E11.5 3D Edge-Aware Refined Atlas Derived from the Allen Developing Mouse Brain Atlas

3D imaging necessitates corresponding 3D anatomical atlases, but generating such atlases is time consuming and challenging. Substantial efforts have generated such atlases including the Allen Developing Mouse Brain Atlas (ADMBA) but are typically limited by the process of serial 2D annotation for 3D reconstruction leading to artifacts. We have developed an automated, edge-aware atlas refinement method to curate existing atlases in a topologically consistent, 3D manner. Applying this approach to the E11.5 atlas in the ADMBA, we smoothed the labels in 3D and realigned labels to the underlying anatomical edges. We also rotated images in 3D and straightened a caudal kink in the spinal cord for midline symmetry, and we used the completed labels to strip regions outside of the central nervous system.