Development of pan-ExM for whole-brain, molecularly annotated connectomics

About This Grant

Project Summary Mapping nanoscale brain architecture and molecular features across the entire mammalian brain remains out of reach using current technologies. Correlative light and electron microscopy (CLEM) is the only method capable of bridging structural and molecular information at this scale, but it is prohibitively slow, expensive, and complex, making it unsuitable for scaling to an entire mouse brain. Panluminate Inc. is developing a whole-organ 20X expansion technology called whole-brain pan-Expansion Microscopy (WBExM) that addresses these limitations directly. By combining ~20-fold linear expansion of intact mouse brains with novel bulk (pan) staining of proteins and lipids, WBExM enables molecularly annotated imaging of ultrastructure at sub-20 nm resolution across sections post-tissue expansion, minimizing alignment errors and enabling accurate tracing of neuronal processes for dense connectomics. Neurites including dendrites and axons can be traced by segmenting the pan-staining channel, while simultaneous immunolabeling identifies molecular targets of interest. Unlike EM/CLEM, WBExM is fully optical, scalable, and cost-effective, making it ideal for tracing brain circuits and investigating neurodegenerative disease mechanisms. Our proposed Phase I project is to develop and validate a complete workflow for brain-wide pan-ExM sample preparation and imaging. In particular, we will: (1) develop and optimize WBExM, including perfusion, embedding, clearing, and isotropic expansion protocols that preserve protein targets and tissue structure across the entire mouse brain; and (2) validate reconstruction of neuronal processes across sections, demonstrating that WBExM enables faithful tracing of long-range neuronal projections, synapses, and local circuits, overcoming alignment errors inherent in slice-based approaches. This work will establish WBExM as a practical and scalable platform for nanoscale brain imaging and prepare it for commercialization in Phase II as a research tool for molecular dense connectomics. Our long-term goal is for WBExM to become a core technology for generating nanoscale molecular brain atlases and for studying circuit-level abnormalities in neurodegenerative disease models, supporting discovery and therapeutic innovation aligned with the NIMH mission.