Literature DB >> 32206433

Deep learning in single-molecule microscopy: fundamentals, caveats, and recent developments [Invited].

Leonhard Möckl1, Anish R Roy1, W E Moerner1.   

Abstract

Deep learning-based data analysis methods have gained considerable attention in all fields of science over the last decade. In recent years, this trend has reached the single-molecule community. In this review, we will survey significant contributions of the application of deep learning in single-molecule imaging experiments. Additionally, we will describe the historical events that led to the development of modern deep learning methods, summarize the fundamental concepts of deep learning, and highlight the importance of proper data composition for accurate, unbiased results.
© 2020 Optical Society of America under the terms of the OSA Open Access Publishing Agreement.

Year:  2020        PMID: 32206433      PMCID: PMC7075610          DOI: 10.1364/BOE.386361

Source DB:  PubMed          Journal:  Biomed Opt Express        ISSN: 2156-7085            Impact factor:   3.732


  60 in total

1.  Imaging intracellular fluorescent proteins at nanometer resolution.

Authors:  Eric Betzig; George H Patterson; Rachid Sougrat; O Wolf Lindwasser; Scott Olenych; Juan S Bonifacino; Michael W Davidson; Jennifer Lippincott-Schwartz; Harald F Hess
Journal:  Science       Date:  2006-08-10       Impact factor: 47.728

2.  Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function.

Authors:  Sri Rama Prasanna Pavani; Michael A Thompson; Julie S Biteen; Samuel J Lord; Na Liu; Robert J Twieg; Rafael Piestun; W E Moerner
Journal:  Proc Natl Acad Sci U S A       Date:  2009-02-11       Impact factor: 11.205

3.  The double-helix microscope super-resolves extended biological structures by localizing single blinking molecules in three dimensions with nanoscale precision.

Authors:  Hsiao-Lu D Lee; Steffen J Sahl; Matthew D Lew; W E Moerner
Journal:  Appl Phys Lett       Date:  2012-04-09       Impact factor: 3.791

4.  Nanoscopy with Focused Light (Nobel Lecture).

Authors:  Stefan W Hell
Journal:  Angew Chem Int Ed Engl       Date:  2015-06-18       Impact factor: 15.336

Review 5.  A survey on deep learning in medical image analysis.

Authors:  Geert Litjens; Thijs Kooi; Babak Ehteshami Bejnordi; Arnaud Arindra Adiyoso Setio; Francesco Ciompi; Mohsen Ghafoorian; Jeroen A W M van der Laak; Bram van Ginneken; Clara I Sánchez
Journal:  Med Image Anal       Date:  2017-07-26       Impact factor: 8.545

6.  Three-dimensional localization microscopy using deep learning.

Authors:  P Zelger; K Kaser; B Rossboth; L Velas; G J Schütz; A Jesacher
Journal:  Opt Express       Date:  2018-12-10       Impact factor: 3.894

7.  Imaging the three-dimensional orientation and rotational mobility of fluorescent emitters using the Tri-spot point spread function.

Authors:  Oumeng Zhang; Jin Lu; Tianben Ding; Matthew D Lew
Journal:  Appl Phys Lett       Date:  2018-07-17       Impact factor: 3.791

8.  Deep learning massively accelerates super-resolution localization microscopy.

Authors:  Wei Ouyang; Andrey Aristov; Mickaël Lelek; Xian Hao; Christophe Zimmer
Journal:  Nat Biotechnol       Date:  2018-04-16       Impact factor: 54.908

9.  Accurate and rapid background estimation in single-molecule localization microscopy using the deep neural network BGnet.

Authors:  Leonhard Möckl; Anish R Roy; Petar N Petrov; W E Moerner
Journal:  Proc Natl Acad Sci U S A       Date:  2019-12-23       Impact factor: 11.205

10.  Extending single-molecule microscopy using optical Fourier processing.

Authors:  Adam S Backer; W E Moerner
Journal:  J Phys Chem B       Date:  2014-05-12       Impact factor: 2.991

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  15 in total

1.  Deep learning-based light scattering microfluidic cytometry for label-free acute lymphocytic leukemia classification.

Authors:  Jing Sun; Lan Wang; Qiao Liu; Attila Tárnok; Xuantao Su
Journal:  Biomed Opt Express       Date:  2020-10-23       Impact factor: 3.732

2.  Single-molecule localization microscopy.

Authors:  Mickaël Lelek; Melina T Gyparaki; Gerti Beliu; Florian Schueder; Juliette Griffié; Suliana Manley; Ralf Jungmann; Markus Sauer; Melike Lakadamyali; Christophe Zimmer
Journal:  Nat Rev Methods Primers       Date:  2021-06-03

Review 3.  Development of Deep-Learning-Based Single-Molecule Localization Image Analysis.

Authors:  Yoonsuk Hyun; Doory Kim
Journal:  Int J Mol Sci       Date:  2022-06-21       Impact factor: 6.208

4.  Single Molecules Are Your Quanta: A Bottom-Up Approach toward Multidimensional Super-resolution Microscopy.

Authors:  Limin Xiang; Kun Chen; Ke Xu
Journal:  ACS Nano       Date:  2021-07-26       Impact factor: 15.881

5.  AutoSmarTrace: Automated chain tracing and flexibility analysis of biological filaments.

Authors:  Mathew Schneider; Alaa Al-Shaer; Nancy R Forde
Journal:  Biophys J       Date:  2021-05-20       Impact factor: 3.699

Review 6.  Single-molecule tracking of transcription protein dynamics in living cells: seeing is believing, but what are we seeing?

Authors:  Timothée Lionnet; Carl Wu
Journal:  Curr Opin Genet Dev       Date:  2021-01-07       Impact factor: 4.665

7.  SSNOMBACTER: A collection of scattering-type scanning near-field optical microscopy and atomic force microscopy images of bacterial cells.

Authors:  Massimiliano Lucidi; Denis E Tranca; Lorenzo Nichele; Devrim Ünay; George A Stanciu; Paolo Visca; Alina Maria Holban; Radu Hristu; Gabriella Cincotti; Stefan G Stanciu
Journal:  Gigascience       Date:  2020-11-24       Impact factor: 6.524

Review 8.  Super-resolution Microscopy with Single Molecules in Biology and Beyond-Essentials, Current Trends, and Future Challenges.

Authors:  Leonhard Möckl; W E Moerner
Journal:  J Am Chem Soc       Date:  2020-10-09       Impact factor: 15.419

9.  Democratising deep learning for microscopy with ZeroCostDL4Mic.

Authors:  Lucas von Chamier; Romain F Laine; Johanna Jukkala; Christoph Spahn; Daniel Krentzel; Elias Nehme; Martina Lerche; Sara Hernández-Pérez; Pieta K Mattila; Eleni Karinou; Séamus Holden; Ahmet Can Solak; Alexander Krull; Tim-Oliver Buchholz; Martin L Jones; Loïc A Royer; Christophe Leterrier; Yoav Shechtman; Florian Jug; Mike Heilemann; Guillaume Jacquemet; Ricardo Henriques
Journal:  Nat Commun       Date:  2021-04-15       Impact factor: 14.919

Review 10.  Light Sheet Illumination for 3D Single-Molecule Super-Resolution Imaging of Neuronal Synapses.

Authors:  Gabriella Gagliano; Tyler Nelson; Nahima Saliba; Sofía Vargas-Hernández; Anna-Karin Gustavsson
Journal:  Front Synaptic Neurosci       Date:  2021-11-24
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