DOI: 10.18129/B9.bioc.tofsims    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see tofsims.

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

Bioconductor version: 3.7

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.

Author: Lorenz Gerber, Viet Mai Hoang

Maintainer: Lorenz Gerber <genfys at>

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biocViews DataImport, ImagingMassSpectrometry, Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version 1.8.0
In Bioconductor since BioC 3.3 (R-3.3) (2.5 years)
License GPL-3
Depends R (>= 3.3.0), methods, utils, ProtGenerics
Imports Rcpp (>= 0.11.2), ALS, ChemometricsWithR, signal, KernSmooth, graphics, grDevices, stats
LinkingTo Rcpp, RcppArmadillo
Suggests EBImage, knitr, rmarkdown, testthat, tofsimsData, BiocParallel, RColorBrewer
Enhances parallel
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