Eurovis: Eurographics Conference on Visualization

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https://diglib.eg.org/handle/10.2312/392

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Browsing Eurovis: Eurographics Conference on Visualization by Subject "Biology and genetics"

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    AVOCADO: Visualization of Workflow-Derived Data Provenance for Reproducible Biomedical Research
    (The Eurographics Association and John Wiley & Sons Ltd., 2016) Stitz, Holger; Luger, Stefan; Streit, Marc; Gehlenborg, Nils; Kwan-Liu Ma and Giuseppe Santucci and Jarke van Wijk
    A major challenge in data-driven biomedical research lies in the collection and representation of data provenance information to ensure that findings are reproducibile. In order to communicate and reproduce multi-step analysis workflows executed on datasets that contain data for dozens or hundreds of samples, it is crucial to be able to visualize the provenance graph at different levels of aggregation. Most existing approaches are based on node-link diagrams, which do not scale to the complexity of typical data provenance graphs. In our proposed approach, we reduce the complexity of the graph using hierarchical and motif-based aggregation. Based on user action and graph attributes, a modular degree-of-interest (DoI) function is applied to expand parts of the graph that are relevant to the user. This interest-driven adaptive approach to provenance visualization allows users to review and communicate complex multi-step analyses, which can be based on hundreds of files that are processed by numerous workflows. We have integrated our approach into an analysis platform that captures extensive data provenance information, and demonstrate its effectiveness by means of a biomedical usage scenario.
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    Cell Lineage Visualisation
    (The Eurographics Association and John Wiley & Sons Ltd., 2015) Pretorius, A. Johannes; Khan, Imtiaz A.; Errington, Rachel J.; H. Carr, K.-L. Ma, and G. Santucci
    Cell lineages describe the developmental history of cell populations and are produced by combining time-lapse imaging and image processing. Biomedical researchers study cell lineages to understand fundamental processes such as cell differentiation and the pharmacodynamic action of anticancer agents. Yet, the interpretation of cell lineages is hindered by their complexity and insufficient capacity for visual analysis. We present a novel approach for interactive visualisation of cell lineages. Based on an understanding of cellular biology and live-cell imaging methodology, we identify three requirements: multimodality (cell lineages combine spatial, temporal, and other properties), symmetry (related to lineage branching structure), and synchrony (related to temporal alignment of cellular events). We address these by combining visual summaries of the spatiotemporal behaviour of an arbitrary number of lineages, including variation from average behaviour, with node-link representations that emphasise the presence or absence of symmetry and synchrony. We illustrate the merit of our approach by presenting a real-world case study where the cytotoxic action of the anticancer drug topotecan was determined.
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    Comparison of Multiple Weighted Hierarchies: Visual Analytics for Microbe Community Profiling
    (The Eurographics Association and Blackwell Publishing Ltd., 2011) Dinkla, Kasper; Westenberg, M. A.; Timmerman, H. M.; Hijum, S.A.F.T. van; Wijk, J. J. van; H. Hauser, H. Pfister, and J. J. van Wijk
    We propose visual analytics techniques to support concurrent comparison of hundreds of cumulatively weighted instances of a single hierarchy. This includes a node-link representation of the hierarchy where nodes depict the weights of all instances with high-density heat maps that are grouped and aligned to ease cross-referencing. Hierarchy exploration is facilitated by smoothly animated expansion and collapse of its branches. Detailed infor- mation about hierarchy structure, weights, and meta-data is provided by secondary linked visualizations. These techniques have been implemented in a prototype tool, in which the computational analysis concerns have been strictly separated from the visualization concerns. The analysis algorithms are extensible via a script engine. We discuss the effectiveness of our techniques for the visual analytic process of microbe community profiling experts.
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    Synthetic Brainbows
    (The Eurographics Association and Blackwell Publishing Ltd., 2013) Wan, Yong; Otsuna, Hideo; Hansen, Charles; B. Preim, P. Rheingans, and H. Theisel
    Brainbow is a genetic engineering technique that randomly colorizes cells. Biological samples processed with this technique and imaged with confocal microscopy have distinctive colors for individual cells. Complex cellular structures can then be easily visualized. However, the complexity of the Brainbow technique limits its applications. In practice, most confocal microscopy scans use different florescence staining with typically at most three distinct cellular structures. These structures are often packed and obscure each other in rendered images making analysis difficult. In this paper, we leverage a process known as GPU framebuffer feedback loops to synthesize Brainbow-like images. In addition, we incorporate ID shuffling and Monte-Carlo sampling into our technique, so that it can be applied to single-channel confocal microscopy data. The synthesized Brainbow images are presented to domain experts with positive feedback. A user survey demonstrates that our synthetic Brainbow technique improves visualizations of volume data with complex structures for biologists.