereby limiting the biological information that can be obtained. Although widefield microscopy provides a very light-efficient way of imaging, obtaining high-quality reconstructions requires deconvolution to remove optical aberrations. Unfortunately, most deconvolution methods perform very poorly at low signal-to-noise ratios, thereby requiring moderate photon doses to obtain acceptable resolution. We present a unique deconvolution method that combines an entropy-based regularization function with kernels that can exploit general spatial characteristics of the fluorescence image to push the required dose to extreme low levels, resulting in an enabling technology for high-resolution in vivo biological imaging.

Keywords:  4D microscopy; low dose microscopy; noise-suppressing regularization

Mesh:

Substances:

Year:  2013        PMID: 24106307      PMCID: PMC3808589          DOI: 10.1073/pnas.1315675110

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  11 in total

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Authors:  Won-Ki Huh; James V Falvo; Luke C Gerke; Adam S Carroll; Russell W Howson; Jonathan S Weissman; Erin K O'Shea
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2.  Fast live simultaneous multiwavelength four-dimensional optical microscopy.

Authors:  Peter M Carlton; Jérôme Boulanger; Charles Kervrann; Jean-Baptiste Sibarita; Jean Salamero; Susannah Gordon-Messer; Debra Bressan; James E Haber; Sebastian Haase; Lin Shao; Lukman Winoto; Atsushi Matsuda; Peter Kner; Satoru Uzawa; Mats Gustafsson; Zvi Kam; David A Agard; John W Sedat
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3.  Enhanced three-dimensional reconstruction from confocal scanning microscope images. II. Depth discrimination versus signal-to-noise ratio in partially confocal images.

Authors:  J A Conchello; J J Kim; E W Hansen
Journal:  Appl Opt       Date:  1994-06-10       Impact factor: 1.980

4.  Richardson-Lucy algorithm with total variation regularization for 3D confocal microscope deconvolution.

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Journal:  Microsc Res Tech       Date:  2006-04       Impact factor: 2.769

5.  Deterministic edge-preserving regularization in computed imaging.

Authors:  P Charbonnier; L Blanc-Feraud; G Aubert; M Barlaud
Journal:  IEEE Trans Image Process       Date:  1997       Impact factor: 10.856

6.  A fast thresholded landweber algorithm for wavelet-regularized multidimensional deconvolution.

Authors:  C Vonesch; M Unser
Journal:  IEEE Trans Image Process       Date:  2008-04       Impact factor: 10.856

7.  Superresolution and convergence properties of the expectation-maximization algorithm for maximum-likelihood deconvolution of incoherent images.

Authors:  J A Conchello
Journal:  J Opt Soc Am A Opt Image Sci Vis       Date:  1998-10       Impact factor: 2.129

8.  Roles for two RecA homologs in promoting meiotic chromosome synapsis.

Authors:  B Rockmill; M Sym; H Scherthan; G S Roeder
Journal:  Genes Dev       Date:  1995-11-01       Impact factor: 11.361

9.  ZIP1 is a synaptonemal complex protein required for meiotic chromosome synapsis.

Authors:  M Sym; J A Engebrecht; G S Roeder
Journal:  Cell       Date:  1993-02-12       Impact factor: 41.582

10.  AIDA: an adaptive image deconvolution algorithm with application to multi-frame and three-dimensional data.

Authors:  Erik F Y Hom; Franck Marchis; Timothy K Lee; Sebastian Haase; David A Agard; John W Sedat
Journal:  J Opt Soc Am A Opt Image Sci Vis       Date:  2007-06       Impact factor: 2.129

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  21 in total

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Authors:  Kasey J Day; Effrosyni Papanikou; Benjamin S Glick
Journal:  Methods Mol Biol       Date:  2016

Review 2.  The Property-Based Practical Applications and Solutions of Genetically Encoded Acetylcholine and Monoamine Sensors.

Authors:  Jun Chen; Katriel E Cho; Daria Skwarzynska; Shaylyn Clancy; Nicholas J Conley; Sarah M Clinton; Xiaokun Li; Li Lin; J Julius Zhu
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Authors:  Barnali Waugh; Sharon G Wolf; Deborah Fass; Eric Branlund; Zvi Kam; John W Sedat; Michael Elbaum
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Authors:  Masakazu Iwai; Melissa S Roth; Krishna K Niyogi
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5.  Fluorescence microscopy datasets for training deep neural networks.

Authors:  Guy M Hagen; Justin Bendesky; Rosa Machado; Tram-Anh Nguyen; Tanmay Kumar; Jonathan Ventura
Journal:  Gigascience       Date:  2021-05-05       Impact factor: 6.524

Review 6.  Faster fluorescence microscopy: advances in high speed biological imaging.

Authors:  Peter W Winter; Hari Shroff
Journal:  Curr Opin Chem Biol       Date:  2014-05-09       Impact factor: 8.822

7.  Low-Dose CBCT Reconstruction Using Hessian Schatten Penalties.

Authors:  Liang Liu; Xinxin Li; Kai Xiang; Jing Wang; Shan Tan
Journal:  IEEE Trans Med Imaging       Date:  2017-12       Impact factor: 10.048

8.  Single-molecule localization microscopy as nonlinear inverse problem.

Authors:  Ji Yu; Ahmed Elmokadem
Journal:  Proc Natl Acad Sci U S A       Date:  2019-09-23       Impact factor: 11.205

9.  Isotropic super-resolution light-sheet microscopy of dynamic intracellular structures at subsecond timescales.

Authors:  Yuxuan Zhao; Meng Zhang; Wenting Zhang; Yao Zhou; Longbiao Chen; Qing Liu; Peng Wang; Rong Chen; Xinxin Duan; Feifan Chen; Huan Deng; Yunfei Wei; Peng Fei; Yu-Hui Zhang
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10.  The mechanism of force transmission at bacterial focal adhesion complexes.

Authors:  Laura M Faure; Jean-Bernard Fiche; Leon Espinosa; Adrien Ducret; Vivek Anantharaman; Jennifer Luciano; Sébastien Lhospice; Salim T Islam; Julie Tréguier; Mélanie Sotes; Erkin Kuru; Michael S Van Nieuwenhze; Yves V Brun; Olivier Théodoly; L Aravind; Marcelo Nollmann; Tâm Mignot
Journal:  Nature       Date:  2016-10-05       Impact factor: 49.962

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