U-FISH：用于基于成像的空间组学分析和人工智能辅助FISH诊断的荧光点检测器

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2025-09-01 DOI:10.1186/s13059-025-03736-x

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

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引用次数: 0

摘要

基于成像的空间组学以亚细胞分辨率和高灵敏度推进生物医学发现，但从不同图像中准确识别信号点仍然具有挑战性。我们开发了U-FISH，这是一种深度学习方法，可以增强图像，以便在各种空间组学数据中进行一致的斑点检测。我们利用7种空间组学方法建立了一个完整的FISH图像数据集。基准分析表明，与现有方法相比，U-FISH具有更高的精度和通用性，可以有效地解码三维FISH数据。U-FISH是第一个集成了大型语言模型的现场检测软件，在人工智能辅助诊断中得到了证明。我们的研究为空间组学分析和诊断提供了一个有价值的工具。

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

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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来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

期刊介绍： Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.