SpotSweeper: spatially aware quality control for spatial transcriptomics.

IF 36.1 1区生物学 Q1 BIOCHEMICAL RESEARCH METHODS

Nature Methods Pub Date : 2025-07-01 Epub Date: 2025-06-06 DOI:10.1038/s41592-025-02713-3

Michael Totty, Stephanie C Hicks, Boyi Guo

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引用次数: 0

Abstract

Quality control (QC) is a crucial step to ensure the reliability of data obtained from RNA sequencing experiments, including spatially resolved transcriptomics (SRT). Existing QC approaches for SRT that have been adopted from single-cell or single-nucleus RNA sequencing methods are confounded by spatial biology and are inappropriate for SRT data. In addition, no methods currently exist for identifying histological tissue artifacts that are unique to SRT. Here, we introduce SpotSweeper, a spatially aware QC method that leverages local neighborhoods to correct for spatial confounding in order to identify both local outliers and regional artifacts in SRT. Using SpotSweeper on publicly available data, we identify a consistent set of Visium barcoded spots as systematically low quality and demonstrate that SpotSweeper accurately identifies two distinct types of regional artifacts. SpotSweeper represents a substantial advancement in spatially resolved transcriptomics QC for SRT, providing a robust, generalizable framework to ensure data reliability across diverse experimental conditions and technologies.

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SpotSweeper：空间转录组学的空间感知质量控制。

质量控制（QC）是确保RNA测序实验（包括空间分辨转录组学（SRT））数据可靠性的关键步骤。现有的SRT质量控制方法采用单细胞或单核RNA测序方法，受空间生物学的影响，不适合SRT数据。此外，目前还没有方法可以识别SRT特有的组织学组织伪影。在这里，我们介绍SpotSweeper，一种空间感知QC方法，它利用局部邻域来纠正空间混淆，以识别SRT中的局部异常值和区域伪影。使用SpotSweeper对公开可用的数据，我们确定了一组一致的Visium条形码点作为系统低质量，并证明SpotSweeper准确地识别了两种不同类型的区域人工制品。SpotSweeper代表了SRT在空间解析转录组学QC方面的重大进步，提供了一个强大的、通用的框架，以确保不同实验条件和技术下数据的可靠性。

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.