LOMAR

An R package to deal with point sets from single molecule localization microscopy. This package provides four sets of functionalities:

• data input: read SMLM data as point sets either from csv files or from TIFF images
• registration: point sets registration using different algorithms
• topological data analysis: compute similarity between point sets using persistent homology
• alpha-shapes: compute alpha-shapes of point sets and derive 3d shape features

A preprint describing the package is available on bioRxiv.

Installation

The package is available on CRAN.

(from the RStudio mirror)

install.packages("LOMAR")

To install the development version of this package, run (from within R):

library(devtools)
install_git('https://git.embl.de/heriche/lomar')

This package depends on these other packages:

• data.table

• FNN

• foreach

• parallel

• doParallel

• proxy

• reshape2

• pracma

• transport

• RANN

• ff

• dbscan

• EBImage (from Bioconductor)

• tools

• rhdf5

• mclust

• alphashape3d