# Collaboratory for atlasing cell type anatomy in the female and male mouse brain

> **NIH NIH U01** · COLD SPRING HARBOR LABORATORY · 2021 · $2,389,198

## Abstract

Even though scientists have been captivated by the diversity of brain cells for well over a century, since the
initial anatomical descriptions by Santiago Ramón y Cajal, it is only recently that the developments in new
technologies allowed us to truly appreciate the astonishing complexity of cell types in the mammalian brain.
Yet, even today, our knowledge of cell type anatomy and function is largely limited to a few brain areas, such
as the sensory cortex or the hippocampus. This lack of whole-brain data has led to generalizations from one
brain area to other regions with similar architecture. However, our preliminary studies applying quantitative
whole brain analyses have revealed unexpected region specific differences in cell type ratios and uncovered
new gender-based differences in cellular anatomy that can inform our understanding of brain development,
wiring and function. We thus believe that closing the gaps in our knowledge of the cellular architecture of the
brain will be a major contribution to enable a modern quantitative understanding of the brain as a system.
Here we propose to establish an Anatomical Collaboratory for Systematic Atlasing of Cell-Type Distribution
and Morphology in female and male brain. This Collaboratory will apply standardized, unbiased and largely
automated methods developed in our laboratories to atlas the distribution and morphology of >80 molecularly
defined cell classes and cell type across all regions of the female and male brain. This work will yield the most
comprehensive characterization of cell type anatomy in the mammalian brain to date, establishing a structural
basis for building an integrated Cell Type Brain Atlas.
Specific Aim 1: Quantify and atlas the brainwide distribution of molecularly defined cell types. This
work will generate a quantitative brain atlas of the distributions of molecularly defined cell classes and cell
types within the Common Coordinated Framework (CCF) of the adult brain.
Specific Aim 2: Quantify and atlas the brainwide morphologies of molecularly defined cell types. This
work will generate a comprehensive structural brain atlas of somatodendritic cell-type morphologies across all
CCF anatomical areas in the female and male brain.
Specific Aim 3: Develop and deploy a neuroinformatics infrastructure: an integrated web portal for
cell-type specific data, tools, and analytics. This work will disseminate the generated data via CSHL cell
type-dedicated BrainArchitecture web portal and through the BRAIN Cell Data Center (BCDC).
!

## Key facts

- **NIH application ID:** 10168627
- **Project number:** 5U01MH114824-05
- **Recipient organization:** COLD SPRING HARBOR LABORATORY
- **Principal Investigator:** PARTHA Pratim MITRA
- **Activity code:** U01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $2,389,198
- **Award type:** 5
- **Project period:** 2017-09-20 → 2023-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10168627

## Citation

> US National Institutes of Health, RePORTER application 10168627, Collaboratory for atlasing cell type anatomy in the female and male mouse brain (5U01MH114824-05). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10168627. Licensed CC0.

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