---
title: "Allen Brain Atlas"
chunk: 2/2
source: "https://en.wikipedia.org/wiki/Allen_Brain_Atlas"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T03:48:26.197389+00:00"
instance: "kb-cron"
---

== Brain explorer ==
The Allen Brain Atlas website contains a downloadable 3-D interactive Brain explorer. The explorer is essentially a search engine for locations of gene expression; this is particularly useful in finding regions that express similar genes. Users can delineate networks and pathways using this application by connecting regions that co-express a certain gene. The explorer uses a multicolor scale and contains multiple planes of the brain that let viewers see differences in density and expression level. The images are a composite of many averaged samples so it is useful when comparing to individuals with abnormally low gene expression.

== Atlases ==

=== Mouse Brain ===
The Allen Mouse Brain Atlas is a comprehensive genome-wide map of the adult mouse brain that reveals where each gene is expressed. The mouse brain atlas was the original project of the Allen Brain Atlas and was finished in 2006. The purpose of the atlas is to aid in the development of neuroscience research. The hope of the project is that it will allow scientists to gain a better understanding of brain diseases and disorders such as autism and depression.

=== Human Brain ===
The Allen Human Brain Atlas was made public in May 2010. It was the first anatomically and genomically comprehensive three-dimensional human brain map. The atlas was created to enhance research in many neuroscience research fields including neuropharmacology, human brain imaging, human genetics, neuroanatomy, genomics and more. The atlas is also geared toward furthering research into mental health disorders and brain injuries such as Alzheimer's disease, autism, schizophrenia and drug addiction.

=== Developing Mouse Brain ===
The Allen Developing Mouse Brain Atlas is an atlas which tracks gene expression throughout the development of a C57BL/6 mouse brain. The project began in 2008 and is currently ongoing. The atlas is based on magnetic resonance imaging (MRI). It traces the growth, white matter, connectivity, and development of the C57BL/6 mouse brain from embryonic day 12 to postnatal day 80.
This atlas enhances the ability of neuroscientists to study how pollutants and genetic mutations effect the development of the brain. Thus, the atlas may be used to determine what toxins pose special threats to children and pregnant mothers.

=== Mouse Brain Connectivity ===
The Allen Mouse Brain Connectivity Atlas was launched in November 2011. Unlike other atlases from the Allen Institute, this atlas focuses on the identification of neural circuitry that govern behavior and brain function. This neural circuitry is responsible for functions like behavior and perception. This map will allow scientists to further understand how the brain works and what causes brain diseases and disorders, such as Parkinson's disease and depression.

=== Mouse Spinal Cord ===
Unveiled in July 2008, the Allen Mouse Spinal Cord Atlas was the first genome-wide map of the mouse spinal cord ever constructed. The spinal cord atlas is a map of genome wide gene expression in the spinal cord of adult and juvenile C57 black mice. The initial unveiling included data for 2,000 genes and an anatomical reference section. A plan for the future includes expanding the amount of data to about 20,000 genes spanning the full length of the spinal cord.
The aim of the spinal cord atlas is to enhance research in the treatment of spinal cord injury, diseases, and disorders such as Lou Gehrig's diseases and spinal muscular atrophy. The project was funded by an array of donors including the Allen Research Institute, Paralyzed Veterans of America Research Foundation, the ALS Association, Wyeth Research, PEMCO Insurance, National Multiple Sclerosis Society, International Spinal Research Trust, and many other organizations, foundations, corporate and private donors.

== See also ==
List of neuroscience databases
EMAGE, the e-Mouse Atlas of Gene Expression

== References ==

Pawel K. Olszewski, "Analysis of the network of feeding neuroregulators using the AllenBrain Atlas" Neuroscience of Behavior, 1 January 2009.
Robert Lee Hotz, "Probing the Brain's Mysteries" The Wall Street Journal, 24 January 2012.
Allan Jones, "The Allen Brain Atlas: 5 years and beyond", Nature, 2009. doi:10.1038/nrn2722.

== External links ==
Official website
Virginia Gewin (2005). "A Golden Age of Brain Exploration". PLOS Biology. 3 (1): e24. doi:10.1371/journal.pbio.0030024. PMC 544547. PMID 15660159. 
"New Brain Atlas Unveils 3-D Gene Map". ABC News. 26 September 2006.