Timothy Lambert

Using Miranda as a first programming language

The functional programming language Miranda has been used as a first programming language at the University of NSW since the beginning of 1989, when a new computer engineering course and a revised computer science course were introduced. This paper explains the reasons for choosing the language, and describes the subject in which Miranda is introduced. Examples of the presentation of the material, and of exercises and assignment used in the course, are given. Finally, an assessment of the experience is given.

Modelling heating of liver tumours with heterogeneous magnetic microsphere deposition

Ferromagnetic embolization hyperthermia (FEH) is a novel treatment for liver cancer. Magnetic microspheres are injected into the hepatic artery and cluster in the periphery of tumours and are heated with externally applied magnetic fields. In order to more accurately simulate FEH, we modelled a three-dimensional heterogeneous distribution of heat sources. We constructed a fractal model of the vasculature in the periphery of a tumour. We used this model to compute the spatial distribution of the microspheres that lodge in capillaries. We used the distribution model as input to a finite-element heat transfer model of the FEH treatment. The overall appearance of the vascular tree is subjectively similar to that of the disorganized vascular network which encapsulates tumours. The microspheres are distributed in the tumour periphery in similar patterns to experimental observations. We expect the vasculature and microsphere deposition models to also be of interest to researchers of any targeted cancer therapies such as localized intra-arterial chemotherapy and selective internal radiotherapy. Our results show that heterogeneous microsphere distributions give significantly different results to those for a homogeneous model and thus are preferable when accurate results are required.

A three-dimensional fractal model of tumour vasculature

We constructed a three-dimensional fractal model of the vascular network in a tumour periphery. We model the highly disorganised structure of the neoplastic vasculature by using a high degree of variation in segment properties such as length, diameter and branching angle. The overall appearance of the vascular tree is subjectively similar to that of the disorganised vascular network which encapsulates tumours. The fractal dimension of the model is within the range of clinically measured values.

The Interactorium: Visualising proteins, complexes and interaction networks in a virtual 3‐D cell

Here, we describe the Interactorium, a tool in which a Virtual Cell is used as the context for the seamless visualisation of the yeast protein interaction network, protein complexes and protein 3‐D structures. The tool has been designed to display very complex networks of up to 40 000 proteins or 6000 multiprotein complexes and has a series of toolboxes and menus to allow real‐time data manipulation and control the manner in which data are displayed. It incorporates new algorithms that reduce the complexity of the visualisation by the generation of putative new complexes from existing data and by the reduction of edges through the use of protein “twins” when they occur in multiple locations. Since the Interactorium permits multi‐level viewing of the molecular biology of the cell, it is a considerable advance over existing approaches. We illustrate its use for Saccharomyces cerevisiae but note that it will also be useful for the analysis of data from simpler prokaryotes and higher eukaryotes, including humans. The Interactorium is available for download at http://www.interactorium.net.

Camera-based OBDP locomotion system

In virtual reality, locomotion is a key factor in making a simulation immersive. Actually walking is the most intuitive way for people to move about, providing a better sense of presence than walking-in-place or flying [Usoh et al. 1999]. We have built a locomotion system with a ball-bearing platform that allows the user to walk in a natural fashion in any direction. The users leg motion is tracked with two cameras and turned into locomotion in the simulation. We also track upper body motion and use this to animate the users avatar. Our approach is less expensive than systems that involve complex mechanical arrangements, such as an omnidirectional treadmill [Darken et al. 1997], and more immersive than simple switch mechanisms such as the Walking-Pad [Bouguila et al. 2004]. Our system delivers real-time performance on mid-tier hardware computer and webcams.

An optimal algorithm for realizing a Delaunay triangulation

Abstract Dillencourt (1990) gives a constructive proof for the realizability as a Delaunay triangulation of any triangulation of the interior of a simple polygon. A naive implementation of the construction will take O ( n 2 ) time. I give a simple O ( n ) algorithm for this problem. An application of this algorithm is generating test data for algorithms that process convex polygons.

3D visualization of the human cerebral vasculature

Computer assisted 3D visualization of the human cerebro-vascular system can help to locate blood vessels during diagnosis and to approach them during treatment. Our aim is to reconstruct the human cerebro-vascular system from the partial information collected from a variety of medical imaging instruments and to generate a 3D graphical representation. This paper describes a tool developed for 3D visualization of cerebro-vascular structures. It also describes a symbolic approach to modeling vascular anatomy. The tool, called Ispline, is used to display the graphical information stored in a symbolic model of the vasculature. The vascular model was developed to assist image processing and image fusion. The model consists of a structural symbolic representation using frames and a geometrical representation of vessel shapes and vessel topology. Ispline has proved to be useful for visualizing both the synthetically constructed vessels of the symbolic model and the vessels extracted from a patients MR angiograms.

AFL and FRL: abstraction and representation for field interchange

The holy grail of biomedical modelling is an integrated model of the entire human body. To this end, research groups around the world need to interchange experimental data, models and model results. A good interchange will have an efficient representation for storage and sharing and will have tools for modelling, data verification, authoring, data conversions and so on. A field is a spatially varying properly. In this paper we present the abstract field layer (AFL) and the field representation language (FRL). The AFL provides the field abstraction together with a set of common field operations. The FRL provides an efficient means for field representation and storage. We show how fields can be used to interchange information between modelling systems and between modelling and visualisation systems. We are currently developing a software system that composes multiple single cell solvers to create a tissue solver.

Pre-integrated deferred subsurface scattering

Related Work  Real-time texture-space diffusion methods [d’Eon and Luebke 2007] achieve high visual quality but not high performance or scalability.  Screen-space subsurface scattering techniques [Jimenez and Gutierrez 2010] are more scalable but use a lot of memory, are expensive, and produce halo artifacts.  Pre-integrated skin scattering methods [Penner and Borshukov 2011] are high quality and fast but cannot be easily applied to a deferred renderer.

Anatomic vascular phantom for the verification of MRA and XRA visualization and fusion

A project is underway to develop automated methods of fusing cerebral magnetic resonance angiography (MRA) and x-ray angiography (XRA) for creating accurate visualizations used in planning treatment of vascular disease. We have developed a vascular phantom suitable for testing segmentation and fusion algorithms with either derived images (psuedo-MRA/psuedo-XRA) or actual MRA or XRA image sequences. The initial unilateral arterial phantom design, based on normal human anatomy, contains 48 tapering vascular segments with lumen diameters from 2.5 millimeter to 0.25 millimeter. The initial phantom used rapid prototyping technology (stereolithography) with a 0.9 millimeter vessel wall fabricated in an ultraviolet-cured plastic. The model fabrication resulted in a hollow vessel model comprising the internal carotid artery, the ophthalmic artery, and the proximal segments of the anterior, middle, and posterior cerebral arteries. The complete model was fabricated but the models lumen could not be cleared for vessels with less than 1 millimeter diameter. Measurements of selected vascular outer diameters as judged against the CAD specification showed an accuracy of 0.14 mm and precision (standard deviation) of 0.15 mm. The plastic vascular model produced provides a fixed geometric framework for the evaluation of imaging protocols and the development of algorithms for both segmentation and fusion.