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

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

(2019) Eran Hershko et al.   OPTICS EXPRESS

Deep learning for cellular image analysis

(2019) Erick Moen et al.   NATURE METHODS

One Pixel Attack for Fooling Deep Neural Networks

(2019) Jiawei Su et al.   IEEE TRANSACTIONS ON EVOLUTIONARY COMPUTATION

In Silico Labeling: Predicting Fluorescent Labels in Unlabeled Images

(2018) Eric M. Christiansen et al.   CELL

Using Deep Neural Networks for Inverse Problems in Imaging: Beyond Analytical Methods

(2018) Alice Lucas et al.   IEEE SIGNAL PROCESSING MAGAZINE

Opportunities and obstacles for deep learning in biology and medicine

(2018) Travers Ching et al.   Journal of the Royal Society Interface

A machine learns to predict the stability of circumbinary planets

(2018) Christopher Lam et al.   MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY

Fast, long-term, super-resolution imaging with Hessian structured illumination microscopy

(2018) Xiaoshuai Huang et al.   NATURE BIOTECHNOLOGY

Deep learning massively accelerates super-resolution localization microscopy

(2018) Wei Ouyang et al.   NATURE BIOTECHNOLOGY

Artificial intelligence faces reproducibility crisis

(2018) Matthew Hutson   SCIENCE

Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms

(2018) Tsung-Li Liu et al.   SCIENCE

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

(2018) Elias Nehme et al.   Optica

Machine learning at the energy and intensity frontiers of particle physics

(2018) Alexander Radovic et al.   NATURE

Image reconstruction by domain-transform manifold learning

(2018) Bo Zhu et al.   NATURE

Deep learning is combined with massive-scale citizen science to improve large-scale image classification

(2018) Devin P Sullivan et al.   NATURE BIOTECHNOLOGY

Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy

(2018) Chawin Ounkomol et al.   NATURE METHODS

Computational modeling of cellular structures using conditional deep generative networks

(2018) Hao Yuan et al.   BIOINFORMATICS

Super-resolution microscopy demystified

(2018) Lothar Schermelleh et al.   NATURE CELL BIOLOGY

Content-aware image restoration: pushing the limits of fluorescence microscopy

(2018) Martin Weigert et al.   NATURE METHODS

U-Net: deep learning for cell counting, detection, and morphometry

(2018) Thorsten Falk et al.   NATURE METHODS

Deep learning enables cross-modality super-resolution in fluorescence microscopy

(2018) Hongda Wang et al.   NATURE METHODS

Light scattering control in transmission and reflection with neural networks

(2018) Alex Turpin et al.   OPTICS EXPRESS

Attenuation artifacts in light sheet fluorescence microscopy corrected by OPTiSPIM

(2018) Jürgen Mayer et al.   Light-Science & Applications

Convolutional Neural Networks for Inverse Problems in Imaging: A Review

(2017) Michael T. McCann et al.   IEEE SIGNAL PROCESSING MAGAZINE

Deep Convolutional Neural Network for Inverse Problems in Imaging

(2017) Kyong Hwan Jin et al.   IEEE TRANSACTIONS ON IMAGE PROCESSING

Beyond a Gaussian Denoiser: Residual Learning of Deep CNN for Image Denoising

(2017) Kai Zhang et al.   IEEE TRANSACTIONS ON IMAGE PROCESSING

DeconvolutionLab2: An open-source software for deconvolution microscopy

(2017) Daniel Sage et al.   METHODS

Dermatologist-level classification of skin cancer with deep neural networks

(2017) Andre Esteva et al.   NATURE

Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging

(2017) Francesco Cutrale et al.   NATURE METHODS

A subcellular map of the human proteome

(2017) Peter J. Thul et al.   SCIENCE

DiffuserCam: lensless single-exposure 3D imaging

(2017) Nick Antipa et al.   Optica

Automated sub-5 nm image registration in integrated correlative fluorescence and electron microscopy using cathodoluminescence pointers

(2017) Martijn T. Haring et al.   Scientific Reports

DehazeNet: An End-to-End System for Single Image Haze Removal

(2016) Bolun Cai et al.   IEEE TRANSACTIONS ON IMAGE PROCESSING

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

(2016) David Silver et al.   NATURE

Adaptive light-sheet microscopy for long-term, high-resolution imaging in living organisms

(2016) Loïc A Royer et al.   NATURE BIOTECHNOLOGY

Fast live-cell conventional fluorophore nanoscopy with ImageJ through super-resolution radial fluctuations

(2016) Nils Gustafsson et al.   Nature Communications

Deep learning

(2015) Yann LeCun et al.   NATURE

Quantitative evaluation of software packages for single-molecule localization microscopy

(2015) Daniel Sage et al.   NATURE METHODS

Efficient processing and analysis of large-scale light-sheet microscopy data

(2015) Fernando Amat et al.   Nature Protocols

Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics

(2015) D. Li et al.   SCIENCE

Hyperspectral light sheet microscopy

(2015) Wiebke Jahr et al.   Nature Communications

Untwisting the Caenorhabditis elegans embryo

(2015) Ryan Patrick Christensen et al.   eLife

Efficient Bayesian-based multiview deconvolution

(2014) Stephan Preibisch et al.   NATURE METHODS

Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy

(2014) Robert Prevedel et al.   NATURE METHODS

Active torque generation by the actomyosin cell cortex drives left–right symmetry breaking

(2014) Sundar Ram Naganathan et al.   eLife

Structured illumination fluorescence microscopy with distorted excitations using a filtered blind-SIM algorithm

(2013) R. Ayuk et al.   OPTICS LETTERS

Annotated high-throughput microscopy image sets for validation

(2012) Vebjorn Ljosa et al.   NATURE METHODS

Elastic volume reconstruction from series of ultra-thin microscopy sections

(2012) Stephan Saalfeld et al.   NATURE METHODS

Structured illumination microscopy using unknown speckle patterns

(2012) E. Mudry et al.   Nature Photonics

Image Denoising in Mixed Poisson–Gaussian Noise

(2010) F Luisier et al.   IEEE TRANSACTIONS ON IMAGE PROCESSING

QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ

(2010) Ricardo Henriques et al.   NATURE METHODS

Fast live simultaneous multiwavelength four-dimensional optical microscopy

(2010) P. M. Carlton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Patch-Based Nonlocal Functional for Denoising Fluorescence Microscopy Image Sequences

(2009) J. Boulanger et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

Three-Dimensional Resolution Doubling in Wide-Field Fluorescence Microscopy by Structured Illumination

(2008) Mats G.L. Gustafsson et al.   BIOPHYSICAL JOURNAL