Project summary, Scalable technologies for brain-wide connectomics of transcriptomic cell types: focus on brainstem This proposal is to develop a scalable pipeline to combine high-resolution morphology and molecular classification of individual neurons to define morpho-molecular cell types in the brain. Complete morphology of individual neurons provides insights of connectivity and information processing in the brain and reveals how neuronal activity is routed across brain areas. Layering transcriptomic information on to morphologically distinct types provides the basis to access these defined neuron types for functional analysis. Such a combined classification of the brain’s cell types is foundational for understanding the role of defined neuron types within neural circuits and how information processing within multi-regional neural circuits orchestrate complex behaviors. Sequencing-based approaches have been used to categorize the brain’s cells into transcriptomic types (t- types) with high throughput. Parallel strategies for a complete description of the morphological types brain-wide are too slow and methods for a combined analysis of these two modalities are lacking. To address this, we will create a brain-wide imaging and neuronal reconstruction platform that provides faster imaging using selective plane illumination microscopy and accelerated reconstructions with modern machine learning tools based on U-Nets and reinforcement learning. We will combine this with post hoc transcriptomic characterization of reconstructed cells with multiplexed fluorescent in situ hybridization to define morpho-molecular types. We will create a data set of 2,000 such dual categorized neuron types from a critical brain area, the medulla, in the mouse. The medulla is comprised of diverse neuronal types organized in numerous inter-related nuclei essential for autonomic functions such as breathing, vasomotor control, integration of ascending inputs from sensory and interoceptive channels and coordination of motor actions such as chewing, licking and swallowing. Our census of morpho-molecular medullary neuron types will lay the foundation for a systematic cell type specific functional interrogation of these neurons within brainstem circuits and in the larger context of multi- regional brain circuits. Furthermore, this will serve as the blueprint for carrying out such studies throughout the mouse brain, and other brains, including that of primates.