Below is a description of what you'll find in the example code & data packages. To the right is a brief walk through of a demonstration application.
This code is contributed by users of the API and is offered to the community with the hope that it will prove useful. All of the code and applications referenced here are made available under the same terms of use as the rest of the Allen Brain Atlas web site. Download the example code & demonstration application here. Be sure to also download the API documentation here (pdf) or here (html) and the extra data sets here.
Code Samples
API Wrapper
This Java class wraps the API URLs in convienience methods. A simple caching scheme is implemented.
3D Volume classes
A set of Java classes for reading & writing 3D expression volume files retrieved through the API. Methods are availble for reading & writing our text-based volume data in MetaImage-compatible binary format; other methods allow the extraction of a slice of volume data as a Java BufferedImage.
Images
Define & download regions of interest or complete images at multiple resolutions.
Visualization
Java classes for displaying and navigating 3D volumes, setting color maps, adjusting image dynamic range.
Analysis
Generate a median expression volume over any input set of expression volumes. Query volume files and compute an overall gene expression "energy" statistic for each region. Calculate ISH image regions of interest based on 3D regions of interest defined in the Atlas coordinate space.
More
Several general purpose Java Swing-based UI forms for tasks like downloading & processing data; classes for efficiently indexing Gene-to-image_series mapping data; define/read/write 2D & 3D ROIs.
Data
Annotated Atlas volumes
3D volume files annotated with the Allen Brain Atlas structure IDs at each voxel. Volumes available at 25, 100 & 200 micron resolution.
Brain structure ontology
The major structures of the Allen Brain Atlas and their parent-child relationships; includes the abbreviations and IDs used throughout the ABA data set.
Gene to image series mapping
A complete list of the genes available in the ABA data set, mapped to the IDs of all of the image series for each. Each entry also references EtrezGene IDs and NCBI accession numbers.
A demonstration application built on the ABA API (view as slideshow)
