RF1MH128841

Scalable Technologies for Brain-Wide Connectomics of Transcriptomic Cell Types: Focus on Brainstem

Project Summary

This proposal aims to develop a scalable pipeline to combine high-resolution morphology and molecular classification of individual neurons in order to define morpho-molecular cell types in the brain. The complete morphology of individual neurons provides insights into connectivity and information processing in the brain, revealing how neuronal activity is routed across different brain areas. By layering transcriptomic information onto morphologically distinct types, we can access these defined neuron types for functional analysis. This 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 orchestrates complex behaviors.

Sequencing-based approaches have been used to categorize the brain's cells into transcriptomic types (T-types) with high throughput. However, 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. This will be combined with post hoc transcriptomic characterization of reconstructed cells using multiplexed fluorescent in situ hybridization to define morpho-molecular types.

We will create a dataset 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.

Allen Institute

93.242 - Mental Health Research Grants

National Institute of Mental Health (NIMH) [HHS - NIH]

Seattle, Washington 98109 United States

Single Zip Code

BRAIN Initiative Cell Census Network (BICCN) Scalable Technologies and Tools for Brain Cell Census (R01 Clinical Trial Not Allowed) (RFA-MH-21-140)