Allen Brain Atlas - Research Techniques

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.