BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

Anisotropic water diffusion in neural fibres such as nerve, white matter in spinal cord, or white matter in brain forms the basis for the utilization of diffusion tensor imaging (DTI) to track fibre pathways. The fact that water diffusion is sensitive to the underlying tissue microstructure provides a unique method of assessing the orientation and integrity of these neural fibres, which may be useful in assessing a number of neurological disorders. The purpose of this review is to characterize the relationship of nuclear magnetic resonance measurements of water diffusion and its anisotropy (i.e. directional dependence) with the underlying microstructure of neural fibres. The emphasis of the review will be on model neurological systems both in vitro and in vivo. A systematic discussion of the possible sources of anisotropy and their evaluation will be presented followed by an overview of various studies of restricted diffusion and compartmentation as they relate to anisotropy. Pertinent pathological models, developmental studies and theoretical analyses provide further insight into the basis of anisotropic diffusion and its potential utility in the nervous system.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/nbm.782

The basis of anisotropic water diffusion in the nervous system – a technical review

The state of the art of reconstruction of the axonal tracts in the central nervous system (CNS) using diffusion tensor imaging (DTI) is reviewed. This relatively new technique has generated much enthusiasm and high expectations because it presently is the only approach available to non-invasively study the three-dimensional architecture of white matter tracts. While there is no doubt that DTI fiber tracking is providing exciting new opportunities to study CNS anatomy, it is very important to understand its limitations. In this review we therefore assess the basic principles and the assumptions that need to be made for each step of the study, including both data acquisition and the elaborate fiber reconstruction algorithms. Special attention is paid to situations where complications may arise, and possible solutions are reviewed. Validation issues and potential future directions and improvements are also discussed.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/nbm.781

Fiber tracking: Principles and strategies - A technical review

Because of their wide use in molecular modeling, methods to compute molecular surfaces have received a lot of interest in recent years. However, most of the proposed algorithms compute the analytical representation of only the solvent-accessible surface. There are a few programs that compute the analytical representation of the solvent-excluded surface, but they often have problems handling singular cases of self-intersecting surfaces and tend to fail on large molecules (more than 10,000 atoms). We describe here a program called MSMS, which is shown to be fast and reliable in computing molecular surfaces. It relies on the use of the reduced surface that is briefly defined here and from which the solvent-accessible and solvent-excluded surfaces are computed. The four algorithms composing MSMS are described and their complexity is analyzed. Special attention is given to the handling of self-intersecting parts of the solvent-excluded surface called singularities. The program has been compared with Connolly's program PQMS [M.L. Connolly (1993) Journal of Molecular Graphics, Vol. 11, pp. 139-141] on a set of 709 molecules taken from the Brookhaven Data Base. MSMS was able to compute topologically correct surfaces for each molecule in the set. Moreover, the actual time spent to compute surfaces is in agreement with the theoretical complexity of the program, which is shown to be O[n log(n)] for n atoms. On a Hewlett-Packard 9000/735 workstation, MSMS takes 0.73 s to produce a triangulated solvent-excluded surface for crambin (1 crn, 46 residues, 327 atoms, 4772 triangles), 4.6 s for thermolysin (3tln, 316 residues, 2437 atoms, 26462 triangles), and 104.53 s for glutamine synthetase (2gls, 5676 residues, 43632 atoms, 476665 triangles).

Reduced surface: An efficient way to compute molecular surfaces

Two- and three-dimensional (3D) white matter atlases were created on the basis of high-spatial-resolution diffusion tensor magnetic resonance (MR) imaging and 3D tract reconstruction. The 3D trajectories of 17 prominent white matter tracts could be reconstructed and depicted. Tracts were superimposed on coregistered anatomic MR images to parcel the white matter. These parcellation maps were then compared with coregistered diffusion tensor imaging color maps to assign visible structures. The results showed (a) which anatomic structures can be identified on diffusion tensor images and (b) where these anatomic units are located at each section level and orientation. The atlas may prove useful for educational and clinical purposes. © RSNA, 2003

Fiber tract-based atlas of human white matter anatomy.

We present a case study evaluating the potential for interactively identifying placental surface blood vessels using magnetic resonance imaging (MRI) scans in virtual reality (VR) environments. We visualized the MRI data using direct volume rendering in a high-fidelity CAVE-like VR system, allowing medical professionals to identify relevant placental vessels directly from volume visualizations in the VR system, without prior vessel segmentation. Participants were able to trace most of the observable vascular structure, and consistently identified blood vessels down to diameters of 1 mm, an important requirement in diagnosing vascular diseases. Qualitative feedback from our participants suggests that our VR visualization is easy to understand and allows intuitive data exploration, but complex user interactions remained a challenge. Using these observations, we discuss implications and requirements for spatial tracing user interaction methods in VR environments. We believe that VR MRI visualizations are the next step towards effective surgery planning for prenatal diseases.

Towards Placental Surface Vasculature Exploration in Virtual Reality

We present a hybrid user interface and gesture-based direct visual editing techniques for quick and rough object creation and manipulation in three-dimensional (3D) virtual environments (VEs). The user interface includes a novel table-prop to resemble an architect's physical workbench. A tracked pinch glove and a stylus pen provide both rough and fingertip level precise spatial input. For quick placement, objects do not float in space, but instead obey a set of constrained physics laws. Experimental results indicate our design is effective for architectural massing study. Our work contributes to the hardware system design and novel gesture-based interaction techniques, which have the potential to bring VEs into practical use in architecture.

Poster: A hybrid direct visual editing method for architectural massing study in virtual environments

We present the design and prototype implementation of a scientific visualization language called Zifazah for composing 3D visualizations of diffusion tensor magnetic resonance imaging (DT-MRI or DTI) data. Unlike existing tools allowing flexible customization of data visualizations that are programmer-oriented, we focus on domain scientists as end users in order to enable them to freely compose visualizations of their scientific data set. We analyzed end-user descriptions extracted from interviews with neurologists and physicians conducting clinical practices using DTI about how they would build and use DTI visualizations to collect syntax and semantics for the language design, and have discovered the elements and structure of the proposed language. Zifazah makes use of the initial set of lexical terms and semantics to provide a declarative language in the spirit of intuitive syntax and usage. This work contributes three, among others, main design principles for scientific visualization language design as well as a practice of such language for DTI visualization with Zifazah. First, Zifazah incorporated visual symbolic mapping based on color, size and shape, which is a sub-set of Bertin's taxonomy migrated to scientific visualizations. Second, Zifazah is defined as a spatial language whereby lexical representation of spatial relationship for 3D object visualization and manipulations, which is characteristic of scientific data, can be programmed. Third, built on top of Bertin's semiology, flexible data encoding specifically for scientific visualizations is integrated in our language in order to allow end users to achieve optimal visual composition at their best. Along with sample scripts representative of our language design features, some new DTI visualizations as the running results created by end users using the novel visualization language have also been presented.

Composing DTI Visualizations with End-user Programming

In recent years, empirical studies have increasingly been seen as a core part of visualization research, and user evaluations have proliferated. It is broadly understood that new techniques and applications must be formally validated in order to be seen as meaningful contributions. However, these efforts continue to face the numerous challenges involved in validating complex software techniques that exist in a wide variety of use contexts. The authors, who represent perspectives from across visualization research and applications, discuss the leading challenges that must be addressed for empirical research to have the greatest possible impact on visualization in the years to come. These include challenges in developing research questions and hypotheses, designing effective experiments and qualitative methods, and executing studies in specialized domains. We discuss those challenges that have not yet been solved and possible approaches to addressing them. This chapter provides an informal survey and proposes a road map for moving forward to a more cohesive and grounded use of empirical studies in visualization research.

Open Challenges in Empirical Visualization Research

In this paper we present the design process of Capsule, an inertial input device to support 3D manipulation of biological datasets. Our motivation is to improve the scientist's workflow during the analysis of 3D biological data such as proteins, CT scans or neuron fibers. We discuss the design process and possibilities for this device.

David H. Laidlaw

Papers

Towards Placental Surface Vasculature Exploration in Virtual Reality

Poster: A hybrid direct visual editing method for architectural massing study in virtual environments

Composing DTI Visualizations with End-user Programming

Open Challenges in Empirical Visualization Research

Designing capsule, an input device to support the manipulation of biological datasets