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3-D Reference Models

The backbone cornerstone of the automated pipeline is an annotated 3-D reference space. For this purpose, a next generation of the common coordinate framework (CCF v3) is being created 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.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 brainan average population of 1675 specimens. See the Allen Mouse Common Coordinate Framework whitepaper for detailed construction information. In this current release, the framework consists of 178 newly drawn structures spanning approximately half the brain. To support whole brain quantification, structures which have not yet been drawn are extracted and merged from the version 2 framework based on the Allen Reference Atlas. The interface between old and new structures were manually inspected and filled to create smooth transitions to create a complete brain map (~700 structures) for quantification.

See the atlas drawings and ontologies page for more information.To avoid possible bias introduced by using a single specimen as a registration target, the Nissl-based 3-D reference volume was not directly used. Instead, a large number of brains were mapped in advanced and averaged to form the registration target. This averaged template may be updated periodically to include more brain specimens and is available for download.

All SectionDataSets are registered to ReferenceSpace id = 9 in PIR orientation (+x = posterior, +y = inferior, +z = right).