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Vis Inf  0, Vol. Issue (): 2-13    DOI: 10.1016/j.visinf.2018.04.002
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摘要: 背景:在大多数物种中,卵母细胞中的钙波被认为是卵子活化的常见现象。但其中钙波的作用机制并不明确。通过与从事秀丽隐杆线虫(一种广为使用的模型生物体)研究的生物学家合作,我们观察到要基于高速体内成像捕获的钙波形成有用的假设必须满足以下条件: ( 1 )该图像能从宏观上展示钙波是如何传播的;( 2 )能展示钙波在窄区域中的传播过程。然而,传统的可视化方法并不能同时满足这两项要求。

贡献:本文提出了一个可视化分析系统, 使用户能够通过对每个点处钙离子荧光强度时间序列数据的互相关分析来理解和研究钙波图像。该系统的界面包括宏观可视化、细节可视化和用户交互。宏观可视化视图可显示由互相关分析计算得到的有向图的聚类,从而使用户能够理解钙波的宏观传播,帮助他们找到感兴趣的区域。细节可视化则可显示用户感兴趣区域与其他区域之间的关系。<br />

结果:用户可以使用可视化系统提供的宏观-细节可视化功能和笔划—连接的探索方式对感兴趣的区域进行语义标记, 并构建假设。本文演示了由秀丽隐杆线虫钙波分析形成新假设的过程,验证了这一可视分析方法的可行性。<br />

关键词: 可视知识展现时间序列数据生物信息可视化     
Abstract: In most species, calcium waves in the oocyte are considered common phenomena in the activation of eggs. However, the mechanism of calcium waves has not yet been clarified. By collaborating with biologists studying Caenorhabditis elegans (C. elegans), which is widely used as a model organism, we observed that the following requirements must be satisfied to form a useful hypothesis based on calcium waves captured using high-speed in vivo imaging: (1) the ability to obtain an overview of how the calcium waves are propagated and (2) the ability to understand the propagation of waves in a narrow region. However, conventional visualization methods cannot satisfy these requirements simultaneously. Therefore, we propose a visual analytics system that allows users to understand and explore calcium wave images using cross-correlation analysis of the time-series data of the Ca2+ fluorescence intensity at each point. The interface of this system comprises an overview visualization, a detail visualization, and user interactions to satisfy these requirements and realize exploratory visualization. Some views present an overview visualization that displays the clustering results of a directed graph calculated using cross-correlation analysis. These views enable the users to understand the overview of wave propagation, thereby helping users find a region of interest. The detail visualization shows the relationship between the region of interest and other areas. Furthermore, users can use the proposed system with overview-detail and brush-link exploration to assign meaning to the region of interest and construct a hypothesis for its role. In this paper, we demonstrate how the proposed visual analytics approach works and how new hypotheses can be formed using the analysis of C. elegans calcium waves.
Key words: Visual Knowledge Discovery    Time Series Data    Bioinformatics Visualization
出版日期: 2018-04-01
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KozenUmezawa, HiroakiNatsukawa, YosukeOnoue, KojiKoyamada. . Vis Inf, 0, (): 2-13.


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