Artificial intelligence for microscopy: what you should know

SMARCAD1 ATPase activity is required to silence endogenous retroviruses in embryonic stem cells

(2019) Parysatis Sachs et al.   Nature Communications

Not-so-supervised: a survey of semi-supervised, multi-instance, and transfer learning in medical image analysis

(2019) Veronika Cheplygina et al.   MEDICAL IMAGE ANALYSIS

Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software

(2019) Daniel Sage et al.   NATURE METHODS

Defining host–pathogen interactions employing an artificial intelligence workflow

(2019) Daniel Fisch et al.   eLife

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

(2019) Chinmay Belthangady et al.   NATURE METHODS

DLBI: deep learning guided Bayesian inference for structure reconstruction of super-resolution fluorescence microscopy

(2018) Yu Li et al.   BIOINFORMATICS

In Silico Labeling: Predicting Fluorescent Labels in Unlabeled Images

(2018) Eric M. Christiansen et al.   CELL

SRRF: Universal live-cell super-resolution microscopy

(2018) Siân Culley et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Deep learning massively accelerates super-resolution localization microscopy

(2018) Wei Ouyang et al.   NATURE BIOTECHNOLOGY

Quantitative mapping and minimization of super-resolution optical imaging artifacts

(2018) Siân Culley et al.   NATURE METHODS

Automated Deep Learning-Based System to Identify Endothelial Cells Derived from Induced Pluripotent Stem Cells

(2018) Dai Kusumoto et al.   Stem Cell Reports

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

Molecular imaging with neural training of identification algorithm (neural network localization identification)

(2018) A. J. Nelson et al.   MICROSCOPY RESEARCH AND TECHNIQUE

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

(2018) Chawin Ounkomol et al.   NATURE METHODS

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

A survey on deep learning in medical image analysis

(2017) Geert Litjens et al.   MEDICAL IMAGE ANALYSIS

Automated analysis of high‐content microscopy data with deep learning

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

Mastering the game of Go without human knowledge

(2017) David Silver et al.   NATURE

Dermatologist-level classification of skin cancer with deep neural networks

(2017) Andre Esteva et al.   NATURE

Deep Learning: A Primer for Radiologists

(2017) Gabriel Chartrand et al.   RADIOGRAPHICS

In situ click chemistry generation of cyclooxygenase-2 inhibitors

(2017) Atul Bhardwaj et al.   Nature Communications

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

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

Segmentation and classification of colon glands with deep convolutional neural networks and total variation regularization

(2017) Philipp Kainz et al.   PeerJ

Classifying and segmenting microscopy images with deep multiple instance learning

(2016) Oren Z. Kraus et al.   BIOINFORMATICS

Deep learning for computational biology

(2016) Christof Angermueller et al.   Molecular Systems Biology

A Deep Convolutional Neural Network for segmenting and classifying epithelial and stromal regions in histopathological images

(2016) Jun Xu et al.   NEUROCOMPUTING

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

(2016) Nils Gustafsson et al.   Nature Communications

Investigating the Consequences of Interference between Multiple CD8+ T Cell Escape Mutations in Early HIV Infection

(2016) Victor Garcia et al.   PLoS Computational Biology

Ultrastructural Characterization of the Lower Motor System in a Mouse Model of Krabbe Disease

(2016) Valentina Cappello et al.   Scientific Reports

Deep learning

(2015) Yann LeCun et al.   NATURE

CellCognition: time-resolved phenotype annotation in high-throughput live cell imaging

(2010) Michael Held et al.   NATURE METHODS

A Survey on Transfer Learning

(2009) Sinno Jialin Pan et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING