Versions Compared


  • This line was added.
  • This line was removed.
  • Formatting was changed.

Developing Human Reference Atlases

To complement the RNA-Seq and microarray gene expression data, reference atlases were created at three developmental stages; 15 pcw, 21 pcw and 34 years. The reference atlas are full-color, high-resolution, Web-based digital brain atlases accompanied by a systematic, hierarchically organized taxonomy of developing brain structures.

From the heatmap view in the BrainSpan Atlas of the Developing Human Brain, you can see the Structure Ontology list from the selected data point in the heatmap. Clicking on the structure link will bring you to the appropriate developmental stage in the Reference Atlas (adult vs. prenatal).

From the In Situ Hybridization data in the BrainSpan Atlas of the Developing Human Brain, 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.

Clicking on the annotation links from the "Reference Atlas" tab in the banner menu will also take you to the Interactive Atlas Viewers. Supporting data used to create these Atlases is also available for viewing or for download.

Interactive Atlas Viewer

The Interactive Atlas Viewer is a valuable tool for exploring the anatomy of the developing human brain and providing a context for the experimental ISH images. The viewer is divided into three windows, a collapsible hierarchy of brain structures on the left and annotated images on the right, and a thumbnail strip along the bottom.

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. Clicking on any structure will highlight that structure in the image viewer to the right.

To find a particular structure, start typing in part of the name or acronym of the structure and a list of structures will be suggested. 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 images of the reference brain in a Zoom and Pan (ZAP) Image Viewer. Thumbnail images of each section of the reference atlas line the bottom of the Webpage; click on any thumbnail image to view it in the main viewing window. You can navigate to any of our other Interactive atlases from the dropdown menu in the top right hand of the viewer. When a structure is selected, navigating to an atlas with the same Ontology (i.e. adult human to prenatal human) will open up that atlas with the same structure highlighted.

Images in the main viewer are annotated with polygons hand-drawn by Allen Institute neuroanatomists. There are four configuration options available from the second drop-down menu in the top-right corner of the image viewer. Cortex - Gyral uses annotations indicating the gyral representation of the cortex. Cortex - Mod. Brodmann uses annotations that delineate cortical Brodmanns areas. Human Brain Atlas Guide illustrates the approximate locations of the structures in the adult human brain. The default view is the Atlas view showing just the neuroanatomists drawings, but you can also view the Nissl images with the anatomy polygons overlaying the cytoarchitecture. The polygons will scale and move with the image as you zoom in and out or move the image in any direction. Moving the computer cursor over the image will highlight individual structures; the name and acronyms of the structure in the Reference Atlas will be displayed at the top of the window. Clicking on a structure will also highlight the structure name in the hierarchy in the left-hand pane.

From the tool dropdown menu in the top right of the viewer, you can choose configuration options. The title metadata, outlines and ontology colors can be removed, which is often most useful when viewing the Nissl images under the polygons.

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 scale bar text with your mouse to toggle between horizontal and vertical orientation.

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

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="6e99d2cbc95c4f3f-a2e9b73d-44cc4c0f-85118f88-50c0a8dd093463ad4508a827"><ac:plain-text-body><![CDATA[


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.