Matching Spatial with Ontological Brain Regions using Java Tools for Visualization, Database Access, and Integrated Data
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Matching Spatial with Ontological Brain Regions using Java Tools for Visualization, Database Access, and Integrated Data Analysis Gleb Bezgin & Andrew T. Reid & Dirk Schubert & Rolf Kötter
Published online: 15 January 2009 # Humana Press Inc. 2009
Abstract Brain atlases are widely used in experimental neuroscience as tools for locating and targeting specific brain structures. Delineated structures in a given atlas, however, are often difficult to interpret and to interface with database systems that supply additional information using hierarchically organized vocabularies (ontologies). Here we discuss the concept of volume-to-ontology mapping in the context of macroscopical brain structures. We present Java tools with which we have implemented this concept for retrieval of mapping and connectivity data on the macaque brain from the CoCoMac database in connection with an electronic version of “The Rhesus Monkey Brain in Stereotaxic Coordinates” authored by George Paxinos and colleagues. The software, including our manually drawn monkey brain template, can be downloaded freely under the GNU General Public License. It adds value to the printed atlas and has a wider (neuro-) informatics application since it can read appropriately annotated data from delineated sections of other species and organs, and turn them into 3D registered stacks. The tools provide additional features, including visualization and analysis of connectivity data, volume and centre-of-mass estimates, and graphical manipulation of entire structures, which are potentially useful for a range of research and teaching applications. G. Bezgin : A. T. Reid : D. Schubert : R. Kötter (*) Donders Institute for Brain, Cognition and Behaviour, Section Neurophysiology and Neuroinformatics, Department of Cognitive Neuroscience, Radboud University Nijmegen Medical Centre, P. O. B. 9101, Route 126, 6500 HB Nijmegen, The Netherlands e-mail: [email protected] G. Bezgin : A. T. Reid : R. Kötter C. & O. Vogt Brain Research Institute, and Institute of Anatomy II, Heinrich Heine University, 40225 Düsseldorf, Germany
Keywords Rhesus macaque atlas . Visualization . Neuroanatomy . Connectivity . Neuroimaging . Primate brain . Database interfaces . Ontology . Path analysis
Introduction and Background Brain atlases are indispensable tools for localizing specific structures and making interindividual comparisons with reference to a variety of markers. Such atlases are typically constructed from stacks of either volume element (voxel) imaging data or serial histological sections. For atlases of the macaque brain in particular, non-invasive imaging data have mainly provided coordinates and shape information, whereas histological sections have been used for microstructural delineations and partitioning. Whereas previous macaque atlases were mostly limited to brain stem structures, occasionally indicating the gyral and sulcal pattern of cerebral cortex (Müssen 1967; Smith et al. 1972; Szabo and Cowan 1984; Martin and Bowden 1996), the first atlas with a complete cortical parcella
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