Deep learning for cellular image analysis

Reprogramming Cdr2-Dependent Geometry-Based Cell Size Control in Fission Yeast

(2019) Giuseppe Facchetti et al.   CURRENT BIOLOGY

idtracker.ai: tracking all individuals in small or large collectives of unmarked animals

(2019) Francisco Romero-Ferrero et al.   NATURE METHODS

Studying Stem Cell Organization using “Label-Free” Methods and a Novel Generative Adversarial Model

(2018) Gregory Johnson et al.   BIOPHYSICAL JOURNAL

Seeing More: A Future of Augmented Microscopy

(2018) Devin P. Sullivan et al.   CELL

In Silico Labeling: Predicting Fluorescent Labels in Unlabeled Images

(2018) Eric M. Christiansen et al.   CELL

Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk

(2018) Jian Zhou et al.   NATURE GENETICS

High-precision automated reconstruction of neurons with flood-filling networks

(2018) Michał Januszewski et al.   NATURE METHODS

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

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

CellProfiler 3.0: Next-generation image processing for biology

(2018) Claire McQuin et al.   PLOS BIOLOGY

Inferring cell state by quantitative motility analysis reveals a dynamic state system and broken detailed balance

(2018) Jacob C. Kimmel et al.   PLoS Computational Biology

Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes

(2018) Jia-Ren Lin et al.   eLife

Encoding Growth Factor Identity in the Temporal Dynamics of FOXO3 under the Combinatorial Control of ERK and AKT Kinases

(2018) Somponnat Sampattavanich et al.   Cell Systems

Phenotypic Image Analysis Software Tools for Exploring and Understanding Big Image Data from Cell-Based Assays

(2018) Kevin Smith et al.   Cell Systems

Fusion of encoder-decoder deep networks improves delineation of multiple nuclear phenotypes

(2018) Mina Khoshdeli et al.   BMC BIOINFORMATICS

Intelligent Image-Activated Cell Sorting

(2018) Nao Nitta et al.   CELL

A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging

(2018) Leeat Keren et al.   CELL

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

(2018) Devin P Sullivan 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

DeepLabCut: markerless pose estimation of user-defined body parts with deep learning

(2018) Alexander Mathis et al.   NATURE NEUROSCIENCE

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

In Toto Imaging and Reconstruction of Post-Implantation Mouse Development at the Single-Cell Level

(2018) Katie McDole et al.   CELL

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

(2018) Thorsten Falk et al.   NATURE METHODS

Fast animal pose estimation using deep neural networks

(2018) Talmo D. Pereira et al.   NATURE METHODS

A Dataset and a Technique for Generalized Nuclear Segmentation for Computational Pathology

(2017) Neeraj Kumar et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

A survey on deep learning in medical image analysis

(2017) Geert Litjens et al.   MEDICAL IMAGE ANALYSIS

TrackMate: An open and extensible platform for single-particle tracking

(2017) Jean-Yves Tinevez et al.   METHODS

A deep learning and novelty detection framework for rapid phenotyping in high-content screening

(2017) Christoph Sommer et al.   MOLECULAR BIOLOGY OF THE CELL

Automated analysis of high‐content microscopy data with deep learning

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

The Human Cell Atlas: from vision to reality

(2017) Orit Rozenblatt-Rosen et al.   NATURE

Dermatologist-level classification of skin cancer with deep neural networks

(2017) Andre Esteva et al.   NATURE

Data-analysis strategies for image-based cell profiling

(2017) Juan C Caicedo et al.   NATURE METHODS

A general method to fine-tune fluorophores for live-cell and in vivo imaging

(2017) Jonathan B Grimm et al.   NATURE METHODS

Prospective identification of hematopoietic lineage choice by deep learning

(2017) Felix Buggenthin et al.   NATURE METHODS

Machine learning phases of matter

(2017) Juan Carrasquilla et al.   Nature Physics

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

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

seqFISH Accurately Detects Transcripts in Single Cells and Reveals Robust Spatial Organization in the Hippocampus

(2017) Sheel Shah et al.   NEURON

A mixed-scale dense convolutional neural network for image analysis

(2017) Daniël M. Pelt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Visualizing long-term single-molecule dynamics in vivo by stochastic protein labeling

(2017) Hui Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A subcellular map of the human proteome

(2017) Peter J. Thul et al.   SCIENCE

Accurate Classification of Protein Subcellular Localization from High-Throughput Microscopy Images Using Deep Learning

(2017) Tanel Pärnamaa et al.   G3-Genes Genomes Genetics

Deep Learning in Microscopy Image Analysis: A Survey

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

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Deep learning microscopy

(2017) Yair Rivenson et al.   Optica

Automated Training of Deep Convolutional Neural Networks for Cell Segmentation

(2017) Sajith Kecheril Sadanandan et al.   Scientific Reports

Classifying and segmenting microscopy images with deep multiple instance learning

(2016) Oren Z. Kraus et al.   BIOINFORMATICS

SuperSegger: robust image segmentation, analysis and lineage tracking of bacterial cells

(2016) Stella Stylianidou et al.   MOLECULAR MICROBIOLOGY

Deep learning for computational biology

(2016) Christof Angermueller et al.   Molecular Systems Biology

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

(2016) Loïc A Royer et al.   NATURE BIOTECHNOLOGY

Microscopy Image Browser: A Platform for Segmentation and Analysis of Multidimensional Datasets

(2016) Ilya Belevich et al.   PLOS BIOLOGY

Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments

(2016) David A. Van Valen et al.   PLoS Computational Biology

Survey statistics of automated segmentations applied to optical imaging of mammalian cells

(2015) Peter Bajcsy et al.   BMC BIOINFORMATICS

Global Linking of Cell Tracks Using the Viterbi Algorithm

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

Oufti: an integrated software package for high-accuracy, high-throughput quantitative microscopy analysis

(2015) Ahmad Paintdakhi et al.   MOLECULAR MICROBIOLOGY

Artificial intelligence called in to tackle LHC data deluge

(2015) Davide Castelvecchi   NATURE

Deep learning

(2015) Yann LeCun et al.   NATURE

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

A benchmark for comparison of cell tracking algorithms

(2014) Martin Maška et al.   BIOINFORMATICS

High-Sensitivity Measurements of Multiple Kinase Activities in Live Single Cells

(2014) Sergi Regot et al.   CELL

Quantitative imaging of cell dynamics in mouse embryos using light-sheet microscopy

(2014) R. S. Udan et al.   DEVELOPMENT

Multiplexed ion beam imaging of human breast tumors

(2014) Michael Angelo et al.   NATURE MEDICINE

Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data

(2014) Fernando Amat et al.   NATURE METHODS

Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution

(2014) Bi-Chang Chen et al.   SCIENCE

scikit-image: image processing in Python

(2014) Stéfan van der Walt et al.   PeerJ

Encoding and Decoding Cellular Information through Signaling Dynamics

(2013) Jeremy E. Purvis et al.   CELL

Annotated high-throughput microscopy image sets for validation

(2012) Vebjorn Ljosa et al.   NATURE METHODS

OMERO: flexible, model-driven data management for experimental biology

(2012) Chris Allan et al.   NATURE METHODS

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

(2012) Johannes Schindelin et al.   NATURE METHODS

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

Robust Growth of Escherichia coli

(2010) Ping Wang et al.   CURRENT BIOLOGY

Deep, Big, Simple Neural Nets for Handwritten Digit Recognition

(2010) Dan Claudiu Cireşan et al.   NEURAL COMPUTATION

A systematic analysis of performance measures for classification tasks

(2009) Marina Sokolova et al.   INFORMATION PROCESSING & MANAGEMENT

The Pascal Visual Object Classes (VOC) Challenge

(2009) Mark Everingham et al.   INTERNATIONAL JOURNAL OF COMPUTER VISION

Tracking in cell and developmental biology

(2009) Erik Meijering et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Robust single-particle tracking in live-cell time-lapse sequences

(2008) Khuloud Jaqaman et al.   NATURE METHODS

GPU Computing

(2008) J.D. Owens et al.   PROCEEDINGS OF THE IEEE