Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows.

IF 36.1 1区生物学 Q1 BIOCHEMICAL RESEARCH METHODS

Nature Methods Pub Date : 2025-04-01 Epub Date: 2025-03-13 DOI:10.1038/s41592-025-02617-2

Sergio Marco Salas, Louis B Kuemmerle, Christoffer Mattsson-Langseth, Sebastian Tismeyer, Christophe Avenel, Taobo Hu, Habib Rehman, Marco Grillo, Paulo Czarnewski, Saga Helgadottir, Katarina Tiklova, Axel Andersson, Nima Rafati, Maria Chatzinikolaou, Fabian J Theis, Malte D Luecken, Carolina Wählby, Naveed Ishaque, Mats Nilsson

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引用次数: 0

Abstract

The Xenium In Situ platform is a new spatial transcriptomics product commercialized by 10x Genomics, capable of mapping hundreds of genes in situ at subcellular resolution. Given the multitude of commercially available spatial transcriptomics technologies, recommendations in choice of platform and analysis guidelines are increasingly important. Herein, we explore 25 Xenium datasets generated from multiple tissues and species, comparing scalability, resolution, data quality, capacities and limitations with eight other spatially resolved transcriptomics technologies and commercial platforms. In addition, we benchmark the performance of multiple open-source computational tools, when applied to Xenium datasets, in tasks including preprocessing, cell segmentation, selection of spatially variable features and domain identification. This study serves as an independent analysis of the performance of Xenium, and provides best practices and recommendations for analysis of such datasets.

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通过质量评估和最佳实践分析工作流程优化 Xenium 原位数据实用性。

Xenium In Situ平台是一种新的空间转录组学产品，由10x Genomics商业化，能够在亚细胞分辨率下原位定位数百个基因。鉴于商业上可获得的空间转录组学技术的众多，在选择平台和分析指南方面的建议越来越重要。在此，我们探索了来自多个组织和物种的25个Xenium数据集，比较了其他8种空间分辨率转录组学技术和商业平台的可扩展性、分辨率、数据质量、容量和局限性。此外，我们对多个开源计算工具的性能进行了基准测试，当应用于Xenium数据集时，包括预处理、细胞分割、空间变量特征选择和域识别。本研究作为Xenium性能的独立分析，并为分析此类数据集提供最佳实践和建议。

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.