PhysioIllustration

Long ago, Leonardo da Vinci enabled major advances in the understanding of human physiology. He excelled as an artist, as an illustrator, and as a scientist. For the PhysioIllustration project at the University of Bergen it was an important assumption that integrating state-of-the-art knowledge about physiology with advanced forms of dissemination can lead to valuable contributions to our knowledge-based society. Previous success stories in illustrative visualization, which demonstrate that the visualization of complex structures can be supported by interactive solutions, motivated us, additionally. Leonardo da Vinci was able to integrate the roles of a scientist, an artist and an illustrator in one person. Today, the substantially advanced state of the art in science and in professional illustration makes it necessary to rely on the fruitful collaboration of different disciplines. Accordingly, the PhysioIllustration project was worked out by an interdisciplinary team of researchers, combining three complementary fields: bioinformatics, scientific illustration, and visualization research. In an early stage, PhysioIllustration made important steps in the illustrative visualization of molecular structures. Then, we concentrated on the physiological process of DNA repair. Regularly, our DNA gets damaged by certain influences, for example, UV radiation. Fortunately, a sophisticated repair mechanism is in place to detect and undo the damage. We researched the design, modelling, and rendering of a scientific animation that is illustrating this process, winning the first place award for the best science and education film at the international film festival 2015 in Nice, France! The short film is available from the project web page. Based on this physiological scenario, we then investigated how current visualization technology can be advanced so that it becomes possible to computationally and visually represent such processes in a comprehensive manner. We developed several acceleration techniques, embedded in a new research software called cellVIEW and we can now render molecular scenes with billions of atoms at an interactive update rate. We researched new methods under the title ?Illustrative Timelapse?, integrating seamless temporal zooming, the visual abstraction of molecular trajectories, and a particular lensing solution in order to jointly visualize the Brownian motion of molecules together with biochemical reaction events. We also engaged in an in-depth study of a general model for the comparative visualization of multiple items within an entire data ensemble, representing a particular physiological phenomenon of interest. We studied how semi-spatial abstraction can be integrated with an automatic optimization process, where a comparative visualization design is computed that best possibly fits to the requirements of the users in terms of her or his interest. This work was presented in Baltimore, USA, at the best-possible visualization conference (IEEE VIS 2016). Following, our research addressed the interactive visualization of physiological processes involving molecular dynamics. Ligands, binding to large-scale proteins, need to access the binding site, which often is ?hidden? within the much bigger protein molecule. Molecular dynamics simulation, leading to large datasets with very many time steps provide challenging data scenarios for interactive visualization. In our project, we worked on solutions, which enable the study of such processes, for example, through comparative visualization techniques, partial spatial abstraction, and the acceleration of visualization techniques, resulting in several related publications. Our work on the comparative visualization of secondary structures, also, was not only presented at the BioVis symposium 2016 in Baltimore, USA, but also won the best paper award at this highly respected event! The PhysioIllustration research has led to many internationally recognized publications, including several high-quality papers in level-2 journals, as well as to many talks and poster presentations (in Norway, but also in the US, UK, Korea, Germany, Austria, Czech Republic, Slovakia, and The Netherlands). The project researchers have (co-)organized two workshops (VisBio 2013 in Bergen, Norway, and VisBio 2014 in Vienna, Austria) and participated in a popular science event (Forskningsdagene 2014). We also organized the joint VCBM and MedViz conference 2016 in Bergen, Norway, with more than 100 participants. Winning the first place award for the best science and education film in an international film festival is also considered a strong acknowledgement of our PhysioIllustration research as well as the success with the best paper award at the BioVis 2016 symposium in the US. Furthermore, we are also implementing our ideas in the framework of research prototype software, which we make available through our web page.

Physiological processes are of multi-scale and multi-system nature. In general they are very difficult to comprehend. This project proposes an entirely novel research agenda within the data visualization research field to enable understanding, communicati on, and evaluation of physiology through interactive and easy-to-understand visualization. The visualization metaphors investigated in the context of this project are inspired by textbook illustrations and handcrafted animated illustrations. My primary fo cus is on development of novel graphics data representations, visual representations, occlusion handling, visual guidance and storytel-ling, zooming, interaction and integration of physiological models and medical imaging. The visualization technology wil l be developed and evaluated on multiple scale levels, from molecular machines, up to the organ level. The physiological context for the technological development and evaluation will be primarily the muscular system. The outcome of the project is new visu alization technology in form of algorithms, con-cepts, and proof of concept implementations. The utilization of the outcome can lead to advances in the field of physiology by providing intuitive visual representation, which the user can observe and intera ct with.