A survey on applications of deep learning in microscopy image analysis

Microscopy cell nuclei segmentation with enhanced U-Net

(2020) Feixiao Long   BMC BIOINFORMATICS

Automatic segmentation of mitochondria and endolysosomes in volumetric electron microscopy data

(2020) Manca Žerovnik Mekuč et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Deep Learning‐Based Single‐Cell Optical Image Studies

(2020) Jing Sun et al.   CYTOMETRY PART A

Deep Learning Models for Classification of Red Blood Cells in Microscopy Images to Aid in Sickle Cell Anemia Diagnosis

(2020) Laith Alzubaidi et al.   Electronics

Rapid Antibiotic Susceptibility Testing Based on Bacterial Motion Patterns With Long Short- Term Memory Neural Networks

(2020) Rafael Iriya et al.   IEEE SENSORS JOURNAL

Development of fan‐shaped tracker for single particle tracking

(2020) Luhong Jin et al.   MICROSCOPY RESEARCH AND TECHNIQUE

Deep learning enables structured illumination microscopy with low light levels and enhanced speed

(2020) Luhong Jin et al.   Nature Communications

Fluorescence microscopy tensor imaging representations for large-scale dataset analysis

(2020) Claudio Vinegoni et al.   Scientific Reports

Test-time augmentation for deep learning-based cell segmentation on microscopy images

(2020) Nikita Moshkov et al.   Scientific Reports

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

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

Deep Reinforcement Learning for Data Association in Cell Tracking

(2020) Junjie Wang et al.   Frontiers in Bioengineering and Biotechnology

Instance-Level Microtubule Tracking

(2020) Samira Masoudi et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

A Bird’s-Eye View of Deep Learning in Bioimage Analysis

(2020) Erik Meijering   Computational and Structural Biotechnology Journal

Weakly Supervised Cell Segmentation by Point Annotation

(2020) Tianyi Zhao et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

A Novel Deep Learning based Framework for the Detection and Classification of Breast Cancer Using Transfer Learning

(2019) SanaUllah Khan et al.   PATTERN RECOGNITION LETTERS

Deep learning for cell image segmentation and ranking

(2019) Flávio H.D. Araújo et al.   COMPUTERIZED MEDICAL IMAGING AND GRAPHICS

Deep learning for cellular image analysis

(2019) Erick Moen et al.   NATURE METHODS

Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images

(2019) Juan C. Caicedo et al.   CYTOMETRY PART A

Assessing micrometastases as a target for nanoparticles using 3D microscopy and machine learning

(2019) Benjamin R. Kingston et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Machine Learning in Medical Imaging

(2019) Qian Wang et al.   IEEE Journal of Biomedical and Health Informatics

GRUU-Net: Integrated convolutional and gated recurrent neural network for cell segmentation

(2019) T. Wollmann et al.   MEDICAL IMAGE ANALYSIS

Phasetime: Deep Learning Approach to Detect Nuclei in Time Lapse Phase Images

(2019) Pengyu Yuan et al.   Journal of Clinical Medicine

Mutual Information based hybrid model and deep learning for Acute Lymphocytic Leukemia detection in single cell blood smear images

(2019) Krishna Kumar Jha et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

Cell mitosis event analysis in phase contrast microscopy images using deep learning

(2019) Yunxiang Mao et al.   MEDICAL IMAGE ANALYSIS

Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl

(2019) Juan C. Caicedo et al.   NATURE METHODS

Three-dimensional virtual refocusing of fluorescence microscopy images using deep learning

(2019) Yichen Wu et al.   NATURE METHODS

Democratized image analytics by visual programming through integration of deep models and small-scale machine learning

(2019) Primož Godec et al.   Nature Communications

Video-rate multi-color structured illumination microscopy with simultaneous real-time reconstruction

(2019) Andreas Markwirth et al.   Nature Communications

Deep-Learning-Based Segmentation of Small Extracellular Vesicles in Transmission Electron Microscopy Images

(2019) Estibaliz Gómez-de-Mariscal et al.   Scientific Reports

Cell Type Classification and Unsupervised Morphological Phenotyping From Low-Resolution Images Using Deep Learning

(2019) Kai Yao et al.   Scientific Reports

Particle Mobility Analysis Using Deep Learning and the Moment Scaling Spectrum

(2019) Marloes Arts et al.   Scientific Reports

A Multi-Organ Nucleus Segmentation Challenge

(2019) Neeraj Kumar et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

In Silico Labeling: Predicting Fluorescent Labels in Unlabeled Images

(2018) Eric M. Christiansen et al.   CELL

Fine-grained leukocyte classification with deep residual learning for microscopic images

(2018) Feiwei Qin et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

Learning to transfer microscopy image modalities

(2018) Liang Han et al.   MACHINE VISION AND APPLICATIONS

Deep learning massively accelerates super-resolution localization microscopy

(2018) Wei Ouyang et al.   NATURE BIOTECHNOLOGY

Deep learning advances super-resolution imaging

(2018) Rita Strack   NATURE METHODS

Real-time 3D single-molecule localization using experimental point spread functions

(2018) Yiming Li et al.   NATURE METHODS

Quanti.us: a tool for rapid, flexible, crowd-based annotation of images

(2018) Alex J. Hughes et al.   NATURE METHODS

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

(2018) Elias Nehme et al.   Optica

Segmentation of Nuclei in Histopathology Images by deep regression of the distance map

(2018) Peter Naylor et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

Deep learning in biomedicine

(2018) Michael Wainberg et al.   NATURE BIOTECHNOLOGY

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

(2018) Nicolas Coudray et al.   NATURE MEDICINE

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

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

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

(2018) Chawin Ounkomol et al.   NATURE METHODS

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

Classification of mice hepatic granuloma microscopic images based on a deep convolutional neural network

(2018) Yu Wang et al.   APPLIED SOFT COMPUTING

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

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

Guided by Light: Optical Control of Microtubule Gliding Assays

(2018) Roderick P. Tas et al.   NANO LETTERS

High-performance medicine: the convergence of human and artificial intelligence

(2018) Eric J. Topol   NATURE MEDICINE

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

Three-dimensional localization microscopy using deep learning

(2018) P. Zelger et al.   OPTICS EXPRESS

A machine learning approach for online automated optimization of super-resolution optical microscopy

(2018) Audrey Durand et al.   Nature Communications

Automatic Mitochondria Segmentation for EM Data Using a 3D Supervised Convolutional Network

(2018) Chi Xiao et al.   Frontiers in Neuroanatomy

Micro-Net: A unified model for segmentation of various objects in microscopy images

(2018) Shan E Ahmed Raza et al.   MEDICAL IMAGE ANALYSIS

Large-Scale Multi-Class Image-Based Cell Classification With Deep Learning

(2018) Nan Meng et al.   IEEE Journal of Biomedical and Health Informatics

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

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

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

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

Analysis of live cell images: Methods, tools and opportunities

(2017) Thomas A. Nketia et al.   METHODS

Deep Learning Segmentation for Epifluorescence Microscopy Images

(2017) Yasmin M. Kassim et al.   MICROSCOPY AND MICROANALYSIS

Automated analysis of high‐content microscopy data with deep learning

(2017) Oren Z Kraus et al.   Molecular Systems Biology

An objective comparison of cell-tracking algorithms

(2017) Vladimír Ulman et al.   NATURE METHODS

Stem cell motion-tracking by using deep neural networks with multi-output

(2017) Yangxu Wang et al.   NEURAL COMPUTING & APPLICATIONS

High-resolution 3D reconstruction of microtubule structures by quantitative multi-angle total internal reflection fluorescence microscopy

(2017) Luhong Jin et al.   OPTICS COMMUNICATIONS

Imaging and reconstruction of cell cortex structures near the cell surface

(2017) Luhong Jin et al.   OPTICS COMMUNICATIONS

Classification of C2C12 cells at differentiation by convolutional neural network of deep learning using phase contrast images

(2017) Hirohiko Niioka et al.   Human Cell

Deep Learning in Microscopy Image Analysis: A Survey

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

LSTM: A Search Space Odyssey

(2017) Klaus Greff et al.   IEEE Transactions on Neural Networks and Learning Systems

White blood cells identification system based on convolutional deep neural learning networks

(2017) A.I. Shahin et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

Topography of Cells Revealed by Variable-Angle Total Internal Reflection Fluorescence Microscopy

(2016) Marcelina Cardoso Dos Santos et al.   BIOPHYSICAL JOURNAL

Photometry unlocks 3D information from 2D localization microscopy data

(2016) Christian Franke et al.   NATURE METHODS

Deep Learning in Label-free Cell Classification

(2016) Claire Lifan Chen et al.   Scientific Reports

SPED Light Sheet Microscopy: Fast Mapping of Biological System Structure and Function

(2015) Raju Tomer et al.   CELL

Intact-Brain Analyses Reveal Distinct Information Carried by SNc Dopamine Subcircuits

(2015) Talia N. Lerner et al.   CELL

Global Linking of Cell Tracks Using the Viterbi Algorithm

(2015) Klas E. G. Magnusson et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

High-Speed Tracking with Kernelized Correlation Filters

(2015) Joao F. Henriques et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging

(2014) Martin Ovesný et al.   BIOINFORMATICS

Efficient Bayesian-based multiview deconvolution

(2014) Stephan Preibisch et al.   NATURE METHODS

Brain-wide 3D imaging of neuronal activity in Caenorhabditis elegans with sculpted light

(2013) Tina Schrödel et al.   NATURE METHODS

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

3-D Reconstruction of Microtubules From Multi-Angle Total Internal Reflection Fluorescence Microscopy Using Bayesian Framework

(2011) Qian Yang et al.   IEEE TRANSACTIONS ON IMAGE PROCESSING

Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging

(2011) Graham T Dempsey et al.   NATURE METHODS

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

(2010) Ricardo Henriques et al.   NATURE METHODS

Quantitative study of single molecule location estimation techniques

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

Three-dimensional sub–100 nm resolution fluorescence microscopy of thick samples

(2008) Manuel F Juette et al.   NATURE METHODS