Biomedical Visualization Research Articles

Biomedical Image Visualization as a Web Application

We aim at building the Web-based Laboratory Information System (LIS) and Radiology Information System (RIS). It is challenging to make the functionality of the dedicated imaging and visualization programs compiled from a native programming language publicly available via a Web based interface. Accessing information of the original image data and algorithmic details should be hidden, thus scripts executed by the webpage browser should be avoided. In this regard, we propose a solution based on the ASP.NET framework. Managed codes in C# are developed for Web controls, server-side GUI and relational database management; whereas unmanaged server-dependent imaging programs are invoked from within the managed programs. We present such a Web application for biomedical imaging and visualization, addressing its capability of implementing comprehensive image processing algorithms at the server side where proprietary datasets reside and direct access to them by client-side applications is restricted. The advantages of such a Web application include (a) high security of the proprietary data which is always a primary consideration in deployment of a networked system, (b) thin-client strategy in which heavy computing tasks are completed on the dedicated server with highperformance hardware, and (c) less demand for network bandwidth as only the rendering results instead of multiple high-dimensional datasets need to be transferred.

Biomedical Imaging and Visualization Model of Mitochondrial Dysfunction and Oxidative Stress in Alzheimer Disease

Mitochondrial dysfunction and oxidative stress are among the earliest events linked to Alzheimer Disease and might play a causative role in disease onset and progression. In this paper, a biomedical imaging and visualization model was set to investigate the mitochondrial dysfunction and oxidative stress in Aβ/Cu2+-treated cells, which contribute in a significant manner to bioenergetic failure and mitochondrial dysfunction, by measuring mitochondrial membrane potential, Ca2+, chromatin condensation and ROS. This evaluating method opens a window for analyzing the protective effect of a certain substance in improving mitochondrial function and preventing oxidative stress in AD development.

Biomedical Super-resolved Imaging Using Special Micro-probe

In this paper, we present a design proposal as well as a preliminary experimental validation of special multi-functional biomedical probe. The probe acts as a very thin endoscope (diameter of 100–200 μm), while maintaining high imaging resolution. This micro-probe was made out of polymers, while the core is made out of polystyrene and the cladding is made out of poly(methyl methacrylate). The micro-probe consists from combining hollow regions (capillaries) of a holey structure together with nonhollow regions to form multiple cores. Experimental results for constructing and imaging a resolution target as well as of Fe micro-beads that are embedded into an agar solution are reported. Two very thin tips with external diameters of 100 and 200 μm have been fabricated. The tip provides localization at which its functionalities can be applied. The high imaging resolution capability of 5,000–10,000 imaged pixels and the fact that the edge of the micro-probe is very thin allows localized biomedical inspection, visualization, and treatment with minimal invasive damage. The proposed probe does not provide only spatial resolution that is as good as the one obtained in common endoscopes but it may also enable medical treatment-related multi-functionalities.

SOA-based digital library services and composition in biomedical applications

Carefully collected, high-quality data are crucial in biomedical visualization, and it is important that the user community has ready access to both this data and the high-performance computing resources needed by the complex, computational algorithms that will process it. Biological researchers generally require data, tools and algorithms from multiple providers to achieve their goals. This paper illustrates our response to the problems that result from this. The Living Human Digital Library (LHDL) project presented in this paper has taken advantage of Web Services to build a biomedical digital library infrastructure that allows clinicians and researchers not only to preserve, trace and share data resources, but also to collaborate at the data-processing level.

Mathematical Methods for Images and Surfaces

The last two decades have witnessed a greatly increasing interest in mathematical methods for images and surfaces that are originated from biomedical and biological applications. The research problems have necessitated the development of mathematical theories of wavelets, frames, harmonic analysis, geometric flows, differential geometry, topology statistical methods, machine learning, and so forth. This theoretical development is enhanced by the related numerical algorithm development and modeling development. Currently, mean curvature flow, Willmore flow, level set, generalized Laplace-Beltrami operator are commonly used mathematical techniques for the analysis of biomedical images and for the generation of biomolecular surfaces. Additionally, wavelets, frames, compressive sensing, and harmonic analysis are popular tools for biomedical visualization and image processing. Moreover, differential geometry, topology, and geometric measure theory are powerful approaches for the multiscale modeling of biomolecular structure, dynamics, and transport. Finally, persistently stable manifold, topological invariant, Euler characteristic, Frenet frame, and machine learning are vital to the dimensionality reduction of extremely massive biomedical and biomolecular data. These ideas have been successfully paired with current investigation and discovery in biomedical and biological systems. However, many mathematical challenges remain in image and surface analysis, such as the well-posedness of mathematical models under physical and biological constraints, maximum-minimum principle for high-order geometric evolution equations, numerical analysis of multiply coupled partial differential equations, effectiveness of approximation theory, and the modeling of complex biomolecular phenomena. This special issue was called to address mathematical difficulties and challenges in image and surface analysis. It consists of seventeen research papers.

A reliable surface reconstruction system in biomedicine

For common biomedical imaging facilities, such as CT, MRI, and confocal microscopy, the acquired scans are sequential parallel sections. The object of interest in each section image can be extracted by segmentation procedure to form serial parallel planar contours. How to reconstruct a trustworthy surface from these contours is a crucial issue in biomedical 3D visualization. In this paper, we propose an automatic, fast, and reliable surface reconstruction system. An improved correspondence-determining algorithm is proposed in the system to provide more reasonable contour-correspondences than the existing algorithms. It can handle more general input data, and does not produce wrong reconstruction results. A hybrid tiling algorithm is presented to tile the corresponding contours without the requirement of a contour-matching procedure. It can also handle the branching problem without any modification. For degenerate cases and branches, intermediate contours are introduced by means of contour interpolation to enhance the reconstruction results. The surface area and volume are also calculated to facilitate the practical applications.

The minds' eye: Biomedical visualization: The most powerful tool in science

The minds' eye: Biomedical visualization: The most powerful tool in science

Building a software experience factory using granular-based models

Software quality is one of the most important practical features of software development. Project managers and developers look for methods and tools supporting software development processes and ensuring a required level of quality. To make such tools relevant, they should provide the designer/manager with some quantitative input useful for purposes of interpretation of the results. Knowledge provided by the tools leads to better understanding of the investigated phenomena. In this paper, we propose a comprehensive development methodology of logic-based models represented by fuzzy neural networks. A process of model development is performed in the stages of structural and parametric optimization. The structural optimization framework utilizes mechanisms of evolutionary computing, which become especially attractive in light of the structural optimization of the models. The parametric optimization is performed using the gradient-base method. The study comprises two detailed case studies dealing with existing software data. The first one deals with the quality assessment of software objects in an exploratory biomedical data analysis and visualization system. The second case is concerned with the model of software development effort discussed in the setting of some medical information system.

3DIVE: An immersive environment for interactive volume data exploration

This paper describes an immersive system, called 3DIVE, for interactive volume data visualization and exploration inside the CAVE virtual environment. Combining interactive volume rendering and virtual reality provides a natural immersive environment for volumetric data visualization. More advanced data exploration operations, such as object level data manipulation, simulation and analysis, are supported in 3DIVE by several new techniques. In particular, volume primitives and texture regions are used for the rendering, manipulation, and collision detection of volumetric objects; and the region-based rendering pipeline is integrated with 3D image filters to provide an image-based mechanism for interactive transfer function design. The system has been recently released as public domain software for CAVE/ImmersaDesk users, and is currently being actively used by various scientific and biomedical visualization projects.