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 0.1mm 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.

[1]  G. Schaltenbrand,et al.  Atlas for Stereotaxy of the Human Brain , 1977 .

[2]  Arthur W. Toga,et al.  Stereotaxic white matter atlas based on diffusion tensor imaging in an ICBM template , 2008, NeuroImage.

[3]  Daniel Rueckert,et al.  A dynamic 4D probabilistic atlas of the developing brain , 2011, NeuroImage.

[4]  Wieslaw Lucjan Nowinski,et al.  A 3D Model of Human Cerebrovasculature Derived from 3T Magnetic Resonance Angiography , 2008, Neuroinformatics.

[5]  Babak A. Ardekani,et al.  Quantitative comparison of algorithms for inter-subject registration of 3D volumetric brain MRI scans , 2005, Journal of Neuroscience Methods.

[6]  Wieslaw L. Nowinski,et al.  Statistical Analysis of 168 Bilateral Subthalamic Nucleus Implantations by Means of the Probabilistic Functional Atlas , 2005, Neurosurgery.

[7]  R. Woods,et al.  Cortical change in Alzheimer's disease detected with a disease-specific population-based brain atlas. , 2001, Cerebral cortex.

[8]  Arno Klein,et al.  Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration , 2009, NeuroImage.

[9]  Colin Studholme,et al.  A spatiotemporal atlas of MR intensity, tissue probability and shape of the fetal brain with application to segmentation , 2010, NeuroImage.

[10]  Max A. Viergever,et al.  A survey of medical image registration , 1998, Medical Image Anal..

[11]  Andres M. Lozano,et al.  Textbook of stereotactic and functional neurosurgery , 2009 .

[12]  Val M Runge,et al.  Simulation and assessment of cerebrovascular damage in deep brain stimulation using a stereotactic atlas of vasculature and structure derived from multiple 3- and 7-tesla scans. , 2010, Journal of neurosurgery.

[13]  H. Duvernoy,et al.  The Human Brain: Surface, Three-Dimensional Sectional Anatomy with MRI, and Blood Supply , 1999 .

[14]  D. Caramella,et al.  3D Image Processing: Techniques and Clinical Applications , 2002 .

[15]  David Metcalf,et al.  A Digital Brain Atlas for Surgical Planning, Model-Driven Segmentation, and Teaching , 1996, IEEE Trans. Vis. Comput. Graph..

[16]  K. Miller.  Biomechanics of the brain , 2011 .

[17]  W. L. Nowinski,et al.  Anatomical and Probabilistic Functional Atlases in Stereotactic and Functional Neurosurgery , 2009 .

[18]  James Kozloski,et al.  Automated Reconstruction of Neural Tissue and the Role of Large-Scale Simulation , 2011, Neuroinformatics.

[19]  M. Eisenstein,et al.  Neural circuits: Putting neurons on the map , 2009, Nature.

[20]  W L Nowinski,et al.  Multiple brain atlas database and atlas-based neuroimaging system. , 1997, Computer aided surgery : official journal of the International Society for Computer Aided Surgery.

[21]  M. Torrens.  Co-Planar Stereotaxic Atlas of the Human Brain—3-Dimensional Proportional System: An Approach to Cerebral Imaging, J. Talairach, P. Tournoux. Georg Thieme Verlag, New York (1988), 122 pp., 130 figs. DM 268 , 1990 .

[22]  James M. Bower,et al.  Neural Modeling with GENESIS , 1998 .

[23]  Stephen L. Senft,et al.  A Brief History of Neuronal Reconstruction , 2011, Neuroinformatics.

[24]  Wieslaw L. Nowinski,et al.  Introduction to Brain Anatomy , 2011 .

[25]  Wieslaw L. Nowinski,et al.  Quantification and Visualization of the Three-Dimensional Inconsistency of the Subthalamic Nucleus in the Schaltenbrand-Wahren Brain Atlas , 2006, Stereotactic and Functional Neurosurgery.

[26]  Wieslaw L. Nowinski,et al.  Computerized Brain Atlases for Surgery of Movement Disorders , 2001 .

[27]  Arthur W. Toga,et al.  Human brain white matter atlas: Identification and assignment of common anatomical structures in superficial white matter , 2008, NeuroImage.

[28]  Rémy Prost,et al.  Variational implicit surface meshing , 2009, Comput. Graph..

[29]  Viergever,et al.  An Overview of Medical Image Registration Methods , 1998 .

[30]  Marcia K. Johnson,et al.  Neuroimaging a Single Thought: Dorsolateral PFC Activity Associated with Refreshing Just-Activated Information , 2002, NeuroImage.

[31]  J. Lieberman,et al.  Time-lapse mapping of cortical changes in schizophrenia with different treatments. , 2009, Cerebral cortex.

[32]  Wieslaw Lucjan Nowinski,et al.  Three-Dimensional Interactive and Stereotactic Human Brain Atlas of White Matter Tracts , 2011, Neuroinformatics.

[33]  Nicholas T. Carnevale,et al.  The NEURON Simulation Environment , 1997, Neural Computation.

[34]  Wieslaw Lucjan Nowinski,et al.  Vascular Editor: From Angiographic Images to 3D Vascular Models , 2010, Journal of Digital Imaging.

[35]  Wieslaw Lucjan Nowinski,et al.  Three-dimensional reference and stereotactic atlas of human cerebrovasculature from 7Tesla , 2011, NeuroImage.

[36]  Wieslaw L. Nowinski,et al.  A Probabilistic Functional Atlas of the VIM Nucleus Constructed from Pre-, Intra- and Postoperative Electrophysiological and Neuroimaging Data Acquired during the Surgical Treatment of Parkinson’s Disease Patients , 2006, Stereotactic and Functional Neurosurgery.

[37]  Nicholas T. Carnevale,et al.  Simulation of networks of spiking neurons: A review of tools and strategies , 2006, Journal of Computational Neuroscience.

[38]  A. Valavanis,et al.  Anatomic relationships along the low-middle convexity: Part I--Normal specimens and magnetic resonance imaging. , 1995, Neurosurgery.

[39]  Arvid Lundervold,et al.  Evaluation of automated brain MR image segmentation and volumetry methods , 2009, Human brain mapping.

[40]  L. Garey.  Brodmann's localisation in the cerebral cortex , 1999 .

[41]  Wolfgang Weinrich,et al.  Neurofunctional Systems: 3D Reconstructions with Correlated Neuroimaging , 1997 .

[42]  Guido Gerig,et al.  Spatiotemporal Atlas Estimation for Developmental Delay Detection in Longitudinal Datasets , 2009, MICCAI.

[43]  Randal A. Koene,et al.  NETMORPH: A Framework for the Stochastic Generation of Large Scale Neuronal Networks With Realistic Neuron Morphologies , 2009, Neuroinformatics.

[44]  W. Nowinski.  Computer-Aided Brain Surgery: Present and Future , 2002 .

[45]  Val M Runge,et al.  A new presentation and exploration of human cerebral vasculature correlated with surface and sectional neuroanatomy , 2009, Anatomical sciences education.

[46]  William E. Lorensen,et al.  Marching cubes: A high resolution 3D surface construction algorithm , 1987, SIGGRAPH.

[47]  J F Evers,et al.  Progress in functional neuroanatomy: precise automatic geometric reconstruction of neuronal morphology from confocal image stacks. , 2005, Journal of neurophysiology.

[48]  J. A. Bewer.  The Book of Genesis , 2011 .

[49]  Wieslaw L. Nowinski,et al.  An Algorithm for Rapid Calculation of a Probabilistic Functional Atlas of Subcortical Structures from Electrophysiological Data Collected during Functional Neurosurgery Procedures , 2003, NeuroImage.

[50]  Wieslaw Lucjan Nowinski,et al.  A Three-Dimensional Interactive Atlas of Cerebral Arterial Variants , 2009, Neuroinformatics.

[51]  Sébastien Ourselin,et al.  A three-dimensional, histological and deformable atlas of the human basal ganglia. I. Atlas construction based on immunohistochemical and MRI data , 2007, NeuroImage.

[52]  H. Ric Harnsberger,et al.  Diagnostic and surgical imaging anatomy : brain, head & neck, spine , 2006 .

[53]  Wieslaw Lucjan Nowinski,et al.  Use of normative distribution of gray to white matter ratio in orthogonal planes in human brain studies and computer-assisted neuroradiology , 2011, International Journal of Computer Assisted Radiology and Surgery.

[54]  H. Markram.  The Blue Brain Project , 2006, Nature Reviews Neuroscience.

[55]  小野 道夫,et al.  Atlas of the Cerebral Sulci , 1990 .