Abstract
Multimodal mass spectrometry imaging (MSI) data presents unique big data challenges in handling and analysis. Here, we present a pipeline for co-registering matrix-assisted laser desorption/ionization MSI and confocal immunofluorescence imaging data for extracting single-cell metabolite signatures. We further describe methods and introduce software for the simultaneous analysis of these concatenated data sets, which are designed to establish a connection between cell traits of interest (shape metrics, position within sample) and the cells' own metabolic signatures.