MSI-Explorer: Napari-Powered Tool for Mass Spectrometry Imaging Data Analysis

Mass spectrometry imaging (MSI) enables label-free spatial localization of biomolecules from single cells to whole tissues, making it a key technology in the growing fields of spatial omics. However, a lack of comprehensive open-source tools for MSI data analysis, visualization, and quantification has hindered its broader adoption. Napari, a widely used interactive Python-based image analysis platform, currently lacks native support for MSI data, limiting its applications in MSI research. To address this gap, we present MSI-Explorer, the first napari plugin that provides an interactive and user-friendly interface for MSI data processing, spectral analysis, molecular annotation, and quantification. By integrating napari's advanced visualization capabilities with MSI-specific functionalities, MSI-Explorer provides image curation, multimodal, and efficient analysis of MSI data sets. As the first dedicated MSI plugin for napari, MSI-Explorer bridges the gap between spatial metabolomics and the broader bioimaging research community, promoting open, accessible, and integrated MSI data analysis.