SlicerAstro: a 3-D interactive visual analytics tool for HI data

SKA precursors are capable of detecting hundreds of galaxies in HI in a single 12 hours pointing. In deeper surveys one will probe more easily faint HI structures, typically located in the vicinity of galaxies, such as tails, filaments, and extraplanar gas. The importance of interactive visualization has proven to be fundamental for the exploration of such data as it helps users to receive immediate feedback when manipulating the data. We have developed SlicerAstro, a 3-D interactive viewer with new analysis capabilities, based on traditional 2-D input/output hardware. These capabilities enhance the data inspection, allowing faster analysis of complex sources than with traditional tools. SlicerAstro is an open-source extension of 3DSlicer, a multi-platform open source software package for visualization and medical image processing. We demonstrate the capabilities of the current stable binary release of SlicerAstro, which offers the following features: i) handling of FITS files and astronomical coordinate systems; ii) coupled 2-D/3-D visualization; iii) interactive filtering; iv) interactive 3-D masking; v) and interactive 3-D modeling. In addition, SlicerAstro has been designed with a strong, stable and modular C++ core, and its classes are also accessible via Python scripting, allowing great flexibility for user-customized visualization and analysis tasks.Comment: 18 pages, 11 figures, Accepted by Astronomy and Computing. SlicerAstro link: https://github.com/Punzo/SlicerAstro/wiki#get-slicerastr

Hybrid rendering of exploded views for medical image atlas visualization

Medical image atlases contain much information about human anatomy, but learning the shapes of anatomical regions and making sense of the overall structure defined in the atlas can be problematic. Atlases may contain hundreds of regions with complex shapes which can be tightly packed together. This makes visualisation difficult since the shapes can fit together in complex ways and visually obscure each other. In this work, we describe a technique which enables interactive exploration of medical image atlases that permits the hierarchical structure of the atlas and the content of an underlying medical image to be investigated simultaneously. Our method enables a user to create visualizations of the atlas similar to the exploded views used in technical illustrations to show the structure of mechanical assemblies. These views are constrained by the geometry of the atlas and the hierarchical structure to reduce the complexity of user interaction. We also enable the user to explode the atlas meshes themselves. The atlas meshes are registered with a medical image which is displayed on the cut surfaces of the meshes using raycasting. Results from the AAL human brain atlas are presented and discussed

Animating Human Muscle Structure

Graphical simulations of human muscle motion and deformation are of great interest to medical education. In this article, the authors present a technique for simulating muscle deformations by combining physically and geometrically based computations to reduce computation cost and produce fast, accurate simulations

Virtual reality training and assessment in laparoscopic rectum surgery

Background: Virtual-reality (VR) based simulation techniques offer an efficient and low cost alternative to conventional surgery training. This article describes a VR training and assessment system in laparoscopic rectum surgery. Methods: To give a realistic visual performance of interaction between membrane tissue and surgery tools, a generalized cylinder based collision detection and a multi-layer mass-spring model are presented. A dynamic assessment model is also designed for hierarchy training evaluation. Results: With this simulator, trainees can operate on the virtual rectum with both visual and haptic sensation feedback simultaneously. The system also offers surgeons instructions in real time when improper manipulation happens. The simulator has been tested and evaluated by ten subjects. Conclusions: This prototype system has been verified by colorectal surgeons through a pilot study. They believe the visual performance and the tactile feedback are realistic. It exhibits the potential to effectively improve the surgical skills of trainee surgeons and significantly shorten their learning curve. © 2014 John Wiley & Sons, Ltd

Accurate geometry reconstruction of vascular structures using implicit splines

3-D visualization of blood vessel from standard medical datasets (e.g. CT or MRI) play an important role in many clinical situations, including the diagnosis of vessel stenosis, virtual angioscopy, vascular surgery planning and computer aided vascular surgery. However, unlike other human organs, the vasculature system is a very complex network of vessel, which makes it a very challenging task to perform its 3-D visualization. Conventional techniques of medical volume data visualization are in general not well-suited for the above-mentioned tasks. This problem can be solved by reconstructing vascular geometry. Although various methods have been proposed for reconstructing vascular structures, most of these approaches are model-based, and are usually too ideal to correctly represent the actual variation presented by the cross-sections of a vascular structure. In addition, the underlying shape is usually expressed as polygonal meshes or in parametric forms, which is very inconvenient for implementing ramification of branching. As a result, the reconstructed geometries are not suitable for computer aided diagnosis and computer guided minimally invasive vascular surgery. In this research, we develop a set of techniques associated with the geometry reconstruction of vasculatures, including segmentation, modelling, reconstruction, exploration and rendering of vascular structures. The reconstructed geometry can not only help to greatly enhance the visual quality of 3-D vascular structures, but also provide an actual geometric representation of vasculatures, which can provide various benefits. The key findings of this research are as follows: 1. A localized hybrid level-set method of segmentation has been developed to extract the vascular structures from 3-D medical datasets. 2. A skeleton-based implicit modelling technique has been proposed and applied to the reconstruction of vasculatures, which can achieve an accurate geometric reconstruction of the vascular structures as implicit surfaces in an analytical form. 3. An accelerating technique using modern GPU (Graphics Processing Unit) is devised and applied to rendering the implicitly represented vasculatures. 4. The implicitly modelled vasculature is investigated for the application of virtual angioscopy

Robust semi-automated path extraction for visualising stenosis of the coronary arteries

Computed tomography angiography (CTA) is useful for diagnosing and planning treatment of heart disease. However, contrast agent in surrounding structures (such as the aorta and left ventricle) makes 3-D visualisation of the coronary arteries difficult. This paper presents a composite method employing segmentation and volume rendering to overcome this issue. A key contribution is a novel Fast Marching minimal path cost function for vessel centreline extraction. The resultant centreline is used to compute a measure of vessel lumen, which indicates the degree of stenosis (narrowing of a vessel). Two volume visualisation techniques are presented which utilise the segmented arteries and lumen measure. The system is evaluated and demonstrated using synthetic and clinically obtained datasets

Shape: A 3D Modeling Tool for Astrophysics

We present a flexible interactive 3D morpho-kinematical modeling application for astrophysics. Compared to other systems, our application reduces the restrictions on the physical assumptions, data type and amount that is required for a reconstruction of an object's morphology. It is one of the first publicly available tools to apply interactive graphics to astrophysical modeling. The tool allows astrophysicists to provide a-priori knowledge about the object by interactively defining 3D structural elements. By direct comparison of model prediction with observational data, model parameters can then be automatically optimized to fit the observation. The tool has already been successfully used in a number of astrophysical research projects.Comment: 13 pages, 11 figures, accepted for publication in the "IEEE Transactions on Visualization and Computer Graphics