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

Mass spectrometry imaging (MSI) is a powerful tool which reveals the contextual distribution of biomolecules in tissues. Acquiring these images involves collecting an information-rich mass spectrum for each pixel of the ion image, which results in large datasets typically exceeding 1 GB. To streamline data processing and interpretation, various toolboxes have been developed for image pre-processing, segmentation, statistical analysis, and visualization. These generally require imaging data to be input in ‘imzML’ format, an Extensible Markup Language file with controlled vocabulary for mass spectrometry and MSI-specific parameters. While major/commercial MSI modalities (e.g. MALDI) come with proprietary file converters, to our knowledge, no open-access user-friendly converters exist for continuously acquired MSI data (e.g. nano-DESI, DESI). Here, we present imzML Writer, an open-access python application which is easy to install and easy to use. imzML Writer has a simple graphical user interface to convert data from MS vendor format into pixel-aligned imzML files suitable for further analysis. We package this application with imzML Scout, a tool to quickly visualize the resulting file(s) and batch export ion images across a range of image/data formats (PNG, TIF, CSV). To demonstrate the utility of files generated by imzML Writer, we processed a nano-DESI image using previously inaccessible toolboxes/data repositories such as Cardinal MSI and METASPACE. Overall, this work provides a simple tool for emerging MSI modality users to access the wealth of advanced MSI processing tools reliant on imzML format.