细胞映射器：一个用于可视化高度多重成像数据的R/Bioconductor软件包。
cytomapper: an R/Bioconductor package for visualization of highly multiplexed imaging data.
作者信息
Eling Nils, Damond Nicolas, Hoch Tobias, Bodenmiller Bernd
机构信息
Department of Quantitative Biomedicine, University of Zurich, 8057 Zurich, Switzerland.
Institute for Molecular Health Sciences, ETH Zurich, 8093 Zurich, Switzerland.
出版信息
Bioinformatics. 2021 Apr 5;36(24):5706-5708. doi: 10.1093/bioinformatics/btaa1061.
SUMMARY
Highly multiplexed imaging technologies enable spatial profiling of dozens of biomarkers in situ. Here, we describe cytomapper, a computational tool written in R, that enables visualization of pixel- and cell-level information obtained by multiplexed imaging. To illustrate its utility, we analysed 100 images obtained by imaging mass cytometry from a cohort of type 1 diabetes patients. In addition, cytomapper includes a Shiny application that allows hierarchical gating of cells based on marker expression and visualization of selected cells in corresponding images.
AVAILABILITY AND IMPLEMENTATION
The cytomapper package can be installed via https://www.bioconductor.org/packages/release/bioc/html/cytomapper.html. Code for analysis and further instructions can be found at https://github.com/BodenmillerGroup/cytomapper_publication.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
高度多重成像技术能够在原位对数十种生物标志物进行空间分析。在此，我们描述了Cytomapper，这是一个用R编写的计算工具，可实现对通过多重成像获得的像素级和细胞级信息的可视化。为说明其效用，我们分析了来自1型糖尿病患者队列的成像质谱流式细胞术获得的100张图像。此外，Cytomapper包含一个Shiny应用程序，可基于标志物表达对细胞进行分层门控，并在相应图像中可视化选定的细胞。
可用性与实现方式
补充信息
补充数据可在《生物信息学》在线获取。
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