ArticleGenome biology2025
U-FISH: a fluorescent spot detector for imaging-based spatial-omics analysis and AI-assisted FISH diagnosis.
Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
11 citing papers in PubMed.
- Craniofacial development: genetics, signaling pathways, teratogenic mechanisms, and clinal significance.Molecular biomedicine · 2026Review
- From descriptive to generative: foundation-model approaches for spatial transcriptomics.Briefings in bioinformatics · 2026Review
- SpotMAX: A generalist framework for multidimensional automatic spot detection and quantification.Science advances · 2026Article
- Establishing MS2-MCP-based single-molecule RNA visualization in Schizosaccharomyces pombe.Journal of cell science · 2026Article
- Imaging-Based Spatial Transcriptomics: Data Interpretation Methods and Biomedical Applications.Biology · 2026Review
- Large RNA polymerase II condensates are promoter-centric assemblies associated with early stages of transcription at all expressed genes.bioRxiv : the preprint server for biology · 2026Article
- autoFISH: a modular toolbox for sequential single-molecule RNA FISH experiments.Communications biology · 2026Article
- Multimodal AI reading of genetic complexity and residual marrow composition in acute promyelocytic leukemia.Frontiers in immunology · 2026Article
- Enhanced FISH Image Classification via CBAM-PPM-Optimized ResNet50 for Precision Cytogenetic Diagnosis.Sensors (Basel, Switzerland) · 2025Article
- GPU-accelerated, self-optimizing processing for 3D multiplexed iterative RNA-FISH experiments.bioRxiv : the preprint server for biology · 2025Article
- U-FISH: a fluorescent spot detector for imaging-based spatial-omics analysis and AI-assisted FISH diagnosis.Genome biology · 2025Article
Corrections and comments
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Authors and funding
15 authors.
Funding
Abstract
Imaging-based spatial-omics advances biomedical discoveries with subcellular resolution and high sensitivity, but accurately identifying signal spots from diverse images remains challenging. We develop U-FISH, a deep learning method that enhances images for consistent spot detection across various spatial-omics data. We establish a comprehensive FISH image dataset from seven spatial-omics methods. Benchmark analysis shows U-FISH has superior accuracy and generalizability compared to existing methods and can effectively decode 3D FISH data. U-FISH is the first spot detection software integrated with large language models, as demonstrated in AI-assisted diagnostics. Our study provides a valuable tool for spatial-omics analysis and diagnostics.
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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.