The Active Atlas: Combining 3D Anatomical Models with Texture Detectors

TL;DR

This paper introduces the Active Atlas, a novel digital brain atlas that integrates 3D anatomical models with texture analysis to automate and improve the localization of brain regions in histological studies.

Contribution

It presents a new methodology combining 3D organization and texture detection, creating detailed, automatically alignable brain atlases for regions lacking existing detailed maps.

Findings

Successfully created an atlas for mouse brainstem and mid-brain.

Enabled automatic alignment of histological data to the atlas.

Reduced manual labor in neuroanatomical localization.

Abstract

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.