Reviving formalin-fixed, paraffin embedded (FFPE) tissues for on-slide and multiscale correlative microscopy

Correlative microscopy integrates complementary imaging modalities to enable structural analysis of biological samples across multiple length scales. Here, we present two correlative workflows for formalin-fixed, paraffin-embedded (FFPE) human tissues that extend the utility of archived clinical specimens for high-resolution imaging. The first, an on-slide correlative light and electron microscopy (CLEM) workflow, enables direct integration of brightfield light microscopy with scanning electron microscopy to resolve ultrastructural features from standard histological sections. The second, a multiscale three-dimensional workflow, combines X-ray micro-computed tomography with serial block-face scanning electron microscopy to enable targeted, volumetric ultrastructural analysis within a defined tissue context. Using these approaches, we demonstrate that FFPE tissues retain sufficient structural integrity to resolve cellular and subcellular architecture across liver, lung, brain, and heart specimens. Finally, we apply artificial intelligence-assisted image processing and segmentation to enable scalable, quantitative analysis of large-volume datasets. Together, these workflows establish FFPE specimens as a versatile and accessible resource for multiscale correlative imaging in both research and clinical settings.