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Multi-omics integration

SpaMTP

Open-source framework for joint analysis, annotation, alignment, integration and visualization of spatial metabolomics and spatial transcriptomics.

Imaging mass spectrometrySpatial metabolomicsMulti-omicsR packageOpen source
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Overview

SpaMTP combines spatial metabolomics and transcriptomics analysis in an R environment built around Seurat objects and Cardinal functionality. It supports m/z-based candidate annotation, statistical comparison and pathway analysis, alongside visualization and multimodal integration.

What can this tool do?

Univariate statisticsMultivariate statisticsPathway enrichmentContainer support

Common uses

  • Compare spatial metabolite patterns and associated pathways.
  • Integrate spatial MS measurements with transcriptomic context.

Scientific fit

Primary function

Multi-omics integration

Other functions

Metabolite annotation and identification, Statistical analysis, Visualization and reporting, Pathway and biological interpretation

Analysis types

Spatial metabolomics, Multi-omics

Data compatibility

Inputs

Imaging data, Feature or peak table, Sample metadata

Outputs

Statistical results, Pathway or reaction data, Human-readable report

Input formats

Spatial-omics data imported into supported R objects, Seurat-compatible expression and coordinate data

Output formats

R analysis objects, statistical tables and visualizations

Scope and considerations

Designed for

  • Joint spatial metabolomics and transcriptomics analysis.

Not designed for

  • Treating m/z-only candidate annotation as definitive identification.

Important requirements

  • R and documented package dependencies, or the supplied container environment.
  • Appropriate spatial coordinates and compatible inputs for the chosen workflow.

Considerations

  • Annotation ambiguity propagates to pathway interpretation.
  • Alignment and statistical comparisons depend on sampling geometry and biological replication.
  • Record the branch, package version and reference databases used.

Access and documentation

Primary accessSource repository

Open-source R package with documented installation and an Apptainer environment. Stable and developmental branches have separate documentation; experimental features should not be assumed part of a reproducible stable workflow.

License: MIT

Evidence and review

Official package documentation, repository license and Nature Methods publication verified on 2026-09-11. Stable and developmental functionality distinguished. No installation, statistical analysis or benchmark performed. RaMP-DB relationship remains queued until that entry is added.

Core publications

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

  1. Causer A, Lu T, Kriel J, et al. SpaMTP: integrative statistical analysis and visualization of spatial metabolomics and transcriptomics data. Nature Methods 23, 1501–1506 (2026). doi:10.1038/s41592-026-03140-8

Related tools

METASPACEComplementary to · An alternative source of spatial annotation evidence; direct interchange was not tested.CardinalDepends on · The project builds on Cardinal MSI functionality.RaMP-DBIntegrates with · Provides pathway context used by SpaMTP; inspect identifier mapping and reference versions.

Entry history

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

  1. 2026-09-12 · Entry update

    Add IDBac and RaMP specialist resources

    View change · Entry at this revision
  2. 2026-09-11 · First committed entry

    Complete supplied spatial tools and connect molecular cartography

    View change · Entry at this revision

Full GitHub history