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<p>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.</p>

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U-FISH: a fluorescent spot detector for imaging-based spatial-omics analysis and AI-assisted FISH diagnosis

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年9月1日

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  • Weize Xu,
  • Huaiyuan Cai,
  • Qian Zhang,
  • Zhengze Wang,
  • Jiajun Yang,
  • Xiaofeng Wu,
  • Chengwen Li,
  • Chenghua Cui,
  • Changzhi Liu,
  • Jin He,
  • Florian Mueller,
  • Jinxia Dai,
  • Chen Hao,
  • Wei Ouyang,
  • Gang Cao

摘要

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.