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

Dendritic action potentials and computation in human layer 2/3 cortical neurons

(2020) Albert Gidon et al.   SCIENCE

High-throughput, high-resolution deep learning microscopy based on registration-free generative adversarial network

(2019) Hao Zhang et al.   Biomedical Optics Express

Adversarial attacks on medical machine learning

(2019) Samuel G. Finlayson et al.   SCIENCE

Multicolor localization microscopy and point-spread-function engineering by deep learning

(2019) Eran Hershko et al.   OPTICS EXPRESS

Automated Stoichiometry Analysis of Single-Molecule Fluorescence Imaging Traces via Deep Learning

(2019) Jiachao Xu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Deep learning for cellular image analysis

(2019) Erick Moen et al.   NATURE METHODS

Information-rich localization microscopy through machine learning

(2019) Taehwan Kim et al.   Nature Communications

Single-Particle Diffusion Characterization by Deep Learning

(2019) Naor Granik et al.   BIOPHYSICAL JOURNAL

Applications, promises, and pitfalls of deep learning for fluorescence image reconstruction

(2019) Chinmay Belthangady et al.   NATURE METHODS

Why deep-learning AIs are so easy to fool

(2019) Douglas Heaven   NATURE

ImJoy: an open-source computational platform for the deep learning era

(2019) Wei Ouyang et al.   NATURE METHODS

Accurate phase retrieval of complex 3D point spread functions with deep residual neural networks

(2019) Leonhard Möckl et al.   APPLIED PHYSICS LETTERS

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

(2019) Leonhard Möckl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2018) Oumeng Zhang et al.   APPLIED PHYSICS LETTERS

Deep learning massively accelerates super-resolution localization microscopy

(2018) Wei Ouyang et al.   NATURE BIOTECHNOLOGY

Machine learning for improved image-based wavefront sensing

(2018) Scott W. Paine et al.   OPTICS LETTERS

Fundamental Precision Bounds for Three-Dimensional Optical Localization Microscopy with Poisson Statistics

(2018) Mikael P. Backlund et al.   PHYSICAL REVIEW LETTERS

Deep-STORM: super-resolution single-molecule microscopy by deep learning

(2018) Elias Nehme et al.   Optica

Deep learning for biology

(2018) Sarah Webb   NATURE

Planning chemical syntheses with deep neural networks and symbolic AI

(2018) Marwin H. S. Segler et al.   NATURE

Artifact-free high-density localization microscopy analysis

(2018) Richard J. Marsh et al.   NATURE METHODS

CDeep3M—Plug-and-Play cloud-based deep learning for image segmentation

(2018) Matthias G. Haberl et al.   NATURE METHODS

Analyzing complex single-molecule emission patterns with deep learning

(2018) Peiyi Zhang et al.   NATURE METHODS

Three-dimensional localization microscopy using deep learning

(2018) P. Zelger et al.   OPTICS EXPRESS

SegNet: A Deep Convolutional Encoder-Decoder Architecture for Image Segmentation

(2017) Vijay Badrinarayanan et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

A survey on deep learning in medical image analysis

(2017) Geert Litjens et al.   MEDICAL IMAGE ANALYSIS

Mastering the game of Go without human knowledge

(2017) David Silver et al.   NATURE

Measurement-based estimation of global pupil functions in 3D localization microscopy

(2017) Petar N. Petrov et al.   OPTICS EXPRESS

Automatic detection of diffusion modes within biological membranes using back-propagation neural network

(2016) Patrice Dosset et al.   BMC BIOINFORMATICS

Mastering the game of Go with deep neural networks and tree search

(2016) David Silver et al.   NATURE

Multicolour localization microscopy by point-spread-function engineering

(2016) Yoav Shechtman et al.   Nature Photonics

Single Molecules, Cells, and Super-Resolution Optics (Nobel Lecture)

(2015) Eric Betzig   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Nanoscopy with Focused Light (Nobel Lecture)

(2015) Stefan W. Hell   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Single-Molecule Spectroscopy, Imaging, and Photocontrol: Foundations for Super-Resolution Microscopy (Nobel Lecture)

(2015) W. E. William E. Moerner   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Single-molecule spectroscopy and imaging over the decades

(2015) W. E. Moerner et al.   FARADAY DISCUSSIONS

Precise Three-Dimensional Scan-Free Multiple-Particle Tracking over Large Axial Ranges with Tetrapod Point Spread Functions

(2015) Yoav Shechtman et al.   NANO LETTERS

Deep learning

(2015) Yann LeCun et al.   NATURE

Deep learning in neural networks: An overview

(2015) Jürgen Schmidhuber   NEURAL NETWORKS

Single-molecule spectroscopy and imaging over the decades

(2015) W. E. Moerner et al.   FARADAY DISCUSSIONS

Extending Single-Molecule Microscopy Using Optical Fourier Processing

(2014) Adam S. Backer et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Optimal Point Spread Function Design for 3D Imaging

(2014) Yoav Shechtman et al.   PHYSICAL REVIEW LETTERS

Characterization and development of photoactivatable fluorescent proteins for single-molecule-based superresolution imaging

(2014) S. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

FALCON: fast and unbiased reconstruction of high-density super-resolution microscopy data

(2014) Junhong Min et al.   Scientific Reports

Photophysics of Fluorescent Probes for Single-Molecule Biophysics and Super-Resolution Imaging

(2012) Taekjip Ha et al.   Annual Review of Physical Chemistry

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

(2012) Hsiao-lu D. Lee et al.   APPLIED PHYSICS LETTERS

Microscopy beyond the diffraction limit using actively controlled single molecules

(2012) W.E. MOERNER   JOURNAL OF MICROSCOPY

Simultaneous, accurate measurement of the 3D position and orientation of single molecules

(2012) M. P. Backlund et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simultaneous multiple-emitter fitting for single molecule super-resolution imaging

(2011) Fang Huang et al.   Biomedical Optics Express

Accuracy of the Gaussian Point Spread Function model in 2D localization microscopy

(2010) Sjoerd Stallinga et al.   OPTICS EXPRESS

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

(2009) S. R. P. Pavani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA