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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 are were also registered to MNI space to enable cross-individual comparisons.


RNA isolated from each sample area was hybridized to a custom Agilent 8x60k microarray chip to measure gene expression over the transcriptome. All least two different probes were available for 93% of genes. Probes were located on different exons as much as possible when multiple probes were available for a gene. For 60 genes, a set sets of tiling probes were probes was designed.

Each sampling site is was associated to a Structure by expert anatomist anatomists using cytoarchitectural information from multiple histological stains. Structures are arranged in a hierarchical organization. Each structure has one parent and denotes a "part-of" relationshiporganized hierarchically into a tree in which children structures are “parts of” their parent structure. Structures are assigned a color to colors that visually emphasize their hierarchical positions in the brainthe hierarchical relationships.

See the structure ontology page for more information.

Gene expression data for samples passing quality control are normalized to enable cross-comparison between batches and of samples processed at different times or samples belonging to different donors.  See the whitepaper for For more details on microarray data generation and processing see the Microarray whitepapers.

Normalized microarray expression values can be downloaded in several ways:


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.

Differential search

Differential The differential search find 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.

The differential  differential search function can be access accessed through the Web application or using the API.


Figure: Screenshot of top returns of a differential search for genes with higher expression in the thalamus than in the cerebral cortex. ZThe z-score heatmap shows enrichment (red) in the thalamus (structure color: light green) compare relative to other brain regions.

Usage of this service is demonstrated in the SPM example application.

Correlative search

Correlative The correlative search function finds probes with similar expression profile similar to the that of a selected seed probe over all samples within a user-specified structure. Pearson's correlation coefficient is computed for all probes and the results ranked in descending order.


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 white paperwhitepapers for more specific scan sequence details for each brain.


All T1 images were registered to MNI space. FreeSurfer's affine registration was used for the in cranio scans. For ex cranio brains, the T1 was first rigidly aligned using FSL (Jenkinson, et. al, 2002) and then non-rigidly aligned using ANTS (Avants, et. al., 2011). The 3-D affine transform from a location in the MR volume to MNI space is encapsulated in the Alignment3d model.

Examples queries:

  • Download links for all MR and DTI data available
    Code Block,
    rma::criteria,products[abbreviation$in'HumanMA','HumanSZ','HumanCtx','HumanSubctx'],organism[name$il'Homo Sapiens'],
  • Download TI MR scan for donor 'H0351.2002'
    Code Block
  • Download the MR to MNI transform parameters
    Code Block,