Synchrotron Radiation-Based Tomography of an Entire Mouse Brain with Sub-Micron Voxels: Augmenting Interactive Brain Atlases with Terabyte Data.

Synchrotron radiation-based X-ray microtomography is uniquely suited for post-mortem 3D visualization of organs such as the mouse brain. Tomographic imaging of the entire mouse brain with isotropic cellular resolution requires an extended field-of-view and produces datasets of multiple terabytes in size. These data must be reconstructed, analyzed, and made accessible to domain experts who may have limited image processing knowledge. Extended-field X-ray microtomography is presented with voxel size covering an entire mouse brain. The 4495 projections from 8 × 8 offset acquisitions are stitched to reconstruct a volume of 15000 voxels. The microtomography volume was non-rigidly registered to the Allen Mouse Brain Common Coordinate Framework v3 based on a combination of image intensity and landmark pairs. The data were block-wise transformed and stored in a public repository with a hierarchical format for navigation and overlay with anatomical annotations in online viewers such as Neuroglancer or siibra-explorer. This study demonstrates X-ray imaging and data processing for a full mouse brain, augmenting current atlases by improving resolution in the third dimension by an order of magnitude. The 3.3-teravoxel dataset is publicly available and easily accessible for domain experts via browser-based viewers.