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Imaging of Biological Tissues by Desorption Electrospray Ionization Mass Spectrometry
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imzML Writer: An Easy-to-Use Python Pipeline for Conversion of Continuously Acquired Raw Mass Spectrometry Imaging
Joseph Monaghan1, Kiera Nguyen1, Nicholas Woytowich1,2
1Department of Chemistry, Vancouver Island University, 900 Fifth Street, Nanaimo, British Columbia, Canada V9R 5S5.
Analytical Chemistry
|March 14, 2025
Summary
A new Python tool, imzML Writer, converts vendor-formatted mass spectrometry imaging (MSI) data into the standard imzML format. This enables users of emerging MSI techniques to access advanced image processing and analysis tools.
Area of Science:
- Analytical Chemistry
- Biotechnology
- Data Science
Background:
- Mass spectrometry imaging (MSI) provides spatial distribution of biomolecules in tissues, generating large datasets.
- Existing MSI analysis tools often require data in the imzML file format.
- Open-access, user-friendly converters for continuously acquired MSI data are lacking.
Purpose of the Study:
- To develop an accessible tool for converting vendor-specific MSI data into the imzML format.
- To facilitate the use of advanced MSI analysis software for emerging MSI techniques.
Main Methods:
- Development of imzML Writer, a Python application with a graphical user interface.
- Integration of imzML Scout for visualization and batch export of ion images.
- Demonstration using nano-DESI data processed with Cardinal MSI and METASPACE.
Main Results:
- imzML Writer successfully converts vendor data to pixel-aligned imzML files.
- imzML Scout enables visualization and export of MSI data in various formats.
- Generated imzML files are compatible with established MSI analysis platforms.
Conclusions:
- imzML Writer provides a crucial open-access solution for users of emerging MSI modalities.
- The tool lowers the barrier to entry for advanced MSI data analysis.
- This work supports broader adoption and utilization of MSI technologies.
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