A realistic phantom dataset for benchmarking cryo-ET data annotation

IF 32.1 1区生物学 Q1 BIOCHEMICAL RESEARCH METHODS

Nature Methods Pub Date : 2025-08-26 DOI:10.1038/s41592-025-02800-5

Ariana Peck, Yue Yu, Jonathan Schwartz, Anchi Cheng, Utz Heinrich Ermel, Joshua Hutchings, Saugat Kandel, Dari Kimanius, Elizabeth A. Montabana, Daniel Serwas, Hannah Siems, Feng Wang, Zhuowen Zhao, Shawn Zheng, Matthias Haury, David A. Agard, Clinton S. Potter, Bridget Carragher, Kyle Harrington, Mohammadreza Paraan

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引用次数: 0

Abstract

Cryo-electron tomography (cryo-ET) is a powerful technique for imaging molecular complexes in their native cellular environments. However, identifying the vast majority of molecular species in cellular tomograms remains prohibitively difficult. Machine learning (ML) methods provide an opportunity to automate the annotation process, but algorithm development has been hindered by the lack of large, standardized datasets. Here we present an experimental phantom dataset with comprehensive ground-truth annotations for six molecular species to spur new algorithm development and benchmark existing tools. This annotated dataset is available on the CryoET Data Portal with infrastructure to streamline access for methods developers across fields. A standardized, realistic phantom dataset consisting of ground-truth annotations for six diverse molecular species is provided as a community resource for cryo-electron-tomography algorithm benchmarking.

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一个真实的模拟数据集，用于基准测试冷冻- et数据注释。

低温电子断层扫描（cryo-ET）是一种强大的成像分子复合物在其原生细胞环境的技术。然而，在细胞断层扫描中识别绝大多数分子物种仍然非常困难。机器学习（ML）方法提供了自动化注释过程的机会，但由于缺乏大型标准化数据集，算法开发受到阻碍。在这里，我们提出了一个具有六种分子物种的综合ground-truth注释的实验性幻影数据集，以刺激新算法的开发和对现有工具进行基准测试。这个带注释的数据集可以在CryoET数据门户上获得，该门户具有基础设施，可以简化跨领域方法开发人员的访问。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Nature Methods 生物-生化研究方法

CiteScore

58.70

自引率

1.70%

发文量

326

审稿时长

1 months

期刊介绍： Nature Methods is a monthly journal that focuses on publishing innovative methods and substantial enhancements to fundamental life sciences research techniques. Geared towards a diverse, interdisciplinary readership of researchers in academia and industry engaged in laboratory work, the journal offers new tools for research and emphasizes the immediate practical significance of the featured work. It publishes primary research papers and reviews recent technical and methodological advancements, with a particular interest in primary methods papers relevant to the biological and biomedical sciences. This includes methods rooted in chemistry with practical applications for studying biological problems.