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.
{"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":"28 1","pages":"15-20"},"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}
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.
{"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":"9 1","pages":"23-28"},"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
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.
{"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":"27 1","pages":"47-52"},"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
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.
{"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":"29 1","pages":"57-62"},"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}
Jian-Kun Shen, B. Matuszewski, L. Shark, A. Skalski, T. Zielinski, C. Moore
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.
本文描述了作者先前提出的柔性弹簧质量系统图像配准技术的定量评价结果。该方法针对Insight Segmentation and registration Toolkit (ITK)中实现的两种著名的配准算法，即Demons和b样条自由形式变形(FFD)进行了评估。利用模拟数据以及放疗后前列腺和头颈部患者的真实CT图像进行评估。而对于模拟数据的配准质量是使用密集位移场来衡量的，而离散的解剖标志则与真实的CT图像一起使用。结果表明，对于无噪声或高斯噪声的数据，使用弹簧质量系统的方法与Demons和b样条FFD的配准精度相当，但当数据中存在结构化噪声时，其配准精度优于这些方法。此外，使用弹簧质量系统的方法可以提供更准确的配准质量，如果一些额外的信息，以特征标志和/或分割的解剖结构的形式，是可用的。在整个论文中，特别注意了结果的有效可视化。
{"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":"41 1","pages":"77-82"},"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}
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.
{"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":"7 1","pages":"63-68"},"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}
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 related sequences, and uses these similarity linkages to create an enhanced node-link diagram of syntenic sequences. We refer to this as Spring Synteny visualization, which is aimed at helping a biologist discover similar gene ordering relationships across species. The paper describes the techniques that are used to support synteny visualization, in terms of computation, visual design, and interaction design.
{"title":"Genomic Spring-Synteny Visualization with IMAS","authors":"C. Shaw","doi":"10.1109/MEDIVIS.2008.17","DOIUrl":"https://doi.org/10.1109/MEDIVIS.2008.17","url":null,"abstract":"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 related sequences, and uses these similarity linkages to create an enhanced node-link diagram of syntenic sequences. We refer to this as Spring Synteny visualization, which is aimed at helping a biologist discover similar gene ordering relationships across species. The paper describes the techniques that are used to support synteny visualization, in terms of computation, visual design, and interaction design.","PeriodicalId":51800,"journal":{"name":"Computer Methods in Biomechanics and Biomedical Engineering-Imaging and Visualization","volume":"11 2 1","pages":"3-8"},"PeriodicalIF":1.6,"publicationDate":"2008-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80395845","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}
This paper proposes a new approach for separation of components in functional MRI sequences using FastICA. In this paper we will demonstrate that if we subtract background (which is separated from sources by PCA) from other principal components, the algorithm converges very fast. The proposed method is more robust and much more computationally efficient than methods, which previously has been applied for separation of components in functional MRI sequences.
{"title":"A New Approach for Separation of Functional MRI Images' Components Using Modified FastICA Algorithm","authors":"H. Larijani, G.R. Rad","doi":"10.1109/MEDIVIS.2008.8","DOIUrl":"https://doi.org/10.1109/MEDIVIS.2008.8","url":null,"abstract":"This paper proposes a new approach for separation of components in functional MRI sequences using FastICA. In this paper we will demonstrate that if we subtract background (which is separated from sources by PCA) from other principal components, the algorithm converges very fast. The proposed method is more robust and much more computationally efficient than methods, which previously has been applied for separation of components in functional MRI sequences.","PeriodicalId":51800,"journal":{"name":"Computer Methods in Biomechanics and Biomedical Engineering-Imaging and Visualization","volume":"73 1","pages":"83-87"},"PeriodicalIF":1.6,"publicationDate":"2008-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73508822","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}
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 results on a synthetic image as well as real 2D and 3D medical images are also shown in the paper with the emphasis on the comparisons between the new hybrid method and the Chan-Vese method.
{"title":"Medical Image Segmentation Using New Hybrid Level-Set Method","authors":"Yan Zhang, B. Matuszewski, L. Shark, C. Moore","doi":"10.1109/MEDIVIS.2008.12","DOIUrl":"https://doi.org/10.1109/MEDIVIS.2008.12","url":null,"abstract":"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 results on a synthetic image as well as real 2D and 3D medical images are also shown in the paper with the emphasis on the comparisons between the new hybrid method and the Chan-Vese method.","PeriodicalId":51800,"journal":{"name":"Computer Methods in Biomechanics and Biomedical Engineering-Imaging and Visualization","volume":"108 1","pages":"71-76"},"PeriodicalIF":1.6,"publicationDate":"2008-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89793049","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}
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