Kummerfeld Erich, Williams Leland, Wang Yinzhao, Peters Samuel T, Schmidt Elizabeth, DuFresne-To Mickayla, Bernlohr David, Robbins Paul, Ikramuddin Sayeed, Adeyi Oyedele, Laux Linshan, Barthel Grant, Johnson Steven, Wang Jinhua, Niedernhofer Laura, Nelson Andrew, Aliferis Constantin
Institute for Health Informatics, University of Minnesota, 8-101 Phillips-Wangensteen Building, 516 Delaware St. SE, Minneapolis, MN 55455, United States.
Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Ave, St Paul, MN 55108, United States.
Brief Bioinform. 2025 Jul 2;26(4). doi: 10.1093/bib/bbaf306.
Data artifacts may induce errors in findings from any spatial transcriptomics platform. To provide protection from these errors, we have developed Border, Location, and edge Artifact DEtection (BLADE). BLADE is a novel collection of automated cross-platform statistical methods for detecting and removing three types of artifacts: (i) border effects, where total gene reads is modified at the border of the capture area; (ii) tissue edge effects, where total gene reads is modified at the edge of the tissue; (iii) location batch malfunctions, where there is a zone in the same location on all slides in a batch with substantially decreased sequencing depth. These artifacts are not mutually exclusive. BLADE has been applied to both Visium and CosMx data, and was used to evaluate our library of 37 10x Visium samples of liver and adipose tissue from humans and mice. Artifacts were found to be both common and impactful in those samples, indicating that artifact detection methods are critical for spatial transcriptomics quality control. Our BLADE software is publicly available.
数据伪影可能会在任何空间转录组学平台的研究结果中引发错误。为了防止这些错误，我们开发了边界、位置和边缘伪影检测（BLADE）方法。BLADE是一种新颖的自动化跨平台统计方法集合，用于检测和去除三种类型的伪影：（i）边界效应，即捕获区域边界处的总基因读数被修改；（ii）组织边缘效应，即组织边缘处的总基因读数被修改；（iii）位置批次故障，即一批中所有载玻片上同一位置存在测序深度大幅降低的区域。这些伪影并非相互排斥。BLADE已应用于Visium和CosMx数据，并用于评估我们包含37个来自人类和小鼠肝脏及脂肪组织的10x Visium样本的文库。在这些样本中发现伪影既常见又有影响，这表明伪影检测方法对于空间转录组学质量控制至关重要。我们的BLADE软件已公开可用。
