tofsims: Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data

This packages offers a pipeline for import, processing and analysis of ToF-SIMS 2D image data. Import of Iontof and Ulvac-Phi raw or preprocessed data is supported. For rawdata, mass calibration, peak picking and peak integration exist. General funcionality includes data binning, scaling, image subsetting and visualization. A range of multivariate tools common in the ToF-SIMS community are implemented (PCA, MCR, MAF, MNF). An interface to the bioconductor image processing package EBImage offers image segmentation functionality.

Package details

AuthorLorenz Gerber, Viet Mai Hoang
Bioconductor views DataImport ImagingMassSpectrometry ImmunoOncology Infrastructure MassSpectrometry Metabolomics Proteomics
MaintainerLorenz Gerber <>
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
if (!requireNamespace("BiocManager", quietly = TRUE))


Try the tofsims package in your browser

Any scripts or data that you put into this service are public.

tofsims documentation built on Nov. 8, 2020, 5:10 p.m.