A visual analytics system to support the formation of a hypothesis from calcium wave data

• Main Authors: Kozen Umezawa, Hiroaki Natsukawa, Yosuke Onoue, Koji Koyamada
• Format: Article
• Language: English
• Published: Elsevier 2018-03-01
• Series: Visual Informatics
• Online Access: http://www.sciencedirect.com/science/article/pii/S2468502X18300081

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. Keywords: Visual Knowledge Discovery, Time Series Data, Bioinformatics Visualization