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Data conversion and import

pyimzML

Python library for reading and writing imzML imaging mass-spectrometry data.

Imaging mass spectrometrySpatial metabolomicsPython packageOpen source
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Overview

pyimzML exposes pixel coordinates, spectra and metadata to Python code. Its parser and writer support custom imaging-data workflows rather than providing a complete graphical analysis environment.

What can this tool do?

Spectral data reading and writing

Common uses

  • Read pixel spectra in a scripted imaging workflow.
  • Write imzML output after custom transformations.

Scientific fit

Primary function

Data conversion and import

Analysis types

Spatial metabolomics

Data compatibility

Inputs

Imaging data

Outputs

Imaging data

Input formats

imzML

Output formats

imzML, Python-accessible spectra, coordinates and metadata

Scope and considerations

Designed for

  • Programmatic imzML input/output and interoperability.

Not designed for

  • An end-to-end MSI statistics or molecular-annotation workflow.

Important requirements

  • Python and the package dependencies; imzML metadata and associated binary data.

Considerations

  • The repository specifies imzML version 1.1.0; check compatibility with the producing software.
  • Preserve coordinates and relevant metadata when transforming data.
  • Validate written files with the intended downstream reader.

Access and documentation

Primary accessDocumentation

Installable Python package with source available under Apache-2.0. Included ontology-derived data have their own attribution notices.

License: Apache-2.0

Evidence and review

Official repository and parser/writer documentation reviewed on 2026-09-11. No dedicated peer-reviewed tool paper verified; no incidental usage paper added. Package installation, round-trip fidelity and interoperability were not tested.

No dedicated scholarly publication is listed. Follow the official documentation and resource-specific citation guidance.

Software and documentation citations

  • Alexandrov Team. pyimzML repository and documentation. Accessed 11 September 2026. Documentation

Related tools

CardinalComplementary to · Cardinal offers imaging analysis in R; exchanging imzML requires compatible files and is not a verified direct integration.M²aiaComplementary to · Open-source environment for interactive processing, visualization and registration of two- and three-dimensional 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 pyimzML and precise spectral data I/O capability

    View change · Entry at this revision

Full GitHub history