Automatically generate two-dimensional gating hierarchy from clustered cytometry data.
Automatically generate two-dimensional gating hierarchy from clustered cytometry data.
复制标题
从聚集的细胞计数数据自动生成二维门控层次结构。
DOI：
10.1002/cyto.a.23577
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发表时间：
2018
期刊：
影响因子：
--
通讯作者：
Qiu,Peng
中科院分区：
文献类型：
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作者：
Yang,Xingyu;Qiu,Peng
细胞计量学是医学和生物学研究中广泛应用的一项重要技术。生物学家传统上通过手动门控来分析单细胞细胞计数数据，这可能是主观和劳动密集型的。为了解决这个问题，已经开发了许多自动化和半自动化的方法。这些先进的方法旨在加速和标准化细胞计数数据的分析，但它们的普及受到其可视化的限制，这些可视化对于习惯于传统双轴门控图的生物学家来说并不直观。在这篇文章中，我们提出了一种新的方法，称为聚类到门（C2G），可以将聚类结果作为输入，并自动生成嵌套的二维门控层次结构，这是生物学家熟悉的可视化表示。该方法可以同时生成多个目标群体的门控序列，并将它们汇总在一个表示门控层次的层次树中。我们已经在通过手动门控、自动聚类算法（例如k均值）和可视化辅助方法（SPADE和tSNE）定义的目标人群上测试了这种方法。我们已经证明，C2G能够产生捕获由各种聚类策略定义的细胞群体的门控序列，并且对过度聚类和重叠的靶群体具有鲁棒性。© 2018国际细胞计数促进学会
Cytometry is an important technique widely used in medicine and biological research. Biologists traditionally analyze single‐cell cytometry data by manual gating, which can be subjective and labor intensive. To address this issue, many automated and semiautomated methods have been developed. These advanced methods are designed to speed up and standardize the analysis of cytometry data, but their popularity is limited by their visualizations which are not intuitive to biologists who are accustomed to the conventional biaxial gating plots. In this article, we present a new method called Cluster‐to‐Gate (C2G) that can take clustering results as input, and automatically generate a nested two‐dimensional gating hierarchy, which is a visualization representation that biologists are familiar with. This method can generate gating sequences for multiple target populations simultaneously and summarize them in one hierarchical tree that represents the gating hierarchy. We have tested this method on target populations defined by manual gating, automated clustering algorithms (k‐means for example), and visualization‐assisted methods (SPADE and tSNE). We have demonstrated that C2G is able to generate gating sequences that capture cell populations defined by the various clustering strategies, and robust to over‐clustered and overlapping target populations. © 2018 International Society for Advancement of Cytometry