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The 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 an 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.

Structures in the common coordinate framework 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 drawings and ontologies page for more information.