BrainMaps Tutorial

For up to date issues or problems with this database please see the wiki.
For more information, please visit BrainMaps.

BrainMaps is an interactive multi-resolution next-generation brain atlas that is based on over 20 million megapixels of sub-micron resolution, annotated, scanned images of serial sections of both primate and non-primate brains and that is integrated with a high-speed database for querying and retrieving data about brain structure and function over the internet.

Therefore, this is a wonderful place to search for and find images of brain regions.

In the following example, we search for Habenula.

Note, whenever possible you should allow the NIF to autocomplete of terms since this will bring back synonyms for your term.  In this case, the Habenula has the synonyms Habenular Nucleus, and HB.

BrainMaps data can be found in the Data Type > Images and brings back 54 histological sections that contain the Habenula or the habenular nucleus.  In some instances, the term Hb will bring back non-specific results. 

Clicking on the blue link, leads to the page in BrainMaps that contains the label for the brain region, Hb. 

Clicking on the arrows will lead to sections adjacent to the current section.  The user can also zoom into all images to a fair degree.  Note that not all sections will have labels, only a few sections are fully labeled.

To get back to the home page for BrainMaps, or the main page for this dataset, the user can click on the blue breadcrumbs at the top of the BrainMaps page.  Below is the result of clicking on the "Giemsa + retinal projections, coronal, histo, Whole-Brain, adult" link.

For more information, please visit BrainMaps.