Dissemin is shutting down on January 1st, 2025

Published in

Oxford University Press, Bioinformatics, 11(33), p. 1703-1711, 2017

DOI: 10.1093/bioinformatics/btx026

Links

Tools

Export citation

Search in Google Scholar

Quantification of fibrous spatial point patterns from single-molecule localization microscopy (SMLM) data

This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

Full text: Download

Green circle
Preprint: archiving allowed
Orange circle
Postprint: archiving restricted
Red circle
Published version: archiving forbidden
Data provided by SHERPA/RoMEO

Abstract

Abstract Motivation Unlike conventional microscopy which produces pixelated images, SMLM produces data in the form of a list of localization coordinates—a spatial point pattern (SPP). Often, such SPPs are analyzed using cluster analysis algorithms to quantify molecular clustering within, for example, the plasma membrane. While SMLM cluster analysis is now well developed, techniques for analyzing fibrous structures remain poorly explored. Results Here, we demonstrate a statistical methodology, based on Ripley’s K-function to quantitatively assess fibrous structures in 2D SMLM datasets. Using simulated data, we present the underlying theory to describe fiber spatial arrangements and show how these descriptions can be quantitatively derived from pointillist datasets. We also demonstrate the techniques on experimental data acquired using the image reconstruction by integrating exchangeable single-molecule localization (IRIS) approach to SMLM, in the context of the fibrous actin meshwork at the T cell immunological synapse, whose structure has been shown to be important for T cell activation. Availability and Implementation Freely available on the web at https://github.com/RubyPeters/Angular-Ripleys-K. Implemented in MatLab. Supplementary information Supplementary data are available at Bioinformatics online.