# A comprehensive whole-brain atlas of cell types in the mouse

> **NIH NIH U19** · ALLEN INSTITUTE · 2021 · $12,859,228

## Abstract

Project Summary (Overall)
For the brain (or any other biological systems), cells are a fundamentally important level of organization
between genes/molecules and networks/systems. The mammalian brain is composed of millions to billions of
neurons and non-neuronal cells with diverse properties and extremely intricate connections to form highly
specific and hierarchically organized circuits and networks. To unravel the principles of information processing
in brain circuits, it is essential to have a systematic understanding of its components – the cell types, and to
have tools to monitor and manipulate them in the living brain to probe their roles in the circuits. However, it is
still unclear how many cell types there are in the brain and how to even define them. Recent high-throughput
technology advancement, especially in the areas of sequencing and imaging, has created an unprecedented
opportunity to collect comprehensive information about individual cells in large scales to enable data-driven cell
type classification. We will form a Comprehensive Center on Mouse Brain Cell Atlas, and our goal is to create
a comprehensive whole-brain atlas of cell types in the mouse encompassing molecular, anatomical and
functional annotations of cell types. We will conduct large-scale single-cell transcriptomic analysis across the
entire mouse brain, as well as systematic sampling of neuronal morphology and connectivity in a wide range of
brain areas. In selected proof-of-principle cases, we will examine the correspondence among the
transcriptomic, morphological, connectional and/or functional properties of the same cells, to gain an
understanding what defines a cell type. Finally, we will generate a census of the number and location of cells
for each type, and new genetic tools targeting selected cell types. We will establish a Data Core to provide
data management systems for integrating the diverse data collections and to provide data processing and
mapping infrastructure and expertise to transform raw data into quantitative cell characterization features. We
will also establish an Administrative Core to address the operational management of the Center, including
fiscal management, project management, strategic planning, progress reporting, and support for collaboration
and communication. Altogether this project will create a first version of a comprehensive cell type atlas for an
entire mammalian brain with enduring values to the community towards the understanding of brain function in
healthy and diseased states.

## Key facts

- **NIH application ID:** 10168628
- **Project number:** 5U19MH114830-05
- **Recipient organization:** ALLEN INSTITUTE
- **Principal Investigator:** David J Anderson
- **Activity code:** U19 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $12,859,228
- **Award type:** 5
- **Project period:** 2017-09-20 → 2023-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10168628

## Citation

> US National Institutes of Health, RePORTER application 10168628, A comprehensive whole-brain atlas of cell types in the mouse (5U19MH114830-05). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10168628. Licensed CC0.

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