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Visualization and reporting

M²aia

Open-source environment for interactive processing, visualization and registration of two- and three-dimensional mass spectrometry imaging data.

Imaging mass spectrometrySpatial metabolomicsDesktop graphical interfaceOpen source
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Overview

M²aia extends the Medical Imaging Interaction Toolkit with MSI signal processing and image interaction. Researchers can inspect ion images and reconstruct or register spatial datasets. The related pyM²aia project exposes programmatic functionality separately.

Also known as: M2aia

What can this tool do?

Spectral data reading and writingPeak or feature detectionContainer support

Common uses

  • Interactively inspect and process MSI spectra and ion images.
  • Register multimodal images and reconstruct three-dimensional MSI datasets.

Scientific fit

Primary function

Visualization and reporting

Other functions

Preprocessing and feature extraction

Analysis types

Spatial metabolomics

Data compatibility

Inputs

Imaging data

Outputs

Imaging data

Input formats

imzML

Output formats

imzML

Scope and considerations

Designed for

  • Interactive spatial-data exploration and MSI image processing.

Not designed for

  • Definitive metabolite identification from image colocalization alone.

Important requirements

  • A compatible Windows or Linux installation, or the documented container environment.
  • The project specifies elastix for image-registration utilities.

Considerations

  • Inspect registration quality and processing parameters before interpreting spatial overlap.
  • Memory and storage requirements depend on image size and processing choices.
  • Python workflows use the companion pyM²aia interface; desktop and Python capabilities are not assumed identical.

Access and documentation

Primary accessSource repository

Source and Windows/Linux packages are available. Dependencies and companion software may carry separate licenses.

License: BSD-3-Clause

Evidence and review

Official project site, repository and publication metadata reviewed on 2026-09-11. The desktop tool paper is included; companion-interface and incidental application papers are not attributed to the desktop release. No installation, registration or benchmarking performed.

Core publications

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

  1. Cordes J, Enzlein T, Marsching C, Hinze M, Engelhardt S, Hopf C, Wolf I. M²aia—Interactive, fast, and memory-efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data. GigaScience 10(7), giab049 (2021). doi:10.1093/gigascience/giab049 PMID 34282451

Related tools

CardinalAlternative to · An R-based alternative for MSI analysis; feature sets and interfaces differ.pyimzMLComplementary to · Programmatic imzML I/O can support preparation of imaging data; direct interoperability was not tested.SCiLS LabAlternative to · Commercial software suite for processing, statistical analysis, segmentation, annotation and 2D/3D visualization of mass spectrometry imaging data.

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 M2aia spatial imaging analysis tool

    View change · Entry at this revision

Full GitHub history