In this issue, Alsema, Wijering, Miedema, Kotah et al. and Lerma-Martin, Badia-i-Mompel et al. demonstrate the ever-growing possibilities of spatial transcriptomics by applying it to the spatially heterogeneous disease multiple sclerosis. They validate the technique by comparison to classic pathology and reveal insights into demyelinated lesion markers, pathological cell types and lesion evolution.