imzML Writer: An Easy-to-Use Python Pipeline for Conversion of Continuously Acquired Raw Mass Spectrometry Imaging Data to imzML Format

Mass spectrometry imaging (MSI) is a technique that uncovers the contextual distribution of biomolecules in tissue. This involves collecting large data sets with information-rich mass spectra in each pixel. To streamline image processing and interpretation, the MSI community has developed toolboxes for image preprocessing, segmentation, statistical analysis, and visualization. These generally require data to be input as imzML files, an Extensible Markup Language file with vocabulary for mass spectrometry and imaging-specific parameters. While commercial systems (e.g., MALDI) come with proprietary file converters, to our knowledge, no open-access user-friendly converters exist for continuously acquired imaging data (e.g., nano-DESI, DESI). Here, we present imzML Writer, an easy-to-use Python application with a graphical user interface to convert data from vendor format into pixel-aligned imzML files. We package this application with imzML Scout, allowing visualization of the resulting file(s) and batch export of ion images across a range of image and data formats (e.g., PNG, TIF, CSV). To demonstrate the utility of files generated by imzML Writer, we processed nano-DESI data with popular tools such as Cardinal MSI and METASPACE. Overall, this work provides a simple open-access tool for emerging MSI modality users to access advanced MSI processing tools reliant on imzML format. ImzML Writer is available as a distributable Python package via pip or as a standalone program for Mac and PC at https://github.com/VIU-Metabolomics/imzML_Writer.