# A Community Resource for Single Cell Data in the Brain

> **NIH NIH U24** · ALLEN INSTITUTE · 2020 · $2,853,216

## Abstract

Project Summary
A detailed census of the structure and role of cell type specific data in the brain is recognized as one of the most
promising avenues for advancing our understanding of the human brain in health and disease. The primary goal
of this project is to build a foundational community resource for housing single-cell centered data content in the
brain. By adopting a three-tiered data, tools, and knowledge paradigm we will lead, together with data generation
partners, in the development and deployment of fundamental data models, common community standards, and
scientific results to improve our understanding of the diverse cell types in the mammalian brain and its three
dimensional organizational logic. This project proposes a unified solution to the development of its resource
beginning with a data collection, quantification, and mapping framework for managing data and information
across diverse repositories. The first step is to support the acquisition of fundamental data types from data
partners by developing the data models and framework for importing structured data into the BRAIN Cell Data
Center (BCDC) in consistent data description standards that describe and facilitate best practices for community
use of multi-modal single cell data and its content. Toward achieving this end, we will partner with the
Neuroscience Information Framework (NIF), International Neuroinformatics Coordinating Facility (INCF),
Neuroscience without Borders (NWB), and other standards promoting organizations to leverage and extend
existing standards to allow external data contributors to utilize the BCDC. For these data to be coherent, spatial
common coordinate frameworks for mapping are essential, and the project develops and extends Allen Institute
Mouse Common Coordinate Framework to enable external mapping of key single cell modalities in a 2D and 3D
anatomic context for access and visualization at cell, nuclei, and/or population level. The entire resulting data,
tools, and knowledge will be made publicly available in a unified and integrated web-accessible Cell Registry
and Portal supporting data retrieval, search, visualization, and analysis of cell specific data and knowledge
synthesis. The BCDC front end will provide data feature summaries, tools, and resulting knowledge, and links to
raw data and high-resolution images, together with a programmable API/SDK that allows the community to build
their own analysis applications and contribute tools. Finally, we will amplify public impact through strong BICCN
partnership management, communication, standards committees, and analysis working groups, and develop
infrastructure for maximizing community usage, publishing standards and tutorials, and coordinating education
and outreach.

## Key facts

- **NIH application ID:** 9934018
- **Project number:** 5U24MH114827-04
- **Recipient organization:** ALLEN INSTITUTE
- **Principal Investigator:** Michael Hawrylycz
- **Activity code:** U24 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $2,853,216
- **Award type:** 5
- **Project period:** 2017-09-20 → 2022-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9934018

## Citation

> US National Institutes of Health, RePORTER application 9934018, A Community Resource for Single Cell Data in the Brain (5U24MH114827-04). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9934018. Licensed CC0.

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