Quality Control for Single Cell Analysis of High-plex Tissue Profiles using CyLinter.
Quality Control for Single Cell Analysis of High-plex Tissue Profiles using CyLinter.
复制标题
使用 CyLinter 对高复合组织概况进行单细胞分析的质量控制。
DOI：
10.1101/2023.11.01.565120
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发表时间：
2024
期刊：
影响因子：
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通讯作者：
Sorger,PeterK
中科院分区：
文献类型：
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作者：
Baker,GregoryJ;Novikov,Edward;Zhao,Ziyuan;Vallius,Tuulia;Davis,JanaeA;Lin,Jia-Ren;Muhlich,JeremyL;Mittendorf,ElizabethA;Santagata,Sandro;Guerriero,JenniferL;Sorger,PeterK
肿瘤是从微米到厘米的空间尺度上形成的细胞和非细胞结构的复杂集合。随着高复合体空间剖面图的引入，对这些组件的研究有了很大的进步。基于图像的图谱方法揭示了每个样本在103-107个细胞中20-100个亚细胞分辨率的蛋白质的强度和空间分布。尽管对从这些图像中提取单细胞数据的方法进行了广泛的研究，但所有组织图像都包含折叠、碎片、抗体聚集、光学像差和图像处理错误等伪影，这些伪影是由于标本准备、数据获取、图像组装和特征提取方面的缺陷造成的。在这里，我们展示了这些人工制品极大地影响了单细胞数据分析，模糊了有意义的生物学解释。我们描述了一个交互式质量控制软件工具CyLint，它可以识别和删除与成像伪影相关的数据。CyLint极大地改进了单细胞分析，特别是对数据收集前多年切片的档案标本，如来自临床试验的标本。
Tumors are complex assemblies of cellular and acellular structures patterned on spatial scales from microns to centimeters. Study of these assemblies has advanced dramatically with the introduction of high-plex spatial profiling. Image-based profiling methods reveal the intensities and spatial distributions of 20–100 proteins at subcellular resolution in 10 3–10 7 cells per specimen. Despite extensive work on methods for extracting single-cell data from these images, all tissue images contain artifacts such as folds, debris, antibody aggregates, optical aberrations and image processing errors that arise from imperfections in specimen preparation, data acquisition, image assembly and feature extraction. Here we show that these artifacts dramatically impact single-cell data analysis, obscuring meaningful biological interpretation. We describe an interactive quality control software tool, CyLinter, that identifies and removes data associated with imaging artifacts. CyLinter greatly improves single-cell analysis, especially for archival specimens sectioned many years before data collection, such as those from clinical trials.