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This document provides a brief overview of the data, database organization and example queries. API database object names are in camel case. See the main API documentation for more information in on data models and query syntax.


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 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 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.

See the atlas drawing and ontology page for more information.

All coronal data is registered to ReferenceSpace id = 9. All sagittal data is registered to ReferenceSpace id = 10.

ReferenceSpace id = 9  PIR orientation (+x = posterior, +y = inferior, +z = right) while, ReferenceSpace id = 10 is in PIL orientation (+x = posterior, +y = inferior, +z = left). The reason for the two spaces is to allow left hemisphere sagittal data to corresponds to the right hemisphere coronal reference atlas.

Figure: The 3-D reference space ReferenceSpace id = 9 is in PIR orientation where x axis = Anterior-to-Posterior, y axis = Superior-to-Inferior and z axis = Left-to-Right.Three


3-D annotation volumes were updated in the June 2013 release to reflect changes in the atlas drawings and ontology. Also note that the volumes are now in a 32-bit format to large structure identifiers.

Four volumetric data files are available for download:

  • atlasVolume: uchar (8bit) grayscale Nissl volume of the reconstructed brain at 25 µm resolution.
  • annotation: ushort uint (16bit32bit) structural annotation volume at 25 µm resolution. The value represents the ID of the finest level structure annotated for the voxel. Note: the 3-D mask for any structure is composed of all voxels annotated for that structure and all of its descendents in the structure hierarchy.
  • gridAnnotation - 200 µm: ushort uint (16bit32bit) structural annotation volume at grid (200 µm) resolution for gene expression analysis.
  • gridAnnotation - 100 µm: ushort uint (16bit32bit) structural annotation volume at grid (100 µm) resolution for axonal projection analysis.

Volumetric data is stored in an uncompressed format with a simple text header file in MetaImage format.