Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Preprocessing and feature extraction

rMSIproc

Open-source R/C++ package for large-scale MSI preprocessing, including smoothing, alignment, recalibration, normalization, peak picking and binning.

Imaging mass spectrometrySpatial metabolomicsR packageOpen source
Access toolSuggest an update

Overview

rMSIproc adds C++ processing routines to the rMSI data model, producing processed images and peak matrices through R functions or a parameter wizard.

What can this tool do?

Peak or feature detection

Common uses

  • Extract peak matrices from imaging datasets.
  • Apply smoothing, mass alignment and calibration before spatial analysis.

Scientific fit

Primary function

Preprocessing and feature extraction

Analysis types

Spatial metabolomics

Data compatibility

Inputs

Imaging data

Outputs

Imaging data, Feature or peak table

Input formats

imzML, rMSI TAR format

Output formats

Processed rMSI TAR datasets and rMSIproc peak-matrix files

Scope and considerations

Designed for

  • MSI preprocessing with rMSI-compatible data.

Not designed for

  • Chromatographic retention-time alignment or definitive compound identification.

Important requirements

  • Working rMSI installation and compatible R/C++ toolchain.
  • FFTW support; follow platform-specific installation instructions.

Considerations

  • Check mass calibration and binning settings against the instrument resolution.
  • Keep preprocessing parameters with output matrices for reproducibility.

Access and documentation

Primary access

R source installation requires compatible native dependencies. The documented GUI uses RGtk2; verify installation on the target operating system before planning an analysis.

License: GPL-3.0

Evidence and review

Official repository README, DESCRIPTION and direct publication metadata reviewed on 2026-09-10. No installation or independent benchmark performed. Ongoing maintenance status has not been established.

Core publications

Resource papers, direct updates and tool-specific methods. Selection policy.

  1. Ràfols P, Heijs B, Del Castillo E, et al. rMSIproc: an R package for mass spectrometry imaging data processing. Bioinformatics 36, 3618–3619 (2020). doi:10.1093/bioinformatics/btaa142 PMID 32108859

Related tools

rMSIComplementary to · Designed to complement rMSI data handling and visualization.

Entry history

Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.

  1. 2026-09-11 · First committed entry

    Add rMSI, rMSIproc and MSiReader spatial tools

    View change · Entry at this revision

Full GitHub history