U-FISH: a fluorescent spot detector for imaging-based spatial-omics analysis and AI-assisted FISH diagnosis.
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Xu W, Cai H, Zhang Q, Wang Z, Yang J, Wu X, Li C, Cui C, Liu C, He J, Mueller F, Dai J, Hao C, Ouyang W, Cao G
Genome Biol. 26 (1) 261 [2025-09-01; online 2025-09-01]
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.
PubMed 40890868
DOI 10.1186/s13059-025-03736-x
Crossref 10.1186/s13059-025-03736-x
pmc: PMC12400573
pii: 10.1186/s13059-025-03736-x