Interactive Visualization of Dense and Multi-Scale Data for Science Outreach

Information

• Publication Type: PhD-Thesis
• Workgroup(s)/Project(s):
  • Visualization Group
• Date: April 2021
• Date (Start): March 2017
• Date (End): April 2021
• Open Access: yes
• 1st Reviewer: Kwan Liu Ma
• 2nd Reviewer: Bernhard Preim
• Rigorosum: 7. April 2021
• First Supervisor: Ivan Viola
• Pages: 123
• Keywords: biological, visualization, multi-scale, dense, navigation

Abstract

This thesis focuses on the problem of navigating complex 3D models composed of large numbers of molecular instances packed densely in the three-dimensional space. Due to the large environment encompassing several magnitudes of scale, the traditional navigational paradigms applied in real-time computer graphics are becoming insufficient when applied to biological environments. In the first part of the thesis, I analyze navigation challenges presented by such a use case and recognize several modes of navigation that can be employed when interfacing a complex 3D visualization system with the end-user. We discuss three such modes of navigation: augmentive, declarative, and automative. First, in augmentive navigation, the user is given fully manual control over all aspects of navigation, such as controlling the camera's position and rotation, or the visibility of the individual model's parts. Their manual exploration is, however, augmented by automatically deployed annotation to help make sense of the environment. In declarative navigation, the user interaction is simplified to declaring their target. The visualization system then takes over the low-level controls of the visualization, e.g., camera path animation and scene visibility transition, which are computed to navigate the user directly to their declared target. The third stage, automative navigation, relieves the user from even this responsibility and places the choice of what gets shown to an algorithmic solution. In this case, such automated fly-through can then be guided by a specific storyline. In the second part of the thesis, I present specific methods addressing technical gaps and contributing to realizing the navigational stages presented in the first part. I start by introducing an approach for textual labeling of multi-scale molecular models inspired by the level-of-detail concept. That way, a scenario of augmentive navigation is provided. Second, I propose a navigational method for traversing a dense molecular model with a hierarchical organization, implementing the declarative navigation concept. The presented method uses textual labels for browsing the three-dimensional model, essentially providing a way of traversing the hierarchical organization and exploring the spatial characteristics of the model. Finally, I propose a pipeline for producing automated tours of molecular models, demonstrating the automative navigation mode.

Additional Files and Images

Weblinks

• Entry in reposiTUm (TU Wien Publication Database)
• DOI: 10.34726/hss.2021.91703

BibTeX

@phdthesis{kouril-2021-phdthesis,
  title =      "Interactive Visualization of Dense and Multi-Scale Data for
               Science Outreach",
  author =     "David Kou\v{r}il",
  year =       "2021",
  abstract =   "This thesis focuses on the problem of navigating complex 3D
               models composed of large numbers of molecular instances
               packed densely in the three-dimensional space. Due to the
               large environment encompassing several magnitudes of scale,
               the traditional navigational paradigms applied in real-time
               computer graphics are becoming insufficient when applied to
               biological environments. In the first part of the thesis, I
               analyze navigation challenges presented by such a use case
               and recognize several modes of navigation that can be
               employed when interfacing a complex 3D visualization system
               with the end-user. We discuss three such modes of
               navigation: augmentive, declarative, and automative. First,
               in augmentive navigation, the user is given fully manual
               control over all aspects of navigation, such as controlling
               the camera's position and rotation, or the visibility of the
               individual model's parts. Their manual exploration is,
               however, augmented by automatically deployed annotation to
               help make sense of the environment. In declarative
               navigation, the user interaction is simplified to declaring
               their target. The visualization system then takes over the
               low-level controls of the visualization, e.g., camera path
               animation and scene visibility transition, which are
               computed to navigate the user directly to their declared
               target. The third stage, automative navigation, relieves the
               user from even this responsibility and places the choice of
               what gets shown to an algorithmic solution. In this case,
               such automated fly-through can then be guided by a specific
               storyline. In the second part of the thesis, I present
               specific methods addressing technical gaps and contributing
               to realizing the navigational stages presented in the first
               part. I start by introducing an approach for textual
               labeling of multi-scale molecular models inspired by the
               level-of-detail concept. That way, a scenario of augmentive
               navigation is provided. Second, I propose a navigational
               method for traversing a dense molecular model with a
               hierarchical organization, implementing the declarative
               navigation concept. The presented method uses textual labels
               for browsing the three-dimensional model, essentially
               providing a way of traversing the hierarchical organization
               and exploring the spatial characteristics of the model.
               Finally, I propose a pipeline for producing automated tours
               of molecular models, demonstrating the automative navigation
               mode.",
  month =      apr,
  pages =      "123",
  address =    "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria",
  school =     "Research Unit of Computer Graphics, Institute of Visual
               Computing and Human-Centered Technology, Faculty of
               Informatics, TU Wien ",
  keywords =   "biological, visualization, multi-scale, dense, navigation",
  URL =        "https://www.cg.tuwien.ac.at/research/publications/2021/kouril-2021-phdthesis/",
}