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SMoLR：R 中的单分子定位显微镜数据的可视化和分析。

SMoLR: visualization and analysis of single-molecule localization microscopy data in R.

机构信息

Erasmus Optical Imaging Centre, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.

Department of Pathology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.

出版信息

BMC Bioinformatics. 2019 Jan 15;20(1):30. doi: 10.1186/s12859-018-2578-3.

DOI:10.1186/s12859-018-2578-3
PMID:30646838
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6334411/
Abstract

BACKGROUND

Single-molecule localization microscopy is a super-resolution microscopy technique that allows for nanoscale determination of the localization and organization of proteins in biological samples. For biological interpretation of the data it is essential to extract quantitative information from the super-resolution data sets. Due to the complexity and size of these data sets flexible and user-friendly software is required.

RESULTS

We developed SMoLR (Single Molecule Localization in R): a flexible framework that enables exploration and analysis of single-molecule localization data within the R programming environment. SMoLR is a package aimed at extracting, visualizing and analyzing quantitative information from localization data obtained by single-molecule microscopy. SMoLR is a platform not only to visualize nanoscale subcellular structures but additionally provides means to obtain statistical information about the distribution and localization of molecules within them. This can be done for individual images or SMoLR can be used to analyze a large set of super-resolution images at once. Additionally, we describe a method using SMoLR for image feature-based particle averaging, resulting in identification of common features among nanoscale structures.

CONCLUSIONS

Embedded in the extensive R programming environment, SMoLR allows scientists to study the nanoscale organization of biomolecules in cells by extracting and visualizing quantitative information and hence provides insight in a wide-variety of different biological processes at the single-molecule level.

摘要

背景

单分子定位显微镜是一种超分辨率显微镜技术，可用于确定生物样本中蛋白质的纳米级定位和组织。为了对数据进行生物学解释，必须从超分辨率数据集提取定量信息。由于这些数据集的复杂性和规模，需要灵活且用户友好的软件。

结果

我们开发了 SMoLR（在 R 中进行单分子定位）：一个灵活的框架，允许在 R 编程环境中探索和分析单分子定位数据。SMoLR 是一个旨在从单分子显微镜获得的定位数据中提取、可视化和分析定量信息的软件包。SMoLR 不仅是一个可视化纳米级亚细胞结构的平台，还提供了获取有关分子在其中分布和定位的统计信息的方法。可以针对单个图像执行此操作，或者可以使用 SMoLR 一次分析大量超分辨率图像。此外，我们描述了一种使用 SMoLR 进行基于图像特征的粒子平均的方法，从而可以识别纳米级结构之间的常见特征。

结论

嵌入广泛的 R 编程环境中，SMoLR 允许科学家通过提取和可视化定量信息来研究细胞中生物分子的纳米级组织，从而在单细胞水平上深入了解各种不同的生物学过程。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1825/6334411/7e521fb7e343/12859_2018_2578_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1825/6334411/2403345f5d65/12859_2018_2578_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1825/6334411/7e521fb7e343/12859_2018_2578_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1825/6334411/2403345f5d65/12859_2018_2578_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1825/6334411/7e521fb7e343/12859_2018_2578_Fig2_HTML.jpg

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