The Active Atlas: Combining 3D Anatomical Models with Texture Detectors
This work addresses the need for detailed, automated brain region localization in neuroanatomy, particularly for regions lacking good atlases, though it is incremental as it builds on existing atlas concepts with new texture-based enhancements.
The authors tackled the problem of localizing brain regions in histological sections, which is labor-intensive and limited by existing low-resolution atlases, by developing an 'active' digital atlas methodology that combines 3D anatomical models with texture detectors, resulting in an atlas for the mouse brainstem and mid-brain that can automatically align histological stacks.
While modern imaging technologies such as fMRI have opened exciting new possibilities for studying the brain in vivo, histological sections remain the best way to study the anatomy of the brain at the level of single neurons. The histological atlas changed little since 1909 and localizing brain regions is a still a labor intensive process performed only by experienced neuro-anatomists. Existing digital atlases such as the Allen Brain atlas are limited to low resolution images which cannot identify the detailed structure of the neurons. We have developed a digital atlas methodology that combines information about the 3D organization of the brain and the detailed texture of neurons in different structures. Using the methodology we developed an atlas for the mouse brainstem and mid-brain, two regions for which there are currently no good atlases. Our atlas is "active" in that it can be used to automatically align a histological stack to the atlas, thus reducing the work of the neuroanatomist.