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ALLEN Human Brain Atlas

This is the online help for the Human Brain Atlas web application.

The Data Set

The Allen Human Brain Atlas consists of two primary sources of gene expression data: microarray numerical value data and in situ hybridization (ISH) image data.

For complete details please see the Microarray Platform Selection, Whole Brain Microarray and In SituHybridization white papers on our Documentation page.

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Brain Explorer 2 Application

Brain Explorer 2 is a desktop software application for viewing human neuroanatomy and the Allen Human Brain Atlas microarray gene expression data in the framework of the Magnetic Resonance Images of the sampled brains.

Once you have chosen a gene of interest (by clicking on the heat map), you can explore a three dimensional representation of its gene expression by clicking on the "Brain Explorer" link over the heat map. When Brain Explorer opens, you will be taken to a screen that displays the Image Viewer, the Structure Ontology Viewer, and the Gene List.

Image Viewer

The Image Viewer will automatically show the 3D expression representations of your gene of interest on every sampled brain. Cortical gene expression is overlaid on an inflated white matter surface for each donor brain, with spots under the white surface representing gene expression in the subcortical regions of the brain. A striped expression pattern on the cortical surface is a result of having sampled from every other slab of cortical tissue. Under each representative brain is the heat map for the probe you selected. Clicking on that heat map will pinpoint the area in the brain from which the sample was taken.

The gene expression colors correspond to the settings in the Atlas with which you were viewing the original heat map. To change the gene expression representation, click on the "Gene" tab in the top left hand corner of your screen and choose either z-score or raw data representations of the gene expression data.

A compass in the right hand corner of the image viewer depicted by a stylized head can be used to rotate the brains by clicking and dragging your cursor. You can look at a single brain by clicking on the magnifying glass above that brain. Choosing a data point, either by clicking on the heat map below the brain or on a brain region itself, will bring up the gene symbol, the location of the sample and the expression level and z-score in the left hand corner of the Image Viewer.

You can zoom using either the wheel on your mouse or using the Zoom scrollbar in the lower right hand corner of the Image Viewer.

Structure Ontology Viewer

The Structure Ontology Viewer shows the entire collapsible ontology for the human brain including the color coding used by our expert annotation team to visualize structural boundaries. Two columns to the right of the ontology determine the type of data displayed in the Image Viewer. "A" represents annotation and when checked, will show a visual representation of that structure in the Image Viewer. "G" represents gene expression and when checked, will show gene expression in that structural domain.

The default organization for the Structure Ontology is the Hierarchical View, but if you are unfamiliar with the ontology, you can click on the Alphabetical View to see the structure list in alphabetical order.

The Bookmarks tab is a space where you can create and save favorite views of the brain. Several default views are already saved that will rotate the brain back into common viewing frames.

Gene List

This section displays the gene probes you have selected and downloaded in this session. When more than one gene probe has been downloaded, clicking on one probe will show its gene expression profile in the image viewer. Right clicking on the gene probe name will bring up a menu where you can view the gene detail page (Get Info), be taken to the Multiplanar View of the probe (View Images) or copy the gene information for use in another application.



Selects cursor rotation tool mode


Selects cursor pan tool mode


Selects cursor selection tool mode


Toggle Sagittal Atlas section viewing


Toggle Coronal Atlas section viewing


Toggle Horizontal Atlas section viewing


Centers the Viewer on the current pinpointed expression data point


Turns on the cutting planes


Toggles the Structure Ontology and Gene List View

Advanced Features

Atlas Tab:

You can show opaque three dimensional structures of the brain by "showing" or "hiding" structures from this menu. The "Transparent" function allows you to see transparent views of the structures to view the anatomical relationships between them.

Selecting the sagittal, coronal or horizontal sections (or clicking on one of the section image buttons in the toolbar) will superimpose a single plane of the MRI images from each brain on your image space. These planes can be moved once the selection tool mode button in the toolbar is selected. Selecting "Show Annotation on Section" from this menu will color the MRI images according to the brain structure ontology.

Gene Tab:

When you have a gene selected, the Gene Tab menu allows to you to show all expression, hide all expression (for instance to then select a single structure) or toggle expression (for instance, unselect your region of interest then toggle to see expression in only that region).

You can also show or remove threshold controls and choose the visual representation of your data (raw data vs. z-score) from this menu.

To be taken to the gene detail page, select "Get Info". To see the Multiplanar view, choose "View Images". These functions are also available by right-clicking on the gene name in the Gene List.

Clipping Planes:

When this function is selected, either by toggling the cutting tools button in the toolbar or selecting "Clipping Planes" from the View drop down menu, you can make coronal, sagittal or horizontal cuts in your view of the brain and related data. To cut in a particular plane, make sure the cursor is in selection tool mode, and then click and drag on the plane you are interested in clipping.

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Image and Probe Navigation

In the image at left you see the 2D images associated with the point selected by the MRI crosshairs. The viewer on the left hand shows a larger view of the brain specimen, with a blue highlight around the chunk of that specimen from which the current sample was taken. The viewer on the right hand shows a detailed view of that chunk, with structure annotations visible.

You can navigate from the image viewers as well. The strip of thumbnail images at the bottom of each viewer shows all of the images from its parent specimen, in sectioning order. Clicking on a thumbnail image in the left hand viewer will move the MRI crosshairs and open a new set of images in the right hand viewer. Click on one of the structures to move the MRI crosshairs to the location where that structure was sampled. As you move your mouse over the structures in the right hand viewer its name will appear in the upper-left corner of the viewer.

Use the toolbar icons to add or remove structure annotations such as structure outline, structure colors, and structure labels. To show all specimen images from this block in order, including the Nissl, ISH, SMI-32 and pre- and post-cut LCM images, click . To see the block face images, click . Use the full-page viewer icon to launch a new full-page viewer in a new window for the current image set.

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Microarray Specimen Magnetic Resonance Images (MRI)

Select the MRI tab to view the Microarray Specimen MRI page, or click on a Donor link in the Gene Detail or Probe Detail pages.

The Microarray Specimen MRI page displays axial, coronal and sagittal planar MRI images of the brain. Drag the red axes in order to change the view coordinates. Donor information including Organism, Age, Sex, Ethnicity, and Postmortem Interval (PMI).

The MRI data files are available for download in NIFTI format by clicking on the T1, T2 and DTI links.

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