The human brain in 1700 pieces: Design and development of a three-dimensional, interactive and reference atlas

As the human brain is the most complex living organ, constructing its detailed model with exploration capabilities in a form of an atlas is a challenge. Our overall goal is to construct an advanced, detailed, parcellated, labeled, accurate, interactive, three-dimensional (3D), and scalable whole human brain atlas of structure, vasculature, tracts and systems. The objectives of this work are three-fold; to present: (1) method of atlas design and development including design principles, accuracy requirements, atlas content, architecture, functionality, user interface, and customized tools; (2) creation of an atlas of structure and systems including its modeling method and validation; and (3) integration of this atlas with the cerebrovasculature and tracts created earlier.The atlas is created from multiple in vivo 3/7 T scans. Its design based on “pyramidal principle” enables scalability while preserving design principles and exploits interaction paradigm “from blocks to brain”. The atlas contains (1) navigator with modules for system/object/object state management, interaction, user interfacing, and rendering; and (2) brain model with cerebrum, cerebellum, brainstem, spinal cord, white matter, deep structures, systems, ventricles, arteries, veins, sinuses, and tracts. The brain model is parcellated, labeled, consistent, realistic, of high resolution, polygonal/volumetric, dissectible, extendable, and deformable. It has over 1700 3D components. The atlas has sub-voxel accuracy of 0.1 mm and the smallest vessels of 80 μm. Brain exploration includes dynamic scene composition, manipulation-independent 3D labeling, interaction combined with animation, meta-labeling, and quantification.This atlas is useful in education, research, and clinical applications. It can potentially be foundation for a multi-level molecular–cellular–anatomical–physiological–behavioral platform.

► A human brain atlas of structure and systems was created and integrated with the cerebrovasculature and white matter tracts constructed earlier from 3/7 T in vivo scans.
► Methods and tools used to construct the atlas are described.
► The atlas contains navigator and brain model with 1700 three-dimensional, fully parcellated and labeled cerebral components.
► The atlas has sub-voxel accuracy of 0.1 mm and the smallest vessels of 80 μm.
► This atlas is useful in education, research, and clinical applications.