A Multimodal Imaging Pipeline for the Discovery of Molecular Markers of Cellular Neighborhoods

We developed an integrated imaging pipeline for spatio-molecular and immunophenotypic tissue analysis, enabling the discovery of molecular markers across spatial scales—from functional tissue units to cell types and neighborhoods. Our approach facilitates single-tissue section analysis, enabling direct cross-modality mining of imaging mass spectrometry and highly multiplexed immunofluorescence microscopy. Demonstrated on human kidney tissue, we identified lipidomic markers of cellular neighborhoods associated with renal cell types and immune cell infiltration.