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$^{3}$ 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.