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 207 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 interfaces between old and new structures were manually inspected and filled to create smooth transitions to create a complete brain map (~700 structures) for quantification.
Figure: The next generation Allen Mouse Common Coordinate Framework is based on shape and intensity average of 1675 specimens from the Allen Mouse Brain Connectivity Atlas. At the time of the October 2016 release, 207 structures have been delineated on the anatomical template.
3-D annotation volumes were updated in the May 2015 October 2016 release to reflect the remapping to the new include newly drawn structures in the Allen Mouse Common Coordinate Framework (CCFv3). Annotation volumes from the October 2014 release (mapped to CCFv2) can be accessed through our data download server (see instructions).
Volumetric data files available download:
USHORT(16 bit) anatomical template of CCFv3 - a shape and intensity average of 1675 specimen brains
FLOAT(32 bit) reconstructed Allen Reference Atlas Nissl deformably registered to the anatomical template of CCFv3
UINT (32 bit) structure gray matter and fiber tract annotation of CCFv3 (October 2016)
UINT (32bit32 bit) structure gray matter and fiber tract annotation of CCFv3 (May 2015)
UINT (32bit32 bit) structure annotation extracted from the coronal Allen Reference Atlas and deformably registered to CCFv3
UINT (32bit32 bit) structure annotation extracted from the P56 Allen Developing Mouse Brain Reference Atlas and deformably registered to CCFv3