Topological data analysis quantifies biological nano-structure from single molecule localization microscopy

Jeremy Pike, Abdullah Khan, Chiara Pallini, Steven Thomas, Markus Mund, Jonas Ries, Natalie Poulter, Iain Styles

Research output: Contribution to journalArticlepeer-review

7 Citations (Scopus)
258 Downloads (Pure)


Motivation: Localization microscopy data is represented by a set of spatial coordinates, each corresponding to a single detection, that form a point cloud. This can be analyzed either by rendering an image from these coordinates, or by analyzing the point cloud directly. Analysis of this type has focused on clustering detections into distinct groups which produces measurements such as cluster area, but has limited capacity to quantify complex molecular organization and nano-structure.

Results: We present a segmentation protocol which, through the application of persistence-based clustering, is capable of probing densely packed structures which vary in scale. An increase in segmentation performance over state-of-the-art methods is demonstrated. Moreover we employ persistent homology to move beyond clustering, and quantify the topological structure within data. This provides new information about the preserved shapes formed by molecular architecture. Our methods are flexible and we demonstrate this by applying them to receptor clustering in platelets, nuclear pore components, endocytic proteins and microtubule networks. Both 2D and 3D implementations are provided within RSMLM, an R package for pointillist-based analysis and batch processing of localization microscopy data.

Availability: RSMLM has been released under the GNU General Public License v3.0 and is available at Tutorials for this library implemented as Binder ready Jupyter notebooks are available at
Original languageEnglish
Pages (from-to)1614–1621
Number of pages8
Issue number5
Early online date18 Oct 2019
Publication statusPublished - Mar 2020

Bibliographical note

© The Author(s) 2019. Published by Oxford University Press.


Dive into the research topics of 'Topological data analysis quantifies biological nano-structure from single molecule localization microscopy'. Together they form a unique fingerprint.

Cite this