Whole human organ clearing and multimodal mapping

Abstract

Human anatomy has traditionally been studied using low-resolution approaches such as cadaveric dissection and conventional medical imaging, limiting our understanding of macroscopic structures. Tissue clearing has emerged as a transformative approach, enabling three-dimensional mapping of organs at microscopic resolution, and offering the opportunity to interrogate anatomy across scales. However, its application to human organs remains challenging due to their size, density and optical properties. Here, we establish multiorgan CleLight (mCleLight) as a generalizable method for clearing, labeling and imaging whole human tissues. mCleLight is broadly applicable across major organ systems and enables the analysis of particularly challenging specimens, including highly heterogeneous samples, dense bones, pigmented tissues and decades-old formalin-fixed archival material. We demonstrate that controlled photoclearing is critical across human tissues both for efficient clearing and for quenching endogenous fluorescence, thereby substantially improving imaging depth as compared to previous methods. mCleLight allows specific labeling and quantitative analysis of complex extended structures such as collagen fibers, vasculature, and innervation, while preserving anatomical relationships, which cannot be easily done with classical histology. We integrated mCleLight into a pipeline with clinical imaging to achieve a comprehensive, multiscale understanding of organ architecture. We demonstrate the voxel-by-voxel alignment between MRI and microscopy datasets, merging cellular-scale detail and protein- specific labeling with macroscopic medical imaging. By bridging the gap between imaging scales and modalities, mCleLight provides a versatile method for integrated three- dimensional histological mapping and macroscopic anatomy of human organs in health and disease.