---
title: "Allen Brain Atlas"
chunk: 1/2
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"
---

The Allen Mouse and Human Brain Atlases are projects within the Allen Institute for Brain Science which seek to combine genomics with neuroanatomy by creating gene expression maps for the mouse and human brain. They were initiated in September 2003 with a $100 million donation from Paul G. Allen and the first atlas went public in September 2006. 
As of May 2012, seven brain atlases have been published: Mouse Brain Atlas, Human Brain Atlas, Developing Mouse Brain Atlas, Developing Human Brain Atlas, Mouse Connectivity Atlas, Non-Human Primate Atlas, and Mouse Spinal Cord Atlas. There are also three related projects with data banks: Glioblastoma, Mouse Diversity, and Sleep. It is the hope of the Allen Institute that their findings will help advance various fields of science, especially those surrounding the understanding of neurobiological diseases. The atlases are free and available for public use online.

== History ==
In 2001, Paul Allen gathered a group of scientists, including James Watson and Steven Pinker, to discuss the future of neuroscience and what could be done to enhance neuroscience research (Jones 2009). During these meetings David Anderson from the California Institute of Technology proposed the idea that a three-dimensional atlas of gene expression in the mouse brain would be of great use to the neuroscience community. The project was set in motion in 2003 with a 100 million dollar donation by Allen through the Allen Institute for Brain Science. 
The project used a technique for mapping gene expression developed by Gregor Eichele and colleagues at the Max Planck Institute for Biophysical Chemistry in Goettingen, Germany. The technique uses colorimetric in situ hybridization to map gene expression. The project set a 3-year goal of finishing the project and making it available to the public.
An initial release of the first atlas, the mouse brain atlas, occurred in December 2004. Subsequently, more data for this atlas was released in stages. The final genome-wide data set was released in September 2006. However, the final release of the atlas was not the end of the project; the Atlas is still being improved upon. Also, other projects including the human brain atlas, developing mouse brain, developing human brain, mouse connectivity, non-human primate atlas, and the mouse spinal cord atlas are being developed through the Allen Institute for Brain Science in conjunction with the Allen Mouse Brain Atlas.

== Goals for the project ==

The overarching goal and motto for all Allen Institute projects is "fueling discovery". The project strives to fulfill this goal and advance science in a few ways. First, they create brain atlases to better understand the connections between genes and brain functioning. They aim to advance the research and knowledge about neurobiological conditions such as Parkinson's, Alzheimer's, and Autism with their mapping of gene expression throughout the brain. 
The Brain Atlas projects also follow the "Allen Institute" motto with their open release of data and findings. This policy is also related to another goal of the Institute: collaborative and multidisciplinary research. Thus, any scientist from any discipline is able to look at the findings and take them into account while designing their own experiments. Also available to the public is the Brain Explorer application.

== Research techniques ==
The Allen Institute for Brain Science uses a project-based philosophy for their research. Each brain atlas focuses on its own project, made up of its own team of researchers. To complete an atlas, each research team collects and synthesizes brain scans, medical data, genetic information and psychological data. With this information, they are able to construct the 3-D biochemical architecture of the brain and figure out which proteins are expressed in certain parts of the brain. To gather the needed data, scientists at the Allen Institute use various techniques. One technique involves the use of postmortem brains and brain scanning technology to discover where in the brain genes are turned on and off. Another technique, called in situ hybridization, or ISH, is used to view gene expression patterns as in situ hybridization images.
Within the Brain Atlases, these 3-D ISH digital images and graphs reveal, in color, the regions where a given gene is expressed. In the Brain Explorer, any gene can be searched for and selected resulting in the in situ image appearing as an easily manipulated and explored fashion. Part of the creation of this anatomy-centred database of gene expression, includes aligning ISH data for each gene with a three-dimensional coordinate space through registration with a reference atlas created for the project.

== Contributions to neuroscience ==
The different types of cells in the central nervous system originate from varying gene expression. A map of gene expression in the brain allows researchers to correlate forms and functions. The Allen Brain Atlas lets researchers view the areas of differing expression in the brain which enables the viewing of neural connections throughout the brain. Viewing these pathways through differing gene expression as well as functional imaging techniques permits researchers to correlate between gene expression, cell types, and pathway function in relation to behaviors or phenotypes.
Even though the majority of research has been done in mice, 90% of genes in mice have a counterpart in humans. This makes the Atlas particularly useful for modeling neurological diseases. The gene expression patterns in normal individuals provide a standard for comparing and understanding altered phenotypes. Extending information learned from mouse diseases will help better the understanding of human neurological disorders. The atlas can show which genes and particular areas are effected in neurological disorders; the action of a gene in a disease can be evaluated in conjunction with general expression patterns and this data could shed light on the role of the particular gene in the disorder.