# The Mouse Connectome Project Phase III: Assembling the global neural networks of the mouse brain

> **NIH NIH R01** · UNIVERSITY OF CALIFORNIA LOS ANGELES · 2020 · $783,743

## Abstract

PROJECT SUMMARY/ABSTRACT
The objective of our Mouse Connectome Project at USC (MCP) is to chart the long-range connectivity of ~800
delineated structures of the mouse brain in an effort to reveal its network organization. In Phase I (2009-2010),
we established an efficient data production, collection, and image processing workflow dedicated to compiling
connectomics data of the highest quality. We adopted an injection strategy that produced data most conducive
for network analysis by simultaneously revealing, for any brain region (i.e. A), its (1) inputs (AB); (2) outputs
(AB); (3) reciprocal or recurrent connections (AB); and (4) intermediate stations, which bridge brain
structures that are not directly connected (ACB). In Phase II (2011-2016), we traced ~2000 pathways from
injections placed across the entire cerebral hemisphere and thalamus. As proposed, in Phase III (2017-2022)
we will collect and analyze connections data for the hypothalamus, midbrain, pons, medulla, and cerebellum
(~1400 additional pathways) (Specific Aim 1). Combined, these pathways will be used to construct the most
comprehensive mesoscale connectome that charts all point-to-point connections of the entire mouse brain.
Compiling these connectivity data sets however is only the first step in constructing the connectome. The ensuing
challenge is to analyze the enormous data to extract information regarding network organization. Based on graph
theoretical analysis of 600 manually annotated pathways, we assembled the global networks of the mammalian
neocortex (Zingg et al., Cell, 2014). Although the gold standard, manual analysis was laborious, time consuming,
and not efficient for our ultimate goal of generating brain-wide connectivity maps and networks. Therefore, in
Phase II, we designed and created an innovative informatics workflow that efficiently and reliably registers,
reconstructs, and annotates large-scale connections data. This workflow will be applied in Phase III to accelerate
image processing, creation of connectivity maps, data annotation, and analysis. In Phase III, we will also initiate
the first stage of constructing cell type specific neural networks (Specific Aim 2). Our connectivity-based cell type
classification strategy will be used to identify all cell types of the medial prefrontal cortex and to gain a census of
each cell type using 2D and 3D images. Novel rabies viral tracing will be employed to systematically reveal the
neuronal inputs to these distinct cell populations. All of our data will be available as open resources
(www.MouseConnctome.org) (Specific Aim 3): (1) the iConnectome viewer is the only visualization tool that
allows users to view images of multiple fluorescently-labeled pathways within their own bright-field Nissl
background and corresponding level of a standard mouse brain atlas; (2) the iConnectome Map Viewer allows
access to connectivity maps, which feature hundreds of reconstructed pathways compiled atop a neuroanatomic
fram...

## Key facts

- **NIH application ID:** 10226677
- **Project number:** 7R01MH094360-10
- **Recipient organization:** UNIVERSITY OF CALIFORNIA LOS ANGELES
- **Principal Investigator:** Hong-Wei Dong
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $783,743
- **Award type:** 7
- **Project period:** 2020-11-06 → 2022-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10226677

## Citation

> US National Institutes of Health, RePORTER application 10226677, The Mouse Connectome Project Phase III: Assembling the global neural networks of the mouse brain (7R01MH094360-10). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10226677. Licensed CC0.

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