Quantitative digital microscopy with deep learning

Fast and Accurate Nanoparticle Characterization Using Deep-Learning-Enhanced Off-Axis Holography

(2021) Benjamin Midtvedt et al.   ACS Nano

Microscopy cell nuclei segmentation with enhanced U-Net

(2020) Feixiao Long   BMC BIOINFORMATICS

DeLTA: Automated cell segmentation, tracking, and lineage reconstruction using deep learning

(2020) Jean-Baptiste Lugagne et al.   PLoS Computational Biology

nucleAIzer: A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer

(2020) Reka Hollandi et al.   Cell Systems

Cut, overlap and locate: a deep learning approach for the 3D localization of particles in astigmatic optical setups

(2020) Simon Franchini et al.   EXPERIMENTS IN FLUIDS

Bright-field holography: cross-modality deep learning enables snapshot 3D imaging with bright-field contrast using a single hologram

(2019) Yichen Wu et al.   Light-Science & Applications

Automatic detection, localization and segmentation of nano-particles with deep learning in microscopy images

(2019) Ayse Betul Oktay et al.   MICRON

Deep learning for cellular image analysis

(2019) Erick Moen et al.   NATURE METHODS

Survey on semantic segmentation using deep learning techniques

(2019) Fahad Lateef et al.   NEUROCOMPUTING

Digital video microscopy enhanced by deep learning

(2019) Saga Helgadottir et al.   Optica

Single-Particle Diffusion Characterization by Deep Learning

(2019) Naor Granik et al.   BIOPHYSICAL JOURNAL

A critique of pure learning and what artificial neural networks can learn from animal brains

(2019) Anthony M. Zador   Nature Communications

Size and Refractive Index Determination of Subwavelength Particles and Air Bubbles by Holographic Nanoparticle Tracking Analysis

(2019) Daniel Midtvedt et al.   ANALYTICAL CHEMISTRY

Deep learning massively accelerates super-resolution localization microscopy

(2018) Wei Ouyang et al.   NATURE BIOTECHNOLOGY

Machine-learning techniques for fast and accurate feature localization in holograms of colloidal particles

(2018) Mark D. Hannel et al.   OPTICS EXPRESS

Advanced Steel Microstructural Classification by Deep Learning Methods

(2018) Seyed Majid Azimi et al.   Scientific Reports

Deep Learning-Based Image Segmentation for Al-La Alloy Microscopic Images

(2018) Boyuan Ma et al.   Symmetry-Basel

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

(2018) Elias Nehme et al.   Optica

Extended depth-of-field in holographic imaging using deep-learning-based autofocusing and phase recovery

(2018) Yichen Wu et al.   Optica

Classification and mutation prediction from non–small cell lung cancer histopathology images using deep learning

(2018) Nicolas Coudray et al.   NATURE MEDICINE

Convolutional neural networks automate detection for tracking of submicron-scale particles in 2D and 3D

(2018) Jay M. Newby et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A deep learning-based algorithm for 2-D cell segmentation in microscopy images

(2018) Yousef Al-Kofahi et al.   BMC BIOINFORMATICS

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

(2018) Thorsten Falk et al.   NATURE METHODS

Three-dimensional localization microscopy using deep learning

(2018) P. Zelger et al.   OPTICS EXPRESS

Accurate Cervical Cell Segmentation from Overlapping Clumps in Pap Smear Images

(2017) Youyi Song et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

Deep Learning Segmentation of Optical Microscopy Images Improves 3-D Neuron Reconstruction

(2017) Rongjian Li et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

Fully Convolutional Networks for Semantic Segmentation

(2017) Evan Shelhamer et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Cell segmentation in histopathological images with deep learning algorithms by utilizing spatial relationships

(2017) Nuh Hatipoglu et al.   MEDICAL & BIOLOGICAL ENGINEERING & COMPUTING

Deep Learning in Microscopy Image Analysis: A Survey

(2017) Fuyong Xing et al.   IEEE Transactions on Neural Networks and Learning Systems

DeepPap: Deep Convolutional Networks for Cervical Cell Classification

(2017) Ling Zhang et al.   IEEE Journal of Biomedical and Health Informatics

Automated Training of Deep Convolutional Neural Networks for Cell Segmentation

(2017) Sajith Kecheril Sadanandan et al.   Scientific Reports

Deep MRI brain extraction: A 3D convolutional neural network for skull stripping

(2016) Jens Kleesiek et al.   NEUROIMAGE

Deep Learning in Label-free Cell Classification

(2016) Claire Lifan Chen et al.   Scientific Reports

Tracking Multiple Particles in Fluorescence Time-Lapse Microscopy Images via Probabilistic Data Association

(2015) William J. Godinez et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

Deep learning

(2015) Yann LeCun et al.   NATURE

A review of progress in single particle tracking: from methods to biophysical insights

(2015) Carlo Manzo et al.   REPORTS ON PROGRESS IN PHYSICS

Objective comparison of particle tracking methods

(2014) Nicolas Chenouard et al.   NATURE METHODS

Precisely and accurately localizing single emitters in fluorescence microscopy

(2014) Hendrik Deschout et al.   NATURE METHODS

Annotated high-throughput microscopy image sets for validation

(2012) Vebjorn Ljosa et al.   NATURE METHODS

Rapid, accurate particle tracking by calculation of radial symmetry centers

(2012) Raghuveer Parthasarathy   NATURE METHODS

Position and orientation estimation of fixed dipole emitters using an effective Hermite point spread function model

(2012) Sjoerd Stallinga et al.   OPTICS EXPRESS

Fast Fourier domain localization algorithm of a single molecule with nanometer precision

(2011) Bin Yu et al.   OPTICS LETTERS

Probing cellular events, one quantum dot at a time

(2010) Fabien Pinaud et al.   NATURE METHODS

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

(2010) Sjoerd Stallinga et al.   OPTICS EXPRESS

Single-particle tracking methods for the study of membrane receptors dynamics

(2009) Damien Alcor et al.   EUROPEAN JOURNAL OF NEUROSCIENCE

Quantitative study of single molecule location estimation techniques

(2009) Anish V. Abraham et al.   OPTICS EXPRESS