Multiscale three-dimensional ultrastructural mapping of intestinal tissues and organoids

Understanding cell biology in native environments requires imaging of subcellular organization in three dimensions. In the intestinal epithelium, multiple cell types organize along the crypt-villus axis, where cell-cell interfaces and subcellular architecture control cell differentiation, tissue organization and epithelial function. Resolving these features volumetrically remains challenging: light microscopy offers molecular specificity but has limited resolution, whereas electron microscopy provides ultrastructural detail but is poorly suited to volumetric acquisition combined with specific protein labeling. Here, we show that expansion microscopy enables the multiscale volumetric study of epithelial ultrastructure in tissue sections and organoid models. Using an optimized workflow, we resolve epithelial tissue architecture, cell types and subcellular features within volumes across scales. Application to a microvillus inclusion disease (MVID) organoid model revealed disease-associated ultrastructural phenotypes that were only observed using electron microscopy. Our results establish expansion microscopy as key technology for studying three-dimensional cell biology within intestinal tissue and tissue mimics.