近日，美国哈佛医学院Peter K. Sorger等研究人员合作使用CyLinter，进行高通量组织特征单细胞分析的质量控制。这一研究成果于2024年10月30日在线发表在国际学术期刊《自然—方法学》上。

研究人员表示，肿瘤是复杂的细胞和非细胞结构的集合，呈现出从微米到厘米的空间尺度。高通量空间剖析的引入使得对这些结构的研究取得了显著进展。基于图像的剖析方法可以在每个样本中以亚细胞分辨率，揭示20到100种蛋白质的强度和空间分布，涵盖10³到10⁷个细胞。

尽管在从这些图像中提取单细胞数据的方法上已有大量研究，但所有组织图像都包含折叠物、碎片、抗体聚集物、光学畸变和图像处理错误等伪影。这些伪影源于样本制备、数据采集、图像组装和特征提取中的不完美之处。

研究人员展示了这些伪影对单细胞数据分析的显著影响，模糊了有意义的生物学解释。研究人员描述了一种互动质量控制软件工具CyLinter，可以识别并去除与成像伪影相关的数据。CyLinter极大地改善了单细胞分析，特别适用于那些在数据收集前许多年就已切割的档案样本，如临床试验中的样本。

附：英文原文

Title: Quality control for single-cell analysis of high-plex tissue profiles using CyLinter

Author: Baker, Gregory J., Novikov, Edward, Zhao, Ziyuan, Vallius, Tuulia, Davis, Janae A., Lin, Jia-Ren, Muhlich, Jeremy L., Mittendorf, Elizabeth A., Santagata, Sandro, Guerriero, Jennifer L., Sorger, Peter K.

Issue&Volume: 2024-10-30

Abstract: 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 103–107 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.

DOI: 10.1038/s41592-024-02328-0

Source: https://www.nature.com/articles/s41592-024-02328-0