A picture is worth a thousand words--the utility of 3D visualization illustrated by a case of survived pancreatic transection

It is one of the most important tasks of the forensic pathologist to explain the forensically relevant medical findings to medical non-professionals. However, it is often difficult to comment on the nature and potential consequences of organ injuries in a comprehensive way to individuals with limited knowledge of anatomy and physiology. This rare case of survived pancreatic transaction after kicks to the abdomen illustrates how the application of dedicated software programs for three-dimensional reconstruction can overcome these difficulties, allowing for clear and concise visualization of complex findings.

The Small Project Observatory: Visualizing Software Ecosystems

Software evolution research has focused mostly on analyzing the evolution of single software systems. However, it is rarely the case that a project exists as standalone, independent of others. Rather, projects exist in parallel within larger contexts in companies, research groups or even the open-source communities. We call these contexts software ecosystems, and on this paper we present The Small Project Observatory, a prototype tool which aims to support the analysis of project ecosystems through interactive visualization and exploration. We present a case-study of exploring an ecosystem using our tool, we describe about the architecture of the tool, and we distill the lessons learned during the tool-building experience.

Angiofil-mediated visualization of the vascular system by microcomputed tomography: a feasibility study

Visualization of the vascular systems of organs or of small animals is important for an assessment of basic physiological conditions, especially in studies that involve genetically manipulated mice. For a detailed morphological analysis of the vascular tree, it is necessary to demonstrate the system in its entirety. In this study, we present a new lipophilic contrast agent, Angiofil, for performing postmortem microangiography by using microcomputed tomography. The new contrast agent was tested in 10 wild-type mice. Imaging of the vascular system revealed vessels down to the caliber of capillaries, and the digital three-dimensional data obtained from the scans allowed for virtual cutting, amplification, and scaling without destroying the sample. By use of computer software, parameters such as vessel length and caliber could be quantified and remapped by color coding onto the surface of the vascular system. The liquid Angiofil is easy to handle and highly radio-opaque. Because of its lipophilic abilities, it is retained intravascularly, hence it facilitates virtual vessel segmentation, and yields an enduring signal which is advantageous during repetitive investigations, or if samples need to be transported from the site of preparation to the place of actual analysis, respectively. These characteristics make Angiofil a promising novel contrast agent; when combined with microcomputed tomography, it has the potential to turn into a powerful method for rapid vascular phenotyping.

MARVIN: a medical research application framework based on open source software

This paper describes the open source framework MARVIN for rapid application development in the field of biomedical and clinical research. MARVIN applications consist of modules that can be plugged together in order to provide the functionality required for a specific experimental scenario. Application modules work on a common patient database that is used to store and organize medical data as well as derived data. MARVIN provides a flexible input/output system with support for many file formats including DICOM, various 2D image formats and surface mesh data. Furthermore, it implements an advanced visualization system and interfaces to a wide range of 3D tracking hardware. Since it uses only highly portable libraries, MARVIN applications run on Unix/Linux, Mac OS X and Microsoft Windows.

Consistent Layout for Thematic Software Maps

Software visualizations can provide a concise overview of a complex software system. Unfortunately, since software has no physical shape, there is no “natural“ mapping of software to a two-dimensional space. As a consequence most visualizations tend to use a layout in which position and distance have no meaning, and consequently layout typical diverges from one visualization to another. We propose a consistent layout for software maps in which the position of a software artifact reflects its \emph{vocabulary}, and distance corresponds to similarity of vocabulary. We use Latent Semantic Indexing (LSI) to map software artifacts to a vector space, and then use Multidimensional Scaling (MDS) to map this vector space down to two dimensions. The resulting consistent layout allows us to develop a variety of thematic software maps that express very different aspects of software while making it easy to compare them. The approach is especially suitable for comparing views of evolving software, since the vocabulary of software artifacts tends to be stable over time.

Visualization and quantification of air embolism structure by processing postmortem MSCT data.

Venous air embolism (VAE) is an often occurring forensic finding in cases of injury to the head and neck. Whenever found, it has to be appraised in its relation to the cause of death. While visualization and quantification is difficult at traditional autopsy, Magnetic Resonance Imaging (MRI) and Computed Tomography (CT) offer a new potential in the diagnosis of VAE. This paper reports the findings of VAE in four cases of massive head injury examined postmortem by Multislice Computed Tomography (MSCT) prior to autopsy. MSCT data of the thorax were processed using 3D air structure reconstruction software to visualize air embolism within the vascular system. Quantification of VAE was done by multiplying air containing areas on axial 2D images by their reconstruction intervals and then by summarizing the air volumes. Excellent 3D visualization of the air within the vascular system was obtained in all cases, and the intravascular gas volume was quantified.

PanPlot - software to visualize profiles and core logs

The program PanPlot was developed as a visualization tool for the information system PANGAEA. It can be used as a stand-alone application to plot data versus depth or time or in a ternary view. Data input format is tab-delimited ASCII (e.g. by export from MS-Excel or from PANGAEA). The default scales and graphic features can individualy be modified. PanPlot graphs can be exported in platform-specific interchange formats (EMF, PICT) which can be imported by graphic software for further processing.

PanPlot 2 - software to visualize profiles and time series

The program PanPlot 2 was developed as a visualization tool for the information system PANGAEA. It can be used as a stand-alone application to plot data versus depth or time. Data input format is tab-delimited ASCII (e.g. by export from MS-Excel or from PANGAEA). The default scales and graphic features can individualy be modified. PanPlot 2 graphs can be exported in several image formats (BMP, PNG, PDF, and SVG) which can be imported by graphic software for further processing.

RADIANCE-A planning software for intra-operative radiation therapy

In the last decades accumulated clinical evidence has proven that intra-operative radiation therapy (IORT) is a very valuable technique. In spite of that, planning technology has not evolved since its conception, being outdated in comparison to current state of the art in other radiotherapy techniques and therefore slowing down the adoption of IORT. RADIANCE is an IORT planning system, CE and FDA certified, developed by a consortium of companies, hospitals and universities to overcome such technological backwardness. RADIANCE provides all basic radiotherapy planning tools which are specifically adapted to IORT. These include, but are not limited to image visualization, contouring, dose calculation algorithms-Pencil Beam (PB) and Monte Carlo (MC), DVH calculation and reporting. Other new tools, such as surgical simulation tools have been developed to deal with specific conditions of the technique. Planning with preoperative images (preplanning) has been evaluated and the validity of the system being proven in terms of documentation, treatment preparation, learning as well as improvement of surgeons/radiation oncologists (ROs) communication process. Preliminary studies on Navigation systems envisage benefits on how the specialist to accurately/safely apply the pre-plan into the treatment, updating the plan as needed. Improvements on the usability of this kind of systems and workflow are needed to make them more practical. Preliminary studies on Intraoperative imaging could provide an improved anatomy for the dose computation, comparing it with the previous pre-plan, although not all devices in the market provide good characteristics to do so. DICOM.RT standard, for radiotherapy information exchange, has been updated to cover IORT particularities and enabling the possibility of dose summation with external radiotherapy. The effect of this planning technology on the global risk of the IORT technique has been assessed and documented as part of a failure mode and effect analysis (FMEA). Having these technological innovations and their clinical evaluation (including risk analysis) we consider that RADIANCE is a very valuable tool to the specialist covering the demands from professional societies (AAPM, ICRU, EURATOM) for current radiotherapy procedures.

Data visualization during the early stages of drug discovery

Multidimensional compound optimization is a new paradigm in the drug discovery process, yielding efficiencies during early stages and reducing attrition in the later stages of drug development. The success of this strategy relies heavily on understanding this multidimensional data and extracting useful information from it. This paper demonstrates how principled visualization algorithms can be used to understand and explore a large data set created in the early stages of drug discovery. The experiments presented are performed on a real-world data set comprising biological activity data and some whole-molecular physicochemical properties. Data visualization is a popular way of presenting complex data in a simpler form. We have applied powerful principled visualization methods, such as generative topographic mapping (GTM) and hierarchical GTM (HGTM), to help the domain experts (screening scientists, chemists, biologists, etc.) understand and draw meaningful decisions. We also benchmark these principled methods against relatively better known visualization approaches, principal component analysis (PCA), Sammon's mapping, and self-organizing maps (SOMs), to demonstrate their enhanced power to help the user visualize the large multidimensional data sets one has to deal with during the early stages of the drug discovery process. The results reported clearly show that the GTM and HGTM algorithms allow the user to cluster active compounds for different targets and understand them better than the benchmarks. An interactive software tool supporting these visualization algorithms was provided to the domain experts. The tool facilitates the domain experts by exploration of the projection obtained from the visualization algorithms providing facilities such as parallel coordinate plots, magnification factors, directional curvatures, and integration with industry standard software. © 2006 American Chemical Society.

DVMS 1.5: A user manual (the data visualization and modeling system)

The data available during the drug discovery process is vast in amount and diverse in nature. To gain useful information from such data, an effective visualisation tool is required. To provide better visualisation facilities to the domain experts (screening scientist, biologist, chemist, etc.),we developed a software which is based on recently developed principled visualisation algorithms such as Generative Topographic Mapping (GTM) and Hierarchical Generative Topographic Mapping (HGTM). The software also supports conventional visualisation techniques such as Principal Component Analysis, NeuroScale, PhiVis, and Locally Linear Embedding (LLE). The software also provides global and local regression facilities . It supports regression algorithms such as Multilayer Perceptron (MLP), Radial Basis Functions network (RBF), Generalised Linear Models (GLM), Mixture of Experts (MoE), and newly developed Guided Mixture of Experts (GME). This user manual gives an overview of the purpose of the software tool, highlights some of the issues to be taken care while creating a new model, and provides information about how to install & use the tool. The user manual does not require the readers to have familiarity with the algorithms it implements. Basic computing skills are enough to operate the software.

miniDVMS v1.8 : A user manual(The data visualization and modeling system)

Today, the data available to tackle many scientific challenges is vast in quantity and diverse in nature. The exploration of heterogeneous information spaces requires suitable mining algorithms as well as effective visual interfaces. miniDVMS v1.8 provides a flexible visual data mining framework which combines advanced projection algorithms developed in the machine learning domain and visual techniques developed in the information visualisation domain. The advantage of this interface is that the user is directly involved in the data mining process. Principled projection methods, such as generative topographic mapping (GTM) and hierarchical GTM (HGTM), are integrated with powerful visual techniques, such as magnification factors, directional curvatures, parallel coordinates, and user interaction facilities, to provide this integrated visual data mining framework. The software also supports conventional visualisation techniques such as principal component analysis (PCA), Neuroscale, and PhiVis. This user manual gives an overview of the purpose of the software tool, highlights some of the issues to be taken care while creating a new model, and provides information about how to install and use the tool. The user manual does not require the readers to have familiarity with the algorithms it implements. Basic computing skills are enough to operate the software.

A flexible, extensible object oriented real-time near photorealistic visualization system:the system framework design

In this paper we describe a novel, extensible visualization system currently under development at Aston University. We introduce modern programming methods, such as the use of data driven programming, design patterns, and the careful definition of interfaces to allow easy extension using plug-ins, to 3D landscape visualization software. We combine this with modern developments in computer graphics, such as vertex and fragment shaders, to create an extremely flexible, extensible real-time near photorealistic visualization system. In this paper we show the design of the system and the main sub-components. We stress the role of modern programming practices and illustrate the benefits these bring to 3D visualization. © 2006 Springer-Verlag Berlin Heidelberg.