Allen Mouse Common Coordinate Framework - Average Brain Template

The reference space or brain template was constructed as a population average of 1,675 young adult C57BL/6J mice brains imaged using serial two photon tomography (STPT) for the Allen Mouse Brain Connectivity Atlas. The average template was created from tissue autofluorescence detected in the red channel. To maximize input data and create a symmetrical atlas, each dataset was reflected across the midline, for a total of 3,350 (2 x 1,675) hemisphere datasets. Creation of the template followed a two-step iterative process: (1) We deformably registered each specimen to the current iteration of the template and computed an intensity average. (2) We then computed the average deformation field, inverted it, and applied it to the intensity average created in (1). This resulted in a volume with an average unbiased shape and intensity to be used as the template in the next iteration until convergence. The axes the average template volume is a +X=Posterior, +Y=Inferior(Ventral) and +Z=Right frame with the origin at the corner of the volume.