A R package for pointillist analysis of single molecule localization microscopy (SMLM) data. This package includes methods for persistence based clustering (ToMATo), alongside DBSCAN, Voronoi tessellation and Ripley's K based clustering. There is also the capacity to simulate dSTORM data.
A set of Binder ready tutorials and demos showcasing this package can be found within the SMLM-tutorials repository. We recommend looking at these before installing the package.
This package is under active devlopment and we havn't released a version on CRAN yet.
The devtools package can be used to install the development version directly from github:
install_github("jeremypike/RSMLM")To run this command you will need devtools. Windows users will also need Rtools.
If RSMLM is useful please cite our pre-print:
Topological data analysis quantifies biological nano-structure from single molecule localization microscopy
Jeremy A Pike, Abdullah O Khan, Chiara Pallini, Steven G Thomas, Markus Mund, Jonas Ries, Natalie S Poulter, Iain B Styles
bioRxiv 400275; doi: https://doi.org/10.1101/400275