MSIGen: An Open-Source Python Package for Processing and Visualizing Mass Spectrometry Imaging Data

06 May 2024, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


Mass spectrometry imaging (MSI) provides information about the spatial localization of molecules in complex samples with high sensitivity and molecular selectivity. Although point-wise data acquisition, in which mass spectra are acquired at pre-defined points in a grid pattern, is common in MSI, several MSI techniques use line-wise data acquisition. In the line-wise mode, the imaged surface is continuously sampled along consecutive parallel lines and MSI data are acquired as a collection of line scans across the sample. Furthermore, aside from the standard imaging mode in which a full mass spectrum is acquired in each pixel of the image, other data acquisition modes have been developed to enhance the molecular specificity, enable separation of isobaric and isomeric species, and improve the sensitivity to facilitate imaging of low abundance species. These methods, including MS/MS-MSI in both MS2 and MS3 modes, multiple-reaction monitoring (MRM)-MSI, and ion mobility spectrometry (IMS)-MSI have all demonstrated their capabilities, but their broader implementation is limited by the existing MSI analysis software. Here, we present MSIGen, an open-source Python package for the visualization of MSI experiments performed in line-wise acquisition mode containing MS1, MS2, and IMS data. The package supports multiple vendor-specific and open-source data formats. It is available for download from the Python Package Index (PyPI) and its source-code is available at This package contains tools for targeted extraction of ion images, and allows for normalization, and exportation as image arrays or publication-style images. MSIGen offers multiple interfaces allowing for accessibility and easy integration with other workflows. Considering its support for a wide variety of MSI imaging modes and vendor formats, MSIGen is a valuable tool for the visualization and analysis of MSI data.


Mass spectrometry imaging
Data visualization
Python package
open access software

Supplementary materials

Supplementary Information
Table S1: Mass list contents for each data type Figure S1. Visual representation of MSIGen’s spectrum and transition grouping algorithm. Figure S2. Specification on MS file name recognition from a representative file.

Supplementary weblinks


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