Machine learning for cluster analysis of localization microscopy data

Research output: Contribution to journalArticle

Authors

  • David J Williamson
  • Garth L Burn
  • Sabrina Simoncelli
  • Juliette Griffié
  • Ruby Peters
  • Daniel M Davis

Colleges, School and Institutes

External organisations

  • King's Health Partners Cancer Biobank, King's College London, London, UK.
  • Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.

Abstract

Quantifying the extent to which points are clustered in single-molecule localization microscopy data is vital to understanding the spatial relationships between molecules in the underlying sample. Many existing computational approaches are limited in their ability to process large-scale data sets, to deal effectively with sample heterogeneity, or require subjective user-defined analysis parameters. Here, we develop a supervised machine-learning approach to cluster analysis which is fast and accurate. Trained on a variety of simulated clustered data, the neural network can classify millions of points from a typical single-molecule localization microscopy data set, with the potential to include additional classifiers to describe different subtypes of clusters. The output can be further refined for the measurement of cluster area, shape, and point-density. We demonstrate this approach on simulated data and experimental data of the kinase Csk and the adaptor PAG in primary human T cell immunological synapses.

Details

Original languageEnglish
Article number1493
JournalNature Communications
Volume11
Issue number1
Publication statusPublished - 20 Mar 2020