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From the above query, gene Pdyn has one sagittal SectionDataSet (id=69782969) and one coronal SectionDataSet (id=71717084). In the web application, images from the experiment are visualized in an experiment detail page. All displayed information, images and structural expression values is also available through the API.

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Figure: Experiment detail page of a sagittal SectionDataSet (id=69782969) for gene Pdyn showing meta-information, images and computed structure expression graph.

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Informatics Data Processing

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The Allen Mouse Brain Atlas (the Atlas) provides genome-wide in situ hybridization (ISH) data for approximately 20,000 genes in male P56 C57BL/6J mice. The informatics data processing pipeline produces results that enable the navigation, analysis and visualization of this data. The informatics data processing pipeline consists of the following components:

  • a an annotated 3-D reference modelspace,
  • an alignment module,
  • an expression detection module,
  • an expression gridding module, and
  • a structure unionizer module.

The output of the pipeline is quantified expression values at a grid voxel level and at a structure level according to the integrated reference atlas ontology. The grid level data are used downstream to provide an on-the-fly a differential and correlative gene search service and to support visualization of spatial relationships.

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The backbone of the automated pipeline is an annotated 3-D reference space based on the same Specimen used for the coronal plates of the integrated reference atlas. A brain volume was reconstructed from the SectionImages SectionImages using a combination of high frequency section-to-section histology registration with low-frequency histology to (ex-cranio) MRI registration. This first-stage reconstructed volume was then aligned with a sagittally sectioned Specimen. Once a straight mid-sagittal plane was achieved, a synthetic symmetric space was created by reflecting one hemisphere to the other side of the volume.

The 3-D ReferenceSpace is in PIR orientation (+x = posterior, +y = inferior, +z = right). Over 800 Structures were extracted from the 2-D coronal reference atlas plates and interpolated to create symmetric 3-D annotations. Structures in the reference atlas are arranged in a hierarchical organization. Each structure has one parent and denotes a "part-of" relationship. Structures are assigned a color to visually emphasize their hierarchical positions in the brain.

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Figure: The 3-D reference space is in PIR orientation where x axis = Anterior-to-Posterior, y axis = Superior-to-Inferior and z axis = Left-to-Right.

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