CCFv3 Highlights: Transgene Expression Data

The Allen Mouse Brain Common Coordinate Framework (CCFv3) is an annotated 3D reference space with 10µm voxel resolution. An average template brain was created from images of 1,675 young adult C57BL/6J mouse brains acquired using serial two-photon tomography.

Transgene expression in conjunction with other reference data was used to parcellated the entire brain directly in 3D, labeling every voxel with a brain structure spanning 43 isocortical areas and their layers, 329 subcortical gray matter structures, 81 fiber tracts, and 8 ventricular structures.

The transgene expression dataset can be accessed in multiple ways:

  • View the high resolution image data on Allen Brain Map
  • Download the downsampled and mapped to CCF 25 micron data for data analysis
  • Download the high resolution data from the Brain Imaging Library

Supplemental table 3 (Wang et al 2020) provide details on which transgene imageset was used to annotate a particular structure.