While modern imaging technologies such as fMRI have opened exciting newpossibilities for studying the brain in vivo, histological sections remain thebest way to study the anatomy of the brain at the level of single neurons. Thehistological atlas changed little since 1909 and localizing brain regions is astill a labor intensive process performed only by experienced neuro-anatomists.Existing digital atlases such as the Allen Brain atlas are limited to lowresolution images which cannot identify the detailed structure of the neurons.We have developed a digital atlas methodology that combines information aboutthe 3D organization of the brain and the detailed texture of neurons indifferent structures. Using the methodology we developed an atlas for the mousebrainstem and mid-brain, two regions for which there are currently no goodatlases. Our atlas is "active" in that it can be used to automatically align ahistological stack to the atlas, thus reducing the work of the neuroanatomist.
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