Adult Human Neuroanatomic Reference Guide

The Neuroanatomic Reference Guide is meant to provide a spatial context for the anatomic structures of the Adult Human Brain.

Clicking on the link at the bottom of the structure ontology list above the heatmap in the Human Brain Atlas,

or clicking on a hotspot in the Human ISH Nissl images,

will bring you to the Interactive Atlas Viewer with the structure of interest highlighted in purple.

You can also reach this guide by selecting "Human Brain Atlas Guide" from the first drop-down menu in the top right-hand corner whilst in any of the reference atlases in the Interactive Atlas Viewer.

Interactive Atlas Viewer

The Interactive Atlas Viewer is a valuable tool for exploring the anatomy of the human brain and providing a context for the ISH images on the Allen Human Brain Atlas. The viewer is divided into two windows, a collapsible hierarchy of brain structures on the left and annotated images of the Nissl-stained reference human brains on the right.

Structure Hierarchy

The anatomical structures of the reference atlas are listed in a hierarchical tree in the left-hand pane of the viewer. The tree can be expanded and collapsed to browse to a structure of interest. Entering a structure name or abbreviation in the text box above the ontology will open up the list to that particular structure, and bring you to that structure in the image viewer to the right. Clicking on any structure name will also highlight that structure in the image viewer.

Structures in the list labeled with a black font have a corresponding structure in the atlas. Structures listed in medium gray have at least one descendent with an annotated structure. Those structures listed in a light gray italic font do not have an annotated structure in the atlas.

Image viewer

The right-hand pane of the interactive atlas viewer displays the drawings of the reference brains in a #Zoom and Pan (ZAP) Image Viewer. Thumbnail images of each section line the lower border of the pane; click on any one thumbnail to view it in the main viewing window.

Images in the main viewer are annotated with polygons hand drawn by Allen Institute neuroanatomists. The polygons will scale and move with the image as the user zooms in and out or moves the image in any direction. Moving the computer cursor over the image will highlight individual structures; the name and acronym of the structure will be displayed at the top of the window. Clicking on a structure will also highlight the structure in the hierarchy of the left-hand pane.

Three configuration options are available from a toolbar at the top of the pane. A text button on the left allows the user to toggle on or off the display of the structure acronym over the top of the selected region. The "Selection Colors" drop-down menu provides the option to color all individual structures with the unique colors of the Allen Reference Atlas, to color only the selected structure or to turn off coloring altogether. The ‘polygon’ button on the right allows a user to toggle on or off the rendering of all structures across the entire brain image.

Zoom and Pan (ZAP) Image Viewer

The Zoom and Pan (ZAP) Image Viewer is a powerful tool to navigate and view the images in an experiment. The main part of the viewer is an interactive window where an image can be repositioned by dragging with a mouse. Use the scroll wheel or the keyboard to zoom in or out.

Scale Bar

Drag the scale bar with your mouse to the desired location. Click the text with your mouse to toggle between horizontal and vertical.

Keyboard Commands

Use the keyboard to navigate through the image series. Keyboard commands include:




Advance to the next image in the series


Go back to the previous image in the series


Advance to the last image in the series


Go back to the first image in the series


Zoom in


Zoom out

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Zoom in. Please note that some keyboards may require the [Shift] key be held down while pressing the [+] key



Zoom out

You can also use the arrow keys to pan the current image.