Abstract Understanding cellular architectures and their connectivity is essential for interrogating system function and dysfunction. However, we lack technologies for mapping the multi-scale details of individual cells in the human organ-scale system. To address this challenge, we developed a platform that simultaneously extracts spatial, molecular, morphological, and connectivity information of individual cells from the same human brain, by integrating novel chemical, mechanical, and computational tools. The platform includes three key tools: (i) a vibrating microtome for ultra-precision slicing of large-scale tissues without losing cellular connectivity (MEGAtome), (ii) a polymer hydrogel-based tissue processing technology for multiplexed multiscale imaging of human organ-scale tissues (mELAST), and (iii) a computational pipeline for reconstructing 3D connectivity across multiple brain slabs (UNSLICE). We demonstrated the transformative potential of our platform by analyzing human Alzheimer’s disease pathology at multiple scales and demonstrating scalable neural connectivity mapping in the human brain. One-Sentence Summary We developed an integrated, scalable platform for highly multiplexed, multi-scale phenotyping and connectivity mapping in the same human brain tissue, which incorporated novel tissue processing, labeling, imaging, and computational technologies.

Integrated platform for multi-scale molecular imaging and phenotyping of the human brain