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Statistical analysis

Cardinal

Open-source R/Bioconductor toolbox for preprocessing, statistical analysis, segmentation, classification and visualization of mass spectrometry imaging data.

Imaging mass spectrometrySpatial metabolomicsR packageOpen source
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Overview

Cardinal provides reproducible analysis of mass spectrometry imaging experiments, including preprocessing, visualization, spatial segmentation, classification and multivariate analysis. Cardinal v3 supports a broad range of MSI workflows and is designed for programmatic analysis in R.

What can this tool do?

Multivariate statistics

Common uses

  • Preprocess and visualize MSI datasets.
  • Segment tissues by chemical composition.
  • Perform classification and multivariate analysis of MSI experiments.

Scientific fit

Primary function

Statistical analysis

Other functions

Preprocessing and feature extraction, Visualization and reporting

Analysis types

Spatial metabolomics

Data compatibility

Inputs

Imaging data

Outputs

Imaging data, Statistical results

Input formats

imzML

Output formats

R analysis objects and statistical or image outputs

Scope and considerations

Designed for

  • Reproducible statistical analysis of MALDI- and DESI-based MSI datasets.

Not designed for

  • Definitive metabolite identification solely from ion images or statistical classification.

Important requirements

  • Compatible imaging-MS data, spatial coordinates and an R/Bioconductor environment.
  • Biological sample metadata and an analysis design appropriate to spatial measurements.

Considerations

  • Pixels from one tissue are not independent biological replicates; preserve sample-level grouping during inference and validation.
  • Interpretation depends on acquisition quality, preprocessing choices and spatial experimental design.

Access and documentation

Primary accessSource repository

Install through Bioconductor with an R version compatible with the selected release. The current source declares Artistic-2.0 or the accompanying license file; package dependencies and versions should be recorded for reproducibility.

License: Artistic-2.0

Evidence and review

Official package metadata and original/version-3 publication identities verified on 2026-09-10. No independent software benchmark or developer verification performed.

Core publications

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

  1. Bemis KA, Föll MC, Guo D, et al. Cardinal v.3: a versatile open-source software for mass spectrometry imaging analysis. Nature Methods 20, 1883–1886 (2023). doi:10.1038/s41592-023-02070-z
  2. Bemis KD, Harry A, Eberlin LS, et al. Cardinal: an R package for statistical analysis of mass spectrometry-based imaging experiments. Bioinformatics 31, 2418–2420 (2015). doi:10.1093/bioinformatics/btv146

Related tools

METASPACEComplementary to · Spatial statistical analysis and molecular annotation address different stages; no automatic integration is implied.M²aiaAlternative to · Open-source environment for interactive processing, visualization and registration of two- and three-dimensional mass spectrometry imaging data.pyimzMLComplementary to · Python library for reading and writing imzML imaging mass-spectrometry data.

Entry history

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

  1. 2026-09-10 · First committed entry

    Begin specialist population with Cardinal and spatial guide entry

    View change · Entry at this revision

Full GitHub history