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

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. ### Competing Interest Statement K.C. is a co-inventor on patent application owned by MIT covering the SHIELD and SWITCH technology (PCT/US2016/064538), the MAP technology (US Provisional Patent Application 62/330,018), and the ELAST technology (US Patent App. 17/308,462). K.C. and J. W. are co-inventors on patent applications owned by MIT covering the MEGAtome technology. MegaSPIM uses patented axial sweeping technology (US10989661B2). K.C. is a co-founder of LifeCanvas Technologies, a startup that provides solutions for 3D tissue processing and analysis.