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ALLEN BRAIN ATLAS API

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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.

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  • Find Structure ID for "thalamus" (id = 4392)
    No Format
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure,
    rma::criteria,[name$il'thalamus'],ontology[name$eq'Human Brain Atlas'],
    rma::options[only$eq'structures.id']
    
  • Find Structure ID for "cerebral cortex" (id = 4008)
    No Format
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure,
    rma::criteria,[name$il'cerebral cortex'],ontology[name$eq'Human Brain Atlas'],
    rma::options[only$eq'structures.id']
    
  • Use Structure IDs as parameters to the connected service
    No Format
    http://api.brain-map.org/api/v2/data/query.xml?criteria=service::human_microarray_differential
    [structures1$eq4008][structures2$eq4392][sort_by$eq'fold-change']
    
  • Visualize the same search result in the Web application 

Image Modified

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

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  • Find Probe ID for probe "CUST_11451_PI416261804" (id = 1052410)
    No Format
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Probe,
    rma::criteria,[name$eq'CUST_11451_PI416261804'],
    rma::options[only$eq'probes.id']
    
  • Find Structure ID for "Brain" (id = 4005)
    No Format
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure,
    rma::criteria,[name$il'brain'],ontology[name$eq'Human Brain Atlas'],
    rma::options[only$eq'structures.id']
    
  • Use Probe and Structure IDs as parameters to the connected service
    No Format
    http://api.brain-map.org/api/v2/data/query.xml?criteria=service::human_microarray_correlation
    [probes$eq1052410][structures$eq4005]
    
  • Visualize the same search result in the Web application

Image Modified

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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  • Download links for all MR and DTI data available
    No Format
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor,
    rma::criteria,products[abbreviation$in'HumanMA','HumanSZ','HumanCtx','HumanSubCtx'],organism[name$il'Homo Sapiens'],
    rma::include,specimens(well_known_files(well_known_file_type[name$in'T1-MRI','T2-MRI','DTI-MRI'])),
    rma::options[only$eq'donors.name,products.name,well_known_files.download_link,specimens.id']
    
  • Download TI MR scan for donor 'H0351.2002'
    No Format
    http://human.brain-map.org/api/v2/well_known_file_download/157723301
    
  • Download the MR to MNI transform parameters
    No Format
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor,
    rma::criteria,products[abbreviation$eq'HumanMA'],
    rma::include,specimens[parent_id$eqnull](alignment3d),
    rma::options[only$eq'donors.id,donors.name,specimens.id']
    

Image Modified

Figure: T1 MR scan for donor 'H0351.2002'

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