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The Allen Human Brain Atlas is a multimodal atlas of the human brain that integrates anatomic and microarray-based gene expression information. Microarray sampling sites (~400-1000 sites per brain) were identified by expert anatomists using cytoarchitectural information from multiple histological stains. Sampling site delineations in the high resolution histological images were subsequently mapped into each individual's MR image space to provide 3-D anatomical context. All brains were also registered to MNI space to enable cross-individual comparisons.

From the API, you can:

Image Modified Download expression values
Image Modified Query the correlative and differential search services
Image Modified Download MRI images

Experimental Overview and Metadata

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ExpressionStructures
ExpressionStructures
Downloading Expression Values

Normalized expression values can be obtained by specifying:

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Usage of this service is demonstrated in the scatter plot and SPM example applications. Also see example code on how to transform each microarray sample to MNI space.

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SearchServices
SearchServices
Differential search

The differential search function finds probes that show the greatest difference between two sets (target and contrast) of user-defined structures. For each probe, a 2-sample t-test is performed followed by Benjamini and Hochberg false discovery rate correction. The null hypothesis is that the average expression level of samples in the contrast set of structures is less than the average expression level of samples in the target set of structures. Resulting p-values are sorted in ascending order. Search results can also be sorted by fold-change (log ratio of expression) in descending order.

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Figure: Screenshot of top returns of a correlative search for probes with similar expression to a PVALB probe with expression values displayed as a z-score heatmap.

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DownloadImages
DownloadImages
Magnetic Resonance Imaging

T1-weighted MPRAGE scans were acquired for the postmortem brains using 3T Siemens Trio MR scanners (TI=900ms, TR=1900ms, TE=3.03ms, 9 degree flip angle, 1mm isotropic voxels). Scans were performed in cranio for some brains and ex cranio for others. See the Microarray whitepapers for more specific scan sequence details for each brain.

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