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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.

From the heatmap view in the Human Brain Atlas, you can see the Structure Ontology list from the selected data point in the heatmap. Clicking on the link at the bottom of the structure ontology list above the heatmap in the Human Brain Atlas will bring you to the Human Brain Atlas Guide.

From the In Situ Hybridization data in the Human Brain Atlas, you can also arrive at the Human Brain Atlas Guide by clicking on a hotspot while viewing an experiment in the High Resolution Image Viewer.

Either of these actions 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 for providing a context for the ISH images in the Allen Human Brain Atlas. The viewer is divided into two windows, a collapsible hierarchy of brain structures on the left and an image viewer showing annotated drawings of a 34yr old human brain 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 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 bring up the name and acronym of the structure in the bar at the top-left 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 the second drop-down menu in the top-right corner of the image viewer. Human Brain Atlas Guide illustrates the approximate locations of the structures in the adult human brain. Cortex - Mod. Brodmann uses annotations that delineate cortical Brodmanns areas. Cortex - Gyral shows the same images with the annotations indicating the gyral representation of the cortex.

The toolbar to the right of the drop-down menus allows you to change the settings of the image viewer. From this menu, you can download individual images and toggle features, such as the Atlas or structure metadata, thumbnail image viewing, or the various annotations.

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 image series. The main part of the viewer is an interactive window where the onscreen tools can be used to navigate the image series. An image can also 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 on 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


Zoom in


Zoom out

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