Robust nonparametric quantification of clustering density of molecules in single-molecule localization microscopy.

Robust nonparametric quantification of clustering density of molecules in single-molecule localization microscopy.

We report a robust nonparametric descriptor, J'(r), for quantifying the density of clustering molecules in single-molecule localization microscopy. J'(r), based on nearest neighbor distribution functions, does not require any parameter as an input for analyzing point patterns. We show that...

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Main Authors: Shenghang Jiang, Seongjin Park, Sai Divya Challapalli, Jingyi Fei, Yong Wang
Format: Article
Language:English
Published: Public Library of Science (PLoS) 2017-01-01
Series:PLoS ONE
Online Access:http://europepmc.org/articles/PMC5479598?pdf=render
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spelling doaj-dda2946d59324adaa189ea383462457e2020-11-24T21:14:19ZengPublic Library of Science (PLoS)PLoS ONE1932-62032017-01-01126e017997510.1371/journal.pone.0179975Robust nonparametric quantification of clustering density of molecules in single-molecule localization microscopy.Shenghang JiangSeongjin ParkSai Divya ChallapalliJingyi FeiYong WangWe report a robust nonparametric descriptor, J'(r), for quantifying the density of clustering molecules in single-molecule localization microscopy. J'(r), based on nearest neighbor distribution functions, does not require any parameter as an input for analyzing point patterns. We show that J'(r) displays a valley shape in the presence of clusters of molecules, and the characteristics of the valley reliably report the clustering features in the data. Most importantly, the position of the J'(r) valley ([Formula: see text]) depends exclusively on the density of clustering molecules (ρc). Therefore, it is ideal for direct estimation of the clustering density of molecules in single-molecule localization microscopy. As an example, this descriptor was applied to estimate the clustering density of ptsG mRNA in E. coli bacteria.http://europepmc.org/articles/PMC5479598?pdf=render
collection DOAJ
language English
format Article
sources DOAJ
author Shenghang Jiang
Seongjin Park
Sai Divya Challapalli
Jingyi Fei
Yong Wang
spellingShingle Shenghang Jiang
Seongjin Park
Sai Divya Challapalli
Jingyi Fei
Yong Wang
Robust nonparametric quantification of clustering density of molecules in single-molecule localization microscopy.
PLoS ONE
author_facet Shenghang Jiang
Seongjin Park
Sai Divya Challapalli
Jingyi Fei
Yong Wang
author_sort Shenghang Jiang
title Robust nonparametric quantification of clustering density of molecules in single-molecule localization microscopy.
title_short Robust nonparametric quantification of clustering density of molecules in single-molecule localization microscopy.
title_full Robust nonparametric quantification of clustering density of molecules in single-molecule localization microscopy.
title_fullStr Robust nonparametric quantification of clustering density of molecules in single-molecule localization microscopy.
title_full_unstemmed Robust nonparametric quantification of clustering density of molecules in single-molecule localization microscopy.
title_sort robust nonparametric quantification of clustering density of molecules in single-molecule localization microscopy.
publisher Public Library of Science (PLoS)
series PLoS ONE
issn 1932-6203
publishDate 2017-01-01
description We report a robust nonparametric descriptor, J'(r), for quantifying the density of clustering molecules in single-molecule localization microscopy. J'(r), based on nearest neighbor distribution functions, does not require any parameter as an input for analyzing point patterns. We show that J'(r) displays a valley shape in the presence of clusters of molecules, and the characteristics of the valley reliably report the clustering features in the data. Most importantly, the position of the J'(r) valley ([Formula: see text]) depends exclusively on the density of clustering molecules (ρc). Therefore, it is ideal for direct estimation of the clustering density of molecules in single-molecule localization microscopy. As an example, this descriptor was applied to estimate the clustering density of ptsG mRNA in E. coli bacteria.
url http://europepmc.org/articles/PMC5479598?pdf=render
work_keys_str_mv AT shenghangjiang robustnonparametricquantificationofclusteringdensityofmoleculesinsinglemoleculelocalizationmicroscopy
AT seongjinpark robustnonparametricquantificationofclusteringdensityofmoleculesinsinglemoleculelocalizationmicroscopy
AT saidivyachallapalli robustnonparametricquantificationofclusteringdensityofmoleculesinsinglemoleculelocalizationmicroscopy
AT jingyifei robustnonparametricquantificationofclusteringdensityofmoleculesinsinglemoleculelocalizationmicroscopy
AT yongwang robustnonparametricquantificationofclusteringdensityofmoleculesinsinglemoleculelocalizationmicroscopy
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