A method for automated location of shape differences in diseased anatomical structures via high resolution biomedical atlases annotated with labels from formal ontologies is described. In particular, a high resolution magnetic resonance image of the myocardium of the human left ventricle was segmented and annotated with structural terms from an extracted subset of the Foundational Model of Anatomy ontology. The atlas was registered to the end systole template of a previous study of left ventricular remodeling in cardiomyopathy using a diffeomorphic registration algorithm. The previous study used thresholding and visual inspection to locate a region of statistical significance which distinguished patients with ischemic cardiomyopathy from those with nonischemic cardiomyopathy. Using semantic technologies and the deformed annotated atlas, this location was more precisely found. Although this study used only a cardiac atlas, it provides a proof-of-concept that ontologically labeled biomedical atlases of any anatomical structure can be used to automate location-based inferences.

BACKGROUND: A critical challenge in neuroscience is organizing, managing, and accessing the explosion in neuroscientific knowledge, particularly anatomic knowledge. We believe that explicit knowledge-based approaches to make neuroscientific knowledge computationally accessible will be helpful in tackling this challenge and will enable a variety of applications exploiting this knowledge, such as surgical planning. RESULTS: We developed ontology-based models of neuroanatomy to enable symbolic lookup, logical inference and mathematical modeling of neural systems. We built a prototype model of the motor system that integrates descriptive anatomic and qualitative functional neuroanatomical knowledge. In addition to modeling normal neuroanatomy, our approach provides an explicit representation of abnormal neural connectivity in disease states, such as common movement disorders. The ontology-based representation encodes both structural and functional aspects of neuroanatomy. The ontology-based models can be evaluated computationally, enabling development of automated computer reasoning applications. CONCLUSION: Neuroanatomical knowledge can be represented in machine-accessible format using ontologies. Computational neuroanatomical approaches such as described in this work could become a key tool in translational informatics, leading to decision support applications that inform and guide surgical planning and personalized care for neurological disease in the future.

The next generation of medical systems will integrate multimodality and multimedia data from a variety of sources to aid individual ysicians in providing the best treatment and care for their patients and to help researchers understand patterns of disease in collections of large databases. We promote a principle of maximum flexibility for the design of these systems to accommodate new developments in medical imaging and bioinformatics. We present several characteristics of flexible systems that support medical multimedia. We illustrate how these characteristics can be applied within diverse medical research and clinical therapy environments through two in-depth case studies. Within these examples, we describe how specific emerging technologies, including the semantic web and publish and subscribe networking, can enhance the flexibility of medical multimedia architectures.

LightKit is a system for lighting three-dimensional synthetic scenes. LightKit simplifies the task of producing visually pleasing, easily interpretable images for visualization while making it harder to produce results where the scene illumination distracts from the visualization process. LightKit is based on lighting designs developed by artists and photographers and shown in previous studies to enhance shape perception. A key light provides natural overhead illumination of the scene, augmented by fill, head, and back lights. By default, lights are attached to a normalized, subject-centric, camera-relative coordinate frame to ensure consistent lighting independent of camera location or orientation. This system allows all lights to be positioned by specifying just six parameters. The intensity of each light is specified as a ratio to the key light intensity, allowing the scene's brightness to be adjusted using a single parameter. The color of each light is specified by a single normalized color parameter called warmth that is based on color temperature of natural sources. LightKit's default values for light position, intensity, and color are chosen to produce good results for a variety of scenes. LightKit is designed to work with both hardware graphics systems and, potentially, higher quality off-line rendering systems. We provide examples of images created using a LightKit implementation within the VTK visualization toolkit software framework.

We describe an animated electro-holographic visualization of brain lesions due to the progression of multiple sclerosis. A research case study is used which documents the expression of visible brain lesions in a series of magnetic resonance imaging (MRI) volumes collected over the interval of one year. Some of the salient information resident within this data is described, and the motivation for using a dynamic spatial display to explore its spatial and temporal characteristics is stated. We provide a brief overview of spatial displays in medical imaging applications, and then describe our experimental visualization pipeline, from the processing of MRI datasets, through model construction, computer graphic rendering, and hologram encoding. The utility, strengths and shortcomings of the electro-holographic visualization are described and future improvements are suggested.

We give an explicit method for mapping any simply connected surface onto the sphere in a manner which preserves angles. This technique relies on certain conformal mappings from differential geometry. Our method provides a new way to automatically assign texture coordinates to complex undulating surfaces. We demonstrate a finite element method that can be used to apply our mapping technique to a triangulated geometric description of a surface.

This paper presents a method for efficiently rendering a sequence of regularly spaced perspectives of a scene. The algorithm presented, called Multiple Viewpoint Rendering (MVR), exploits perspective coherence by rendering epipolar plane images. The computer graphics camera geometry is constrained to produce epipolar plane images with linear features. Transformation and shading operations can be performed once per image sequence instead of once per view. Geometric position, color, and texture coordinates can be computed using linear interpolation. Both view independent and dependent shading algorithms are supported. Both one and two-dimensional grids of perspectives can be rendered. Details of a hardware-accelerated implementation of a multiple viewpoint polygon renderer are given. 1 Introduction Most of the time, photography captures information about the world as seen from a single viewpoint. A still camera's single lens records a scene as it appears at one instant, while a movie cam...