Research graph
References from From Pixels to Discovery: Microscopy Image Analysis in the Age of Artificial Intelligence. Local targets link to admitted publications; unresolved targets remain external evidence.
A review of uncertainty quantification in deep learning: techniques, applications and challenges
10.1016/j.inffus.2021.05.008 · 2021 · External reference
CellSighter: a neural network to classify cells in highly multiplexed images
10.1038/s41467-023-40066-7 · 2023 · External reference
Segment anything for microscopy
10.1038/s41592-024-02580-4 · 2025 · External reference
Computational principles and challenges in single-cell data integration
10.1038/s41587-021-00895-7 · 2021 · External reference
Multi-omics factor analysis—a framework for unsupervised integration of multi-omics data sets
2018 · External reference
LABKIT: labeling and segmentation toolkit for big image data
10.3389/fcomp.2022.777728 · 2022 · External reference
Microplit: semantic unmixing of fluorescent microscopy data
2025 · External reference
denoiSplit: a method for joint microscopy image splitting and unsupervised denoising
2025 · External reference
Deep learning-enabled virtual histological staining of biological samples
10.1038/s41377-023-01104-7 · 2023 · External reference
Red blood cell image generation for data augmentation using conditional generative adversarial networks
2019 · External reference
Enabling global image data sharing in the life sciences
10.1038/s41592-024-02585-z · 2025 · External reference
Generative adversarial networks for augmenting training data of microscopic cell images
10.3389/fcomp.2019.00010 · 2019 · External reference
Autoencoders
2023 · External reference
ilastik: interactive machine learning for (bio)image analysis
10.1038/s41592-019-0582-9 · 2019 · External reference
Multimodal bioimaging across disciplines and scales: challenges, opportunities and breaking down barriers
10.1038/s44303-024-00010-w · 2024 · External reference
Unresolved reference
2024 · External reference
The perception-distortion tradeoff
2018 · External reference
Combining labeled and unlabeled data with co-training
1998 · External reference
Content aware image restoration improves spatiotemporal resolution in luminescence imaging
10.1038/s42003-023-04886-z · 2023 · External reference
Ultrack: pushing the limits of cell tracking across biological scales
10.1038/s41592-025-02778-0 · 2025 · External reference
Random forests
10.1023/a:1010933404324 · 2001 · External reference
Cryo-CARE: content-aware image restoration for cryo-transmission electron microscopy data
2019 · External reference
MicroVQA: a multimodal reasoning benchmark for microscopy-based scientific research
2025 · External reference
Data-analysis strategies for image-based cell profiling
10.1038/nmeth.4397 · 2017 · External reference
Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl
10.1038/s41592-019-0612-7 · 2019 · External reference
SAM 3: segment anything with concepts
2025 · External reference
Light-sheet microscopy of cleared tissues with isotropic, subcellular resolution
10.1038/s41592-019-0615-4 · 2019 · External reference
Image-based profiling for drug discovery: due for a machine-learning upgrade?
10.1038/s41573-020-00117-w · 2021 · External reference
Universal light-sheet generation with field synthesis
10.1038/s41592-019-0327-9 · 2019 · External reference
Towards a general-purpose foundation model for computational pathology
10.1038/s41591-024-02857-3 · 2024 · External reference
A simple framework for contrastive learning of visual representations
2020 · External reference
In silico labeling: predicting fluorescent labels in unlabeled images
10.1016/j.cell.2018.03.040 · 2018 · External reference
The crucial role of bioimage analysts in scientific research and publication
10.1242/jcs.262322 · 2024 · External reference
Support-vector networks
10.1023/a:1022627411411 · 1995 · External reference
Towards multimodal foundation models in molecular cell biology
10.1038/s41586-025-08710-y · 2025 · External reference
Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation
10.1038/s41592-022-01639-4 · 2022 · External reference
Approximation by superpositions of a sigmoidal function
10.1007/bf02551274 · 1989 · External reference
Using AI in bioimage analysis to elevate the rate of scientific discovery as a community
10.1038/s41592-023-01929-5 · 2023 · External reference
Isotropic imaging across spatial scales with axially swept light-sheet microscopy
10.1038/s41596-022-00706-6 · 2022 · External reference
Scaling vision transformers to 22 billion parameters
2023 · External reference
MorphGen: controllable and morphologically plausible generative cell-imaging
2025 · External reference
The HaloTag as a general scaffold for far-red tunable chemigenetic indicators
10.1038/s41589-021-00775-w · 2021 · External reference
Better research software tools to elevate the rate of scientific discovery or why we need to invest in research software engineering
10.3389/fbinf.2023.1255159 · 2023 · External reference
Objective assessment of stored blood quality by deep learning
10.1073/pnas.2001227117 · 2020 · External reference
Multi-layered maps of neuropil with segmentation-guided contrastive learning
10.1038/s41592-023-02059-8 · 2023 · External reference
Unbiased single-cell morphology with self-supervised vision transformers
2023 · External reference
An image is worth 16x16 words: transformers for image recognition at scale
2020 · External reference
The importance of skip connections in biomedical image segmentation
2016 · External reference
A call for public archives for biological image data
10.1038/s41592-018-0195-8 · 2018 · External reference
Unresolved reference
2018 · External reference
A model zoo of vision transformers
2025 · External reference
U-Net: deep learning for cell counting, detection, and morphometry
10.1038/s41592-018-0261-2 · 2019 · External reference
A comparison of data-driven shape quantification methods for 2D microscopy images
External reference
ShapeEmbed: a self-supervised learning framework for 2D contour quantification
External reference
TRACKASTRA: transformer-based cell tracking for live-cell microscopy
2025 · External reference
In focus: data management and data analysis in microscopy
10.1007/s00418-023-02226-0 · 2023 · External reference
Unresolved reference
2016 · External reference
Blessing of dimensionality: mathematical foundations of the statistical physics of data
10.1098/rsta.2017.0237 · 2018 · External reference
On calibration of modern neural networks
2017 · External reference
SubCell: proteome-aware vision foundation models for microscopy capture single-cell biology
2024 · External reference
Benchmarking large language models for bio-image analysis code generation
2024 · External reference
The BioImage Archive – building a home for life-sciences microscopy data
10.1016/j.jmb.2022.167505 · 2022 · External reference
Unresolved reference
2009 · External reference
UNETR: transformers for 3D medical image segmentation
2022 · External reference
Masked autoencoders are scalable vision learners
2022 · External reference
Momentum contrast for unsupervised visual representation learning
2020 · External reference
Deep residual learning for image recognition
2016 · External reference
Localization atomic force microscopy
10.1038/s41586-021-03551-x · 2021 · External reference
Decoding life's inner workings: advances in quantitative bioimaging
10.1098/rsob.230329 · 2023 · External reference
The promise and peril of deep learning in microscopy
10.1038/s41592-020-01035-w · 2021 · External reference
An introduction to flow matching and diffusion models
2025 · External reference
LoRA: low-rank adaptation of large language models
2021 · External reference
Kernel density steering: inference-time scaling via mode seeking for image restoration
2025 · External reference
Aleatoric and epistemic uncertainty in machine learning: an introduction to concepts and methods
10.1007/s10994-021-05946-3 · 2021 · External reference
Has it all been solved?
2023 · External reference
10.1038/s41592-020-01008-z · 2021 · Admitted local publication
nnInteractive: redefining 3D promptable segmentation
2025 · External reference
Fully unsupervised deep mode of action learning for phenotyping high-content cellular images
10.1093/bioinformatics/btab497 · 2021 · External reference
High-precision automated reconstruction of neurons with flood-filling networks
10.1038/s41592-018-0049-4 · 2018 · External reference
What is the best multi-stage architecture for object recognition?
2009 · External reference
Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and exchange-PAINT
10.1038/nmeth.2835 · 2014 · External reference
10.1038/s41746-019-0096-y · 2019 · Admitted local publication
Semi-supervised learning with deep generative models
2014 · External reference
Reexamining the aleatoric and epistemic uncertainty dichotomy
2025 · External reference
Segment anything
2023 · External reference
Self-supervised deep learning encodes high-resolution features of protein subcellular localization
10.1038/s41592-022-01541-z · 2022 · External reference
Big Transfer (BiT): general visual representation learning
2020 · External reference
Masked autoencoders for microscopy are scalable learners of cellular biology
2024 · External reference
ImageNet classification with deep convolutional neural networks
10.1145/3065386 · 2017 · External reference
Connectome-constrained networks predict neural activity across the fly visual system
10.1038/s41586-024-07939-3 · 2024 · External reference
Deep learning
10.1038/nature14539 · 2015 · External reference
Backpropagation applied to handwritten zip code recognition
10.1162/neco.1989.1.4.541 · 1989 · External reference
Gradient-based learning applied to document recognition
10.1109/5.726791 · 1998 · External reference
Octopi 2.0: open and scalable microscopy platform for AI-powered diagnostic applications
2025 · External reference
Microscopy image reconstruction with physics-informed denoising diffusion probabilistic model
10.1038/s44172-024-00331-z · 2024 · External reference
Feature Pyramid Networks for object detection
2017 · External reference
Flow matching for generative modeling
2022 · External reference
Bayesian deep-learning structured illumination microscopy enables reliable super-resolution imaging with uncertainty quantification
10.1038/s41467-025-60093-w · 2025 · External reference
Robust virtual staining of landmark organelles with Cytoland
10.1038/s42256-025-01046-2 · 2025 · External reference
Annotated high-throughput microscopy image sets for validation
10.1038/nmeth.2083 · 2012 · External reference
HaloTag: a novel protein labeling technology for cell imaging and protein analysis
10.1021/cb800025k · 2008 · External reference
Open-source deep-learning software for bioimage segmentation
10.1091/mbc.e20-10-0660 · 2021 · External reference
Pretraining a foundation model for generalizable fluorescence microscopy-based image restoration
10.1038/s41592-024-02244-3 · 2024 · External reference
The multimodality cell segmentation challenge: toward universal solutions
10.1038/s41592-024-02233-6 · 2024 · External reference
Petascale neural circuit reconstruction: automated methods
2021 · External reference
Event-driven acquisition for content-enriched microscopy
10.1038/s41592-022-01589-x · 2022 · External reference
Why rankings of biomedical image analysis competitions should be interpreted with care
10.1038/s41467-018-07619-7 · 2018 · External reference
Metrics reloaded: recommendations for image analysis validation
10.1038/s41592-023-02151-z · 2024 · External reference
Wisdom of crowds for robust gene network inference
10.1038/nmeth.2016 · 2012 · External reference
All biology is computational biology
10.1371/journal.pbio.2002050 · 2017 · External reference
The Cell Tracking Challenge: 10 years of objective benchmarking
10.1038/s41592-023-01879-y · 2023 · External reference
A benchmark for comparison of cell tracking algorithms
10.1093/bioinformatics/btu080 · 2014 · External reference
In toto imaging and reconstruction of post-implantation mouse development at the single-cell level
10.1016/j.cell.2018.09.031 · 2018 · External reference
UMAP: Uniform Manifold Approximation and Projection
10.21105/joss.00861 · 2018 · External reference
Challenges in applying the EU AI act research exemptions to contemporary AI research
10.1038/s41746-025-02263-0 · 2026 · External reference
Functional connectomics spanning multiple areas of mouse visual cortex
10.1038/s41586-025-08790-w · 2025 · External reference
Why bioimage informatics matters
10.1038/nmeth.2024 · 2012 · External reference
DINOv2: learning robust visual features without supervision
2023 · External reference
Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy
10.1038/s41592-018-0111-2 · 2018 · External reference
BioImage Model Zoo: a community-driven resource for accessible deep learning in bioimage analysis
2022 · External reference
Can you trust your model's uncertainty? Evaluating predictive uncertainty under dataset shift
2019 · External reference
Cellpose-SAM: superhuman generalization for cellular segmentation
2025 · External reference
Cellpose 2.0: how to train your own model
10.1038/s41592-022-01663-4 · 2022 · External reference
Predicting cell morphological responses to perturbations using generative modeling
10.1038/s41467-024-55707-8 · 2025 · External reference
Equivariant bootstrapping for uncertainty quantification in imaging inverse problems
2024 · External reference
Improving reproducibility in machine learning research (a report from the NeurIPS 2019 reproducibility program)
2021 · External reference
Petascale pipeline for precise alignment of images from serial section electron microscopy
10.1038/s41467-023-44354-0 · 2024 · External reference
Brillouin microscopy: an emerging tool for mechanobiology
10.1038/s41592-019-0543-3 · 2019 · External reference
HazeMatching: dehazing light microscopy images with guided conditional flow matching
External reference
ResMatching: noise-resilient computational super-resolution via guided conditional flow matching
External reference
The ethics of using artificial intelligence in scientific research: new guidance needed for a new tool
10.1007/s43681-024-00493-8 · 2025 · External reference
Cellpose as a reliable method for single-cell segmentation of autofluorescence microscopy images
10.1038/s41598-024-82639-6 · 2025 · External reference
Antoni van Leeuwenhoek 1723–2023: a review to commemorate Van Leeuwenhoek's death, 300 years ago
10.1007/s10482-023-01859-4 · 2023 · External reference
High-resolution image synthesis with latent diffusion models
2022 · External reference
U-Net: convolutional networks for biomedical image segmentation
2015 · External reference
The perceptron: a probabilistic model for information storage and organization in the brain
10.1037/h0042519 · 1958 · External reference
Omega — harnessing the power of large language models for bioimage analysis
10.1038/s41592-024-02310-w · 2024 · External reference
Learning representations by back-propagating errors
10.1038/323533a0 · 1986 · External reference
A versatile oblique plane microscope for large-scale and high-resolution imaging of subcellular dynamics
10.7554/elife.57681 · 2020 · External reference
A connectome and analysis of the adult Drosophila central brain
10.7554/elife.57443 · 2020 · External reference
Whole-brain annotation and multi-connectome cell typing of Drosophila
10.1038/s41586-024-07686-5 · 2024 · External reference
A practical guide to bioimaging research data management in core facilities
10.1111/jmi.13317 · 2024 · External reference
Cell detection with star-convex polygons
2018 · External reference
Community-developed checklists for publishing images and image analyses
10.1038/s41592-023-01987-9 · 2024 · External reference
Inhibitory specificity from a connectomic census of mouse visual cortex
10.1038/s41586-024-07780-8 · 2025 · External reference
Model zoos: a dataset of diverse populations of neural network models
2022 · External reference
FeatureForest: the power of foundation models, the usability of random forests
10.1038/s44303-025-00089-9 · 2025 · External reference
The unreasonable effectiveness of deep learning in artificial intelligence
10.1073/pnas.1907373117 · 2020 · External reference
MAPS: pathologist-level cell type annotation from tissue images through machine learning
10.1038/s41467-023-44188-w · 2024 · External reference
Application of artificial intelligence and digital tools in cancer pathology
10.1016/j.landig.2025.100933 · 2025 · External reference
A survey on image data augmentation for deep learning
10.1186/s40537-019-0197-0 · 2019 · External reference
Live-cell imaging powered by computation
10.1038/s41580-024-00702-6 · 2024 · External reference
Ladder variational autoencoders
2016 · External reference
Score-based generative modeling through stochastic differential equations
2020 · External reference
Statistical significance for genomewide studies
10.1073/pnas.1530509100 · 2003 · External reference
Benchmarking cellular segmentation methods against Cellpose
2024 · External reference
Cellpose: a generalist algorithm for cellular segmentation
10.1038/s41592-020-01018-x · 2021 · External reference
Energy and policy considerations for modern deep learning research
2020 · External reference
Mean teachers are better role models: Weight-averaged consistency targets improve semi-supervised deep learning results
2017 · External reference
Parameter efficient fine-tuning of Segment Anything Model for biomedical imaging
2025 · External reference
Speed up neural network learning by GPGPU
2011 · External reference
Making the most of bioimaging data through interdisciplinary interactions
10.1242/jcs.262139 · 2024 · External reference
NVAE: a deep hierarchical variational autoencoder
2020 · External reference
Joint embedding versus reconstruction: provable benefits of latent space prediction for self supervised learning
2025 · External reference
Visualizing data using t-SNE
2008 · External reference
Attention is all you need
2017 · External reference
A foundation model for clinical-grade computational pathology and rare cancers detection
10.1038/s41591-024-03141-0 · 2024 · External reference
Methods for segmentation and classification of digital microscopy tissue images
10.3389/fbioe.2019.00053 · 2019 · External reference
Object detection networks and augmented reality for cellular detection in fluorescence microscopy
10.1083/jcb.201903166 · 2020 · External reference
Scientific discovery in the age of artificial intelligence
10.1038/s41586-023-06221-2 · 2023 · External reference
Prediction of cellular morphology changes under perturbations with a transcriptome-guided diffusion model
10.1038/s41467-025-63478-z · 2025 · External reference
A pathology foundation model for cancer diagnosis and prognosis prediction
10.1038/s41586-024-07894-z · 2024 · External reference
A field guide to cultivating computational biology
10.1371/journal.pbio.3001419 · 2021 · External reference
Nuclei instance segmentation and classification in histopathology images with StarDist
2022 · External reference
Content-aware image restoration: pushing the limits of fluorescence microscopy
10.1038/s41592-018-0216-7 · 2018 · External reference
Star-convex polyhedra for 3D object detection and segmentation in microscopy
2020 · External reference
AI-powered virtual tissues from spatial proteomics for clinical diagnostics and biomedical discovery
2025 · External reference
SegFormer: simple and efficient design for semantic segmentation with transformers
2021 · External reference
Instant super-resolution imaging in live cells and embryos via analog image processing
10.1038/nmeth.2687 · 2013 · External reference
AI governance in a complex and rapidly changing regulatory landscape: a global perspective
10.1057/s41599-024-03560-x · 2024 · External reference
Scaling vision transformers
2022 · External reference
Conditional image synthesis with diffusion models: a survey
2025 · External reference
Photoswitchable fluorescent proteins: ten years of colorful chemistry and exciting applications
10.1016/j.cbpa.2013.05.031 · 2013 · External reference
MorphoFeatures for unsupervised exploration of cell types, tissues, and organs in volume electron microscopy
10.7554/elife.80918 · 2023 · External reference
MIFA: metadata, incentives, formats and accessibility guidelines to improve the reuse of AI datasets for bioimage analysis
10.1038/s41592-025-02835-8 · 2025 · External reference
