AI-driven framework to map the brain metabolome in three dimensions

IF 18.9 1区医学 Q1 ENDOCRINOLOGY & METABOLISM

Nature metabolism Pub Date : 2025-03-18 DOI:10.1038/s42255-025-01242-9

Xin Ma, Cameron J. Shedlock, Terrymar Medina, Roberto A. Ribas, Harrison A. Clarke, Tara R. Hawkinson, Praveen K. Dande, Hari K. R. Golamari, Lei Wu, Borhane EC. Ziani, Sara N. Burke, Matthew E. Merritt, Craig W. Vander Kooi, Matthew S. Gentry, Nirbhay N. Yadav, Li Chen, Ramon C. Sun

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引用次数: 0

Abstract

High-resolution spatial imaging is transforming our understanding of foundational biology. Spatial metabolomics is an emerging field that enables the dissection of the complex metabolic landscape and heterogeneity from a thin tissue section. Currently, spatial metabolism highlights the remarkable complexity in two-dimensional (2D) space and is poised to be extended into the three-dimensional (3D) world of biology. Here we introduce MetaVision3D, a pipeline driven by computer vision, a branch of artificial intelligence focusing on image workflow, for the transformation of serial 2D MALDI mass spectrometry imaging sections into a high-resolution 3D spatial metabolome. Our framework uses advanced algorithms for image registration, normalization and interpolation to enable the integration of serial 2D tissue sections, thereby generating a comprehensive 3D model of unique diverse metabolites across host tissues at submesoscale. As a proof of principle, MetaVision3D was utilized to generate the mouse brain 3D metabolome atlas of normal and diseased animals (available at https://metavision3d.rc.ufl.edu) as an interactive online database and web server to further advance brain metabolism and related research.

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人工智能驱动的框架，以三维方式绘制大脑代谢组

高分辨率空间成像正在改变我们对基础生物学的理解。空间代谢组学是一个新兴的领域，能够从薄组织切片解剖复杂的代谢景观和异质性。目前，空间代谢突出了二维（2D）空间的显著复杂性，并准备扩展到三维（3D）生物学世界。在这里，我们介绍MetaVision3D，一个由计算机视觉驱动的流水线，一个专注于图像工作流的人工智能分支，用于将连续2D MALDI质谱成像切片转换为高分辨率的3D空间代谢组。我们的框架使用先进的算法进行图像配准、归一化和插值，以实现连续二维组织切片的集成，从而在亚中尺度上生成宿主组织中独特多样代谢物的综合3D模型。作为原理验证，利用MetaVision3D生成正常和患病小鼠脑三维代谢组图谱（可在https://metavision3d.rc.ufl.edu上获得），作为交互式在线数据库和web服务器，进一步推进脑代谢及相关研究。

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来源期刊

Nature metabolism ENDOCRINOLOGY & METABOLISM-

CiteScore

27.50

自引率

2.40%

发文量

170

期刊介绍： Nature Metabolism is a peer-reviewed scientific journal that covers a broad range of topics in metabolism research. It aims to advance the understanding of metabolic and homeostatic processes at a cellular and physiological level. The journal publishes research from various fields, including fundamental cell biology, basic biomedical and translational research, and integrative physiology. It focuses on how cellular metabolism affects cellular function, the physiology and homeostasis of organs and tissues, and the regulation of organismal energy homeostasis. It also investigates the molecular pathophysiology of metabolic diseases such as diabetes and obesity, as well as their treatment. Nature Metabolism follows the standards of other Nature-branded journals, with a dedicated team of professional editors, rigorous peer-review process, high standards of copy-editing and production, swift publication, and editorial independence. The journal has a high impact factor, has a certain influence in the international area, and is deeply concerned and cited by the majority of scholars.