ArticleNucleic acids research2021
deepBlink: threshold-independent detection and localization of diffraction-limited spots.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers, 1 of them a synthesis that pooled it.
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Who cites it
24 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Classification of neurodegenerative diseases using brain effective connectivity and machine learning techniques: a systematic review.Frontiers in neurology · 2025Pooled it
- SpotMAX: A generalist framework for multidimensional automatic spot detection and quantification.Science advances · 2026Article
- Imaging-Based Spatial Transcriptomics: Data Interpretation Methods and Biomedical Applications.Biology · 2026Review
- Machine Learning in Single-Molecule Tracking Analysis of Superresolution Optical Microscopy Data.Cells · 2026Review
- The Evolution of Spatial Omics Technologies Introduces A Novel Avenue for Lung Cancer Research.Genomics, proteomics & bioinformatics · 2026Review
- Brain-wide mapping reveals temporal and sexually dimorphic opioid actions.Communications biology · 2026Article
- Live-cell single-vRNP imaging identifies viral gene expression signatures that shape influenza infection heterogeneity.Cell systems · 2026Article
- Applications and development of in situ nucleic acid visualization techniques.Frontiers in bioengineering and biotechnology · 2026Review
- TrueSpot: a robust automated tool for quantifying signal puncta in fluorescent imaging.Genome biology · 2025Article
- U-FISH: a fluorescent spot detector for imaging-based spatial-omics analysis and AI-assisted FISH diagnosis.Genome biology · 2025Article
- Altered cofactor recruitment and nucleosome dynamics underlie bisphenol A's impact on ERα-mediated transcriptional bursting.iScience · 2025Article
- TrueSpot: A robust automated tool for quantifying signal puncta in fluorescent imaging.bioRxiv : the preprint server for biology · 2025Article
- Enhancing ultra-high density single-molecule localization with deep spatiotemporal networks.Biomedical optics express · 2025Article
- Chronic lymphocytic leukemia (CLL) screening and abnormality detection based on multi-layer fluorescence imaging signal enhancement and compensation.Journal of cancer research and clinical oncology · 2025Article
- EASI-ORC: A pipeline for the efficient analysis and segmentation of smFISH images for organelle-RNA colocalization measurements in yeast.Communications biology · 2025Article
- Spatial Transcriptomics in Human Cardiac Tissue.International journal of molecular sciences · 2025Review
- Homebuilt Imaging-Based Spatial Transcriptomics: Tertiary Lymphoid Structures as a Case Example.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Sialic acid and PirB are not required for targeting of neural circuits by neurotropic mammalian orthoreovirus.mSphere · 2024Article
- Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning.Cell systems · 2024Article
- A guidebook of spatial transcriptomic technologies, data resources and analysis approaches.Computational and structural biotechnology journal · 2023Review
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Detection of diffraction-limited spots in single-molecule microscopy images is traditionally performed with mathematical operators designed for idealized spots. This process requires manual tuning of parameters that is time-consuming and not always reliable. We have developed deepBlink, a neural network-based method to detect and localize spots automatically. We demonstrate that deepBlink outperforms other state-of-the-art methods across six publicly available datasets containing synthetic and experimental data.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.