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The following topics are dealt with: genomics; biomedical visualisation; medical and biomedical informatics; medical data set visualisation; and medical imaging techniques.
This paper presents a synteny visualization and analysis tool developed in connection with IMAS - the Interactive Multigenomic Analysis System. This visual analysis tool enables biologists to analyze the relationships among genomes of closely related organisms in terms of the locations of genes and clusters of genes. A biologist starts IMAS with the DNA sequence, uses BLAST to find similar genes in...
In molecular biology, Gene Ontology (GO) has often been used for annotation and as a data mining dimension. A frequently performed step in microarray analytics is the clustering of co-expressed genes by their GO bioprocesses. Biological deductions are then made from the visual representation of the cluster pattern. Thus far, the question of how different representations of GO-annotated clusters affect...
High-throughput technologies have established themselves as indispensable for the study of biological systems, from gene expression level changes, protein concentrations, to their modifications and interactions in complex diseases and systems. This kind of data analysis is not well served by the biostatistical techniques traditionally applied to biomedical and clinical data sets. Non-trivial patterns...
We created a computer model with a user-friendly graphical interface that could tell an accurate and engaging story about the management of patients with behavioural and psychological symptoms of dementia (BPSD) in Alzheimerpsilas disease. The agent-based model was built using the AnyLogic development platform and calibrated with data on prevalence and incidence of dementia in the Australian population...
This paper describes an interactive data exploration system for molecular and clinical data in the field of personalized medicine. It addresses the essential but to date unsolved problem of how to identify connections between genetic variants and their corresponding diseases or the response to certain drugs and treatments, respectively. It is therefore necessary to connect genetic with clinical data...
In recent years, comprehensive studies of protein and domain networks have produced large amounts of interaction data. Further work has revealed that alternative splicing is a major cause of the observed protein and interaction diversity. Special microarrays now allow for measuring gene expression at the exon level, which enables the identification of alternative splicing events. We developed the...
A 3D multiscale view has been developed for medical datasets that are composed of multiple images of very different spatial sizes. The example data consisted of 3 volume images of bone: a 400 mm femur; a 20 mm micro-CT image of trabeculae; and a 0.5 mm nano-CT image of a single trabecula. The images were nested, the nano-CT being inside the micro-CT, which was within the head of the femur. The images...
Preceding this report, a proof-of-concept pilot study was conducted on the REAMS database. The REAMS database associates skeletal dysplasia (SD) and their conditions, clinical and radiographic features, with exemplar X-ray images. This study reports on the 3D visualisation of the interconnectedness of the various terms used in the REAMS database. Preliminary results show predictable clustering and...
Collaboration on the storage, processing and visualisation of medical data via the Internet is a considerable challenge and one that is growing in importance due to the escalating interest in the Virtual Physiological Human. Investigations into possible approaches for distributed, realtime visualisation are important in this context. This paper presents a Web Services approach to distributed visualisation...
This paper describes the Medical Visualizer, a real-time visualization system for analyzing medical volumetric data in various virtual environments, such as autostereoscopic displays, dual-projector screens and immersive environments such as the CAVE. Direct volume rendering is used for visualizing the details of medical volumetric data sets without intermediate geometric representations. By interactively...
In this paper, a new hybrid medical image segmentation method in the level-set framework is proposed. The method uses both the objectpsilas boundary and region information to achieve robust and accurate segmentation results. The boundary information can help to detect the precise location of the target object and the region information can help to prevent the boundary leakage problem. Experimental...
This paper describes results of a quantitative evaluation of a flexible spring mass system image registration technique previously proposed by the authors. The method is assessed against two well-known registration algorithms namely the Demons and the B-spline free form deformations (FFD) implemented in Insight Segmentation and Registration Toolkit (ITK). The evaluation has been performed using simulated...
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