Welcome

The Allen Brain Atlas API consists of a set of URLs that make most of the data behind the project available for download.  Much of this data is publicly available for the first time through the API; some of it has been available for some time, but has been documented here for the first time.  This API is an attempt to present both the old and new data sets, as well as previously documented & programmatically available data all under a single, relatively consistent interface.  For complete documentation of the API, see the ABA_API file on the "Attachments" tab above or click here to open the document in pdf format or here to open it as html

What's new about the API release?

• Image data

• • You can now download high resolution images for our complete data set.  You can also specify regions of interest and/or lower resolutions in order to download only the data you need.  Information about the images is now available as XML.

• Expression data

• • 3D volumes are available for the first time for most of our image series. These volumes contain a smoothed expression energy value for each point in the Allen Brain Atlas that has been registered to a particular image series specimen. Another API method returns a mapping file that indicates which atlas points have been registered to the specimen used in a particular image series, along with the coordinates of the closest point within the corresponding ISH image. 

• Atlas data

• • 3D volume files annotated to indicate which brain structure occupies each 3D coordinate location.  These are available at 25, 100 & 200 micron resolutions.

• NeuroBlast data

• • While the NeuroBlast search function has been available for some time through our web site, the returned data is now available as XML for the first time through the API.
    

API Update - October 8, 2008

Today we posted a small update to the API. The change includes one new method that provides a binary download of the expression energy volume. This method differs from the orginal expression energy download in three ways--

• The data includes an value for every voxel in the volume. For voxels that were not mapped, the value is -1. The original method returned a sparse volume which only contained values where the expression energy was greater than 0.
• The new volume format does not include coordinates for each voxel. Rather it is a set of four-byte sagittaly-arranged floating point values. The original format included (x,y,z) coordinates for each value.
• The data is in binary format. The original method used text.

The original method is still and will continue to be supported. Here's an example of the volume in the original format: http://www.brain-map.org/aba/api/expression/75144618.sva And here in the new format: http://www.brain-map.org/aba/api/expression/75144618.bva

Demonstration applications

Getting Started

1. Download the API documentation here (pdf) or here (html).
2. Get more details on the example code and demonstration application here
3. And download data sets here and the example code here

Let Us Hear From You

Comments?  Suggestions?  Requests?  Something to share with other ABA API users?  Please let us know!  Use the "Add Comment" link below to post your thoughts here, or drop an email to ABA_API@alleninstitute.org.