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The tofsims project is an R/Bioconductor toolkit designed for processing, analyzing, and visualizing imaging mass spectrometry data from Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) instruments. It supports importing raw and preprocessed data from popular instrument platforms (e.g. IONTOF, Ulvac-Phi) and provides methods for mass calibration, peak picking, and peak integration. The package allows transformation of spectra into 2D image structures (mass images), with operations such as binning, scaling, subsetting, and visual rendering. For data exploration and dimensionality reduction, it includes multivariate methods common in the ToF-SIMS community: PCA (Principal Component Analysis), MCR (Multivariate Curve Resolution), MAF (Maximum Autocorrelation Factors), and MNF (Minimum Noise Fraction). It also interoperates with Bioconductor’s imaging stack (e.g. EBImage) so users can apply segmentation and image analysis operations on mass images.
Features
- Import of raw and preprocessed ToF-SIMS data from multiple instrument platforms
- Mass calibration, peak picking, and peak integration workflows
- Construction and manipulation of 2D mass images (binning, scaling, subsetting)
- Multivariate decomposition: PCA, MAF, MCR, MNF for dimension reduction and signal separation
- Integration with imaging tools (e.g. EBImage) for segmentation and spatial mask operations
- Example workflows and vignettes to guide end-to-end data processing
Project Samples
