# Quantitative Neuroanatomy

> **NIH NIH U19** · UNIVERSITY OF CALIFORNIA, SAN DIEGO · 2024 · $1,070,228

## Abstract

Abstract
Core 2: Quantitative Neuroanatomy
 The neuroanatomy of orofacial circuitry has grown in complexity as viral-genetic tracing methods uncover
neuronal projections of a myriad of premotor and pre2motor neurons. New methodologies for brain-wide
localization of functionally labelled neuron populations at scale and techniques for reconstruction of the entire
extent of single neurons out to its most distal axonal projections will provide a comprehensive view of the
distribution and detailed connectivity of these cells within the orofacial circuitry.
 Aim 1 of the Quantitative Neuroanatomy Core will, in close partnership with Allen Brain Institute, provide a
mature pipeline for SPIM (selective plane illumination microscopy, a.k.a., light sheet microscopy) imaging of
brain-wide maps of labelled populations of premotor and pre2motor neurons, as well as localization of multi-
electrode arrays in the brain. In further samples provided by Project 4, the fine scale axonal projections of
individual premotor neurons as well as those of its inputs will be systematically reconstructed and examined.
These pipelines will serve to co-register labeled neuronal populations from different experiments onto a common
reference space, the Allen CCF: this is crucial for identification of neighborhoods of different types of neurons as
proximity can be predictive of functional interactions for coordination of multiple orofacial behaviors.
 Aim 2 of the Quantitative Neuroanatomy Core addresses the challenge of effective data-sharing across
neuroanatomy laboratories. Recently, the UCSD's site initiated the use of NeuroGlancer, an open-source 3D
volumetric visualization platform to visualize Cryojane (tape transfer) serially sectioned whole mouse brains with
premotor neuron fluorescent transsynaptic neuronal labeling from peripheral muscles. These samples parallel
our recent publications. We propose to prepare additional Cryojane samples (Projects 1, 3-5) to map new
premotor neuron populations in the context of the counter-stained cytoarchitecture. These are complementary
to samples run through whole-brain clearing and SPIM (see Aim 1).
 It is critical to the scientific success of the Team to have inter-project review of annotated histology files,
including data from the Allen Institute, for decisions about regional boundary annotations. To access these
NeuroGlancer files across laboratories, Core 2 will introduce BrainSharer, a Web-accessible platform for hosting
NeuroGlancer files initially developed in a collaboration (Samuel Wang laboratory in Princeton). Importantly, this
platform improves cross-laboratory interactions through real-time peer-to-peer review of three-dimensional data
sets with user-generated tools that support annotation of cells and of regions across Performance Sites.

## Key facts

- **NIH application ID:** 10930314
- **Project number:** 1U19NS137920-01
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN DIEGO
- **Principal Investigator:** Beth Friedman
- **Activity code:** U19 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $1,070,228
- **Award type:** 1
- **Project period:** 2024-08-15 → 2029-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10930314

## Citation

> US National Institutes of Health, RePORTER application 10930314, Quantitative Neuroanatomy (1U19NS137920-01). Retrieved via AI Analytics 2026-06-12 from https://api.ai-analytics.org/grant/nih/10930314. Licensed CC0.

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