U-FISH: a fluorescent spot detector for imaging-based spatial-omics analysis and AI-assisted FISH diagnosis
Weize Xu, Huaiyuan Cai, Qian Zhang, Zhengze Wang, Jiajun Yang, Xiaofeng Wu, Chengwen Li, Chenghua Cui, Changzhi Liu, He Jin, Florian Mueller, Jinxia Dai, Hao Chen, Wei Ouyang, Gang Cao
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.