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

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Raw Microarray Data Download

To download the raw microarray data for tissue samples in the Allen Human Brain Atlas, click on the Download tab.

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For each tissue sample, the Microarray Data Download page has an entry listing the Tissue Sample ID, the Structure name, the RNA Integrity Number, the Experiment number, the Array number, the sample Type, the RNA in Labeling Reaction, the RNA in Array and a link to the raw microarray data file for the tissue sample in Agilent Feature Extraction output file format.

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Ontology Browser

Click on a Structure acronym link in the Microarray Search page or the Microarray Multiplanar View to open a new window with the Ontology Browser for the Allen Human Brain Atlas.

The expandable tree view of the anatomical structures is color coded and serves as a legend to the anatomic structures on other pages in the Allen Human Brain Atlas.

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In Situ Hybridization (ISH) Data

Gene expression data is available as colorimetric in situ hybridization (ISH) for specific brain regions. Images are grouped into image series that comprise an experiment. Experiments consist of slides from the same specimen that receive the same treatment, whether it is Nissl staining or ISH with a probe for a particular gene.

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  • Search by Gene Category (from the tag cloud)
  • Gene Search
  • Search by Study

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ISH Gene Search

Gene Search

You can search for experiments associated with a gene using its gene symbol, name, Homologene Group ID, or Entrez Gene ID. First, select the "Gene" radio button, type the search term in the input box and click the "Search" button. You will be offered suggestions to choose from while you type, but you can also search by typing the first three or more letters in its name or symbol and appending an asterisk ( * ) as a wildcard.

Search by Study

Data includes ISH experiments from three separate projects including: 1,000 Gene Survey in Cortex (Cortex Study), Schizophrenia Study, and Subcortex study. Please refer to the In Situ Hybridization white paper in the ALLEN Human Brain Atlas and the gene list for details.

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Select an image series by clicking the checkbox in the first column, then click the "View Selected Experiments" button to view all of your selections' images. Click "Clear Selection" to deselect all of your selections, or click "View Cart" to manage them.

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Viewing Images

Zoom and Pan (ZAP) Image Viewer

The ZAP Image Viewer allows you to navigate through an image series' thumbnails to select an image to view at higher resolution. Once selected, you can manipulate it with your mouse and use the keyboard or toolbar to take additional actions.

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Thumbnails for the entire image series are displayed across the bottom of the viewer in section order. Click a thumbnail to select it for viewing, or use the keyboard to navigate through the set. The current selection is outlined in black.

Side by Side Nissl Viewing

Once you click on the full screen viewer button, you will be taken to a screen with side by side viewers. The left hand viewer shows the ISH image series and the right hand viewer displays the Nissl image series from the same specimen block. To show the nearest Nissl section to the ISH image you are interested in, click the "Sync" checkbox. Clicking on another ISH image will automatically display its nearest Nissl section. Clicking on an image thumbnail in the Nissl image series will automatically take you to the nearest ISH image. While the "Sync" box is checked the Pan and Zoom functions will affect both ISH and Nissl images.

Scale Bar

Shows the current viewing resolution of the image, in microns. This value dynamically changes as you zoom in/out of the image. You can position the scale bar anywhere on the main image by dragging the scale bar by its ruler.

You can toggle the orientation of the scale bar from horizontal to vertical by clicking on the scale bar text.

Toolbar

 

Show current image in a full-screen viewer, on its own page

 

Open a new window to view the image series' details

 

Select ISH, Nissl, or Expression image type

 

Move the slider bar to the left to intensify the contrast or color

Keyboard Commands

F

Advance to the next image in the series

D

Go back to the previous image

R

Advance to the last image in the series

E

Go back to the first image in the series

A

Zoom in

Z

Zoom out

+

Zoom in (may need to press shift key)

-

Zoom out

Expression Mask Colors

The Expression Mask image display highlights those cells that have the highest probability of gene expression using a heat map color scale (from low/blue to high/red).

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Specimen Detail Information

Specimen Block Layout

Specimens are received as variable sized blocks of frozen tissue. Before they are sectioned for ISH experiments they are divided into a number of sub-specimens. Throughout this site, when we refer to a specimen we are actually referring to one of these sub-specimens.

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In the block diagram, the green block represents the current sub-specimen. Sibling sub-specimens are shown as grey blocks. Clicking on one of the siblings updates the current page to show the sibling's information.

Donor/Specimen Metadata

pH - tissue sample pH
RNA Integrity Number - metric indicating RNA integrity from tissue. Ranges from 1 to 10 (degraded to intact RNA)
Postmortem Interval - hours between time of death and time tissue samples frozen
Hemisphere - right or left hemisphere tissue origination
Tissue Location - tissue origination in brain
Specimen ID - internal ID
Sex - male or female
Race - ethnicity
Age - years
Handedness - right, left, or ambidextrous
Disease Categories - control or schizophrenia
Smoker - yes or no
Donor ID - internal ID

Sectioning Diagram

The sectioning diagram attempts to depict the relationship between the sections taken from a specimen, the position of each section, and the genes for which experiments have been run on those sections.

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You can click your mouse on the rectangles to go to an Image Summary page, where you can get more information about the section images generated from a particular treatment, and get summary information about gene probes.

Diagram tools

On the right of the titlebar of the Sectioning Diagram, you will find two diagram display tools, which are described below.

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Click this button to sort the section diagram by gene rather than section index. Click it again to return to the default ordering.

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Gene Detail Information

This page summarizes the data regarding the selected gene. The main section details its full name, entrez gene id, alternate gene symbols, chromosome, organism, links to related data in other projects, and gene categories that have been applied to it. A link below this section allows you to bring up a summary of all of the experiments (image series) for this gene.

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Image Series Information

The image series details include the gene and probe associated with the experiment, as well as information regarding the specimen.

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