  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.
