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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 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 May 2015 release, 178 structures on have been delineated on the anatomical template.
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3-D annotation volumes were updated in the May 2015 release to reflect the remapping to the new Allen Mouse Common Coordinate Framework (CCFv3). Annotation volumes from the October 2014 release (mapped to CCFv2) can be access accessed through our data download server (see instructions). |
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Each image in a dataset is divided into a 10 x 10 µm grid. In each division, the sum of the number of detected pixels and the sum of detected pixel intensity were collected. A second set of these same summations was computed for the regions manually identified as belonging to the injection site for injection site quantification. The resulting 3-D grid is then transformed into the standard reference space using linear interpolation to generate sub-grid values.
From these summation the summations we obtained measures for:
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| Warning |
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3-D grids were updated in the May 2015 release to reflect the remapping to the new Allen Mouse Common Coordinate Framework (CCFv3), higher resolution computation and a new compress data format. 3-D grids from the October 2014 release (mapped to CCFv2) can be access accessed through our data download server (see instructions). |
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