H. Muller, K. Zatloukal, M. Streit, D. Schmalstieg
{"title":"Interactive Exploration of Medical Data Sets","authors":"H. Muller, K. Zatloukal, M. Streit, D. Schmalstieg","doi":"10.1109/MEDIVIS.2008.13","DOIUrl":"https://doi.org/10.1109/MEDIVIS.2008.13","url":null,"abstract":"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 order to categorize specific subgroups of patients with certain disease features. The huge amount of data provided by molecular analytical methods (e.g. data on genetic alterations, proteomic or metabolomic data) can only be analyzed by applying statistical methods and bioinformatics. However, even standard methods of statistics and bioinformatics fail when the data is inhomogeneous - as is the case with clinical data - and when data structures are obscured by noise and dominant patterns. The structure of large medical data sets is made visible by using so called object- and attribute-glyphs, which can be arranged in a two dimensional space and synchronized with a set of visualization views.","PeriodicalId":51800,"journal":{"name":"Computer Methods in Biomechanics and Biomedical Engineering-Imaging and Visualization","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2008-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87363448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Visualizing the Gene Ontology-Annotated Clusters of Co-expressed Genes: A Two-Design Study","authors":"D. Fung, Seok-Hee Hong, Kai Xu, D. Hart","doi":"10.1109/MEDIVIS.2008.9","DOIUrl":"https://doi.org/10.1109/MEDIVIS.2008.9","url":null,"abstract":"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 biological interpretation and usability has not been investigated. In this paper, we evaluated two representations of GO-annotated clusters of co-expressed genes. Using a published cDNA microarray dataset, we tested the effect of each representation on biological interpretation. We also reported the results of the user evaluation conducted with bench biologists from different areas of expertise. Our study suggests that the bipartite graph may be more suitable for microarray analytics.","PeriodicalId":51800,"journal":{"name":"Computer Methods in Biomechanics and Biomedical Engineering-Imaging and Visualization","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2008-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87521309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
D. Emig, K. Klein, A. Kunert, Petra Mutzel, M. Albrecht
{"title":"Visualizing Domain Interaction Networks and the Impact of Alternative Splicing Events","authors":"D. Emig, K. Klein, A. Kunert, Petra Mutzel, M. Albrecht","doi":"10.1109/MEDIVIS.2008.16","DOIUrl":"https://doi.org/10.1109/MEDIVIS.2008.16","url":null,"abstract":"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 Cytoscape plugin DomainGraph that facilitates the construction and visualization of protein and domain interaction networks. This plugin additionally supports the integration of exon expression data to highlight the effects of alternative splicing on the networks. We also designed and implemented a radial layout algorithm that specifically takes the integrated biological information for the networks into account and improves the visual presentation of the protein domain graphs considerably.","PeriodicalId":51800,"journal":{"name":"Computer Methods in Biomechanics and Biomedical Engineering-Imaging and Visualization","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2008-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87115412","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"3D Visualisation of the Radiological Features of Type II Collagenopathies Associated with Skeletal Dysplasias","authors":"T. Wyeld, A. Zankl","doi":"10.1109/MEDIVIS.2008.19","DOIUrl":"https://doi.org/10.1109/MEDIVIS.2008.19","url":null,"abstract":"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 outliers based on shared common terms. In 1994 Spranger et al. reported on the identification of the 6 type II collagenopathy conditions associated with SDs. To test the accuracy and usefulness of our 3D visualisation of the REAMS database the 6 known type II collagenopathies were colour coded to distinguish their location within the larger database. Distinct clustering was detected. However, we also discovered 10 non type II collagenopathy conditions that share 2 or more common clinical and/or radiographic features with at least 1 of the 6 known type II collagenopathy conditions. This result confirms and quantifies the clinical radiographical overlap among the type II collagenopathies as originally predicted by Spranger et al.","PeriodicalId":51800,"journal":{"name":"Computer Methods in Biomechanics and Biomedical Engineering-Imaging and Visualization","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2008-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87831847","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"From Microarrays to Promoters: The Visual Story of Stat3","authors":"U. Cvek, M. Trutschl, Z. Syed, J. Clifford","doi":"10.1109/MEDIVIS.2008.18","DOIUrl":"https://doi.org/10.1109/MEDIVIS.2008.18","url":null,"abstract":"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 are most often discovered using visual and other computational tools applied to this data. We derive patterns and information from a series of differentially expressed genes on eight microarrays combined with analysis of promoter regions using regular expression-driven examination of short representative sequences called motifs. These non-trivial patterns are used to aid the discovery process through the use of information visualization and by harnessing userpsilas perceptual and cognitive capabilities.","PeriodicalId":51800,"journal":{"name":"Computer Methods in Biomechanics and Biomedical Engineering-Imaging and Visualization","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2008-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88516978","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Visualisation of Clinical and Non-clinical Characteristics of Patients with Behavioural and Psychological Symptoms of Dementia","authors":"V. Vickland, H. Brodaty","doi":"10.1109/MEDIVIS.2008.20","DOIUrl":"https://doi.org/10.1109/MEDIVIS.2008.20","url":null,"abstract":"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. The graphical user interface of the model consisted of multiple screens and was intended as a tool for information visualisation and virtual experiments. The dynamic progression of the symptoms and each patientpsilas individual characteristics such as age, gender and place of residence were integrated into one model. The preliminary results indicate that simulation modelling approach and application of multiple icons in graphical representation of each individual patient are efficient tools for information visualisation in agent-based model. The dual graphical representation of individual patients allowed for simultaneous display of clinical e.g. symptom-specific and non-clinical e.g. accommodation characteristics.","PeriodicalId":51800,"journal":{"name":"Computer Methods in Biomechanics and Biomedical Engineering-Imaging and Visualization","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2008-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79831167","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
N.J.B. McFarlane, G. Clapworthy, A. Agrawal, M. Viceconti, F. Taddei, E. Schileo, F. Baruffaldi
{"title":"3D Multiscale Visualisation for Medical Datasets","authors":"N.J.B. McFarlane, G. Clapworthy, A. Agrawal, M. Viceconti, F. Taddei, E. Schileo, F. Baruffaldi","doi":"10.1109/MEDIVIS.2008.14","DOIUrl":"https://doi.org/10.1109/MEDIVIS.2008.14","url":null,"abstract":"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 were visualised using a volume slice view. The dataset was multiscale in that each image could not be usefully resolved at the scale of the next larger image. The multiscale interaction within the system is based on the replacement of sub-scale images by small click-and-zoom tokens. Issues relating to interaction with the tokens are discussed and early outcomes from this form representation are described.","PeriodicalId":51800,"journal":{"name":"Computer Methods in Biomechanics and Biomedical Engineering-Imaging and Visualization","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2008-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74803881","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xia Zhao, E. Liu, G. Clapworthy, P. Quadrani, D. Testi, M. Viceconti
{"title":"Using Web Services for Distributed Medical Visualisation","authors":"Xia Zhao, E. Liu, G. Clapworthy, P. Quadrani, D. Testi, M. Viceconti","doi":"10.1109/MEDIVIS.2008.15","DOIUrl":"https://doi.org/10.1109/MEDIVIS.2008.15","url":null,"abstract":"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 that has been developed within the LHDL project. The processing and visualisation Web Services that have been created are based on existing MAF applications; this has formed a useful testbed for transforming legacy software into Web Services. On the client side, a Rich Internet Application concept was adopted, while a web-based, user friendly Flex client has been implemented.","PeriodicalId":51800,"journal":{"name":"Computer Methods in Biomechanics and Biomedical Engineering-Imaging and Visualization","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2008-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84282454","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"MedVis: A Real-Time Immersive Visualization Environment for the Exploration of Medical Volumetric Data","authors":"Rui Shen, P. Boulanger, M. Noga","doi":"10.1109/MEDIVIS.2008.10","DOIUrl":"https://doi.org/10.1109/MEDIVIS.2008.10","url":null,"abstract":"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 manipulating the color and transparency functions through the friendly user interface, radiologists can either inspect the data set as a whole or focus on a specific region. In our system, 3D texture hardware is employed to accelerate the rendering process. The system is designed to be platform independent, as all virtual reality functions are separated from kernel functions. Due to its modular design, our system can be easily extended to other virtual environments, and new functions can be incorporated rapidly.","PeriodicalId":51800,"journal":{"name":"Computer Methods in Biomechanics and Biomedical Engineering-Imaging and Visualization","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2008-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73597907","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jian-Kun Shen, B. Matuszewski, L. Shark, A. Skalski, T. Zielinski, C. Moore
{"title":"Deformable Image Registration - A Critical Evaluation: Demons, B-Spline FFD and Spring Mass System","authors":"Jian-Kun Shen, B. Matuszewski, L. Shark, A. Skalski, T. Zielinski, C. Moore","doi":"10.1109/MEDIVIS.2008.11","DOIUrl":"https://doi.org/10.1109/MEDIVIS.2008.11","url":null,"abstract":"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 data as well as real CT images of the radiotherapy prostate and the head and neck patients. Whereas for the simulated data the quality of registration has been measured using the dense displacement field, the discrete anatomical landmarks have been used with the real CT images. The results show the method using spring mass system achieves comparable registration accuracy with the Demons and B-spline FFD for the data with no noise or Gaussian noise, but it outperforms these methods when structured noise is present in the data. Moreover, the method using spring mass system can offer more accurate registration quality if some additional information, in the form of feature landmarks and/or segmented anatomical structures, is available. Throughout the paper a special attention has been given to the effective visualisation of the results.","PeriodicalId":51800,"journal":{"name":"Computer Methods in Biomechanics and Biomedical Engineering-Imaging and Visualization","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2008-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76285202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}