The focus of the project is is to develop 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 will be developed and evaluated on multiple scale levels, from molecular machines, up to the organ level.
Our Resilient Genome
Our Resilient Genome is a short science animation by filmmaker Pina Kingman. It was developed as part of the PhysioIllustration Project with the Visualization Group, Department of Informatics at the University of Bergen. The aim of this project is to research novel visual communication techniques and advance knowledge translation methods, specifically in the field of molecular and cellular biology. This research culminated in the creation of a short film describing DNA Repair and is intended for the general public. In addition to showcasing our novel visual communication methods, the film also highlights research undertaken by the Department of Molecular Biology, UiB. The film tells the story of our DNA, how it is constantly breaking and rebuilding over and over again to keep us alive, and provides a glimpse into the fascinating world of cellular biology.
St. Tropez International Film Festival in Nice, France
The Nice in South of France International Film and Television Festival of World Cinema held in the South of France at the same time as the World famous Cannes film festival, in its 4th year is a global industry event that will reach out to the many filmmakers who always place film at the centre of our acts as a truly international film industry event, being held a week before the Cannes International film festival so filmmakers can be in the south of France for both events bringing together films from around the world.
We have built a small but exceptional professional network of industry professional that will look at all films entered and will give business and commercial advice, in some cases the distributors attending will make offers to the filmmakers for their work and to work together to put your movies in the market place, we have the people and skills in our professional team to make this happen, if the professional attending feel there is a market for your movie, they will as with many films over the years of our other festival make it happen. We are unique in the amount of platforms and festival we offer filmmakers, we can create a ripple for your movie to be seen around the world, it all starts here by entering your movie.
Generally, to take nothing into account other than the art of film and the pre-eminence of artistic talent, and finally to facilitate transmission, so that tomorrow’s Festival can continue the adventure with the combined strengths of experience and modernity, for those that enter the Festival will truly be the future filmmakers of the film industry.
Acknowledgements
Funding and Support for this project comes from NFR (project #218023), The Bergen University Fund (Universitetsfondet), and BEK/ Bergen senter for elektronisk kunst http://www.bek.no.
Related links
- http://filmfestinternational.com/nice-iff-2015-filmmaker-award-winners/
- http://www.rivieratimes.com/index.php/provence-cote-dazur-article/items/st-tropez-and-nice-film-festival-in-full-swing.html
- http://niceinternationalfilmfestival.com/
- http://www.imdb.com/title/tt4328486/
- https://vimeo.com/124913016
Interactive molecular illustration
Physiological processes are of the temporal and spatial multi-scale and ranges from molecular level to the whole organism. Many of the processes have their begining in the molecular scale. Important processes such as polymerization, diffusion, reactions are all happening in the crowded environment full of different molecules. Also those processes have vast temporal range from nanoseconds (diffusion) to seconds (polymerization). Our first focus is therefore on the illustrative visualization of physiological processes in the molecular scale to provide intuitive visual representation, which the user can observe and interact with.
Illustrating Polymerization using Three-level Model Fusion
Feel free to download the unity prototype of our current research project here: UnityProject. It contains Unity project, which can be opened by the Unity Editor. In the prototype project hierarchy there are models and materials used to create scenes and simulation, 7 scenes which covers the demonstration bundle of project and the scripts.
The demonstration bundle consist of 7 unity scenes. Three of the scenes: parp, cellulose and tubulin, are biological examples of our prototype described in the paper. For additional demonstration of approach there are examples: starpolymer, copolymer and showcase. StarPolymer scene demonstrates the creation of star polymer with our approach, copolymer on the other hand presents the creation of block linear copolymer. Showcase demonstration is described in more detail in the paper. The last scene demonstrates more advanced visualization of our system mentioned in the Discussion section of the paper.
Every scene have predefined GameObjects for important parts pf the system: LSystem and Agent system (see Fig. 1). Those objects contains their respective scripts, which handles the initialization and update of systems. For managing and setting the parameters of those system, there is provided Editor custom GUI in the Inspector panel.
LSystem GUI is divided to three parts. First is the part managing the alphabet of the L-System. Here are specified symbols, which are later used to define the rules and the axiom. The description and semantic meaning of those rules are detaily described in the paper. Second part manages the axiom, which is the starting point of the process. The axiom can only be a communication symbol, which tells by which subprocess it should start. Last section manages the rules. User can change/remove the existing rules or add the new ones.
Agent system is steered by the system of densities, which is another modeling layer described in more detail in System of Densities subsection in the paper. In thiswindow user can add or remove the type of molecule which is in environment. Every molecule has its own image preview and the density can be adjusted.
Simulation have two global parameters: time delta of the simulation, and the number of monomers of the resulting polymer. This variables are accesible from the editor window, which can be opened from LSystem or Agent system inspector.
Comparative VIsualization of Spatial Ensemble Data
Nowadays, generation and study of spatial ensemble data is becoming more and more important for the research in the central scientific fields, such as medicine, biology, physics. A comparative visualization is highly suitable for the exploration of the ensemble members, especially if the spatial aspect is of upmost importance. The usefullness of the comparative visualization highly depends on the number of compared members, and on the visibility of the important characteristics of the members.
A Fractional Cartesian Composition Model for Semi-spatial Comparative Visualization Design
Feel free to download the unity project: Prototype, which contains a prototype implementation of our model. The project can be opened by the Unity Editor. In the prototype project hierarchy there are ensmeble input data (stored in xml format), 3 scenes which covers the demonstration of project and the scripts.
Three scenes (ivy, parp, city) covers the demonstration of the model described in the paper (Wall-covering Ivy, PARP polymerization, Parametrized Cities). Every scene have predefined GameObject (*manager) for accessing user interface of the model (for ivy example see Fig. 1).
The first step of the interaction with the model is to load an ensemble (Fig. 1a)—then the characteristics for the example are shown (Fig. 1b). Here, the user adjusts the importance of the characteristics for the optimization. After pressing “Build Samples” (Fig. 1c), our prototype picks ensemble members (randomly), applies the available abstractions and computes the selected characteristics in order to approximate the cost function for the optimization. For all the examples in this paper, we used an empirically-determined sample size of 10 ensemble members. Clearly, this is only a prototype implementation of the otherwise more general framework and ample opportunities for optimization are given here.
After the initial setup, the user interacts with the model parameters, characteristics, and axes (see Fig. 1d, b, e, respectively). After each parameter change, a preview of how the ensemble members will be positioned and how much visual space is available for each member is shown. If the user is satisfied, he/she can then create the final visualization (Fig. 1g).
Publications
2017
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[Bibtex] @ARTICLE {Kolesar-2017-FCC,
author = "Ivan Kolesar and Stefan Bruckner and Ivan Viola and Helwig Hauser",
title = "A Fractional Cartesian Composition Model for Semi-spatial Comparative Visualization Design",
journal = "IEEE Transactions on Visualization and Computer Graphics",
year = "2017",
volume = "23",
number = "1",
pages = "851--860",
month = "jan",
abstract = "The study of spatial data ensembles leads to substantial visualization challenges in a variety of applications. In this paper, we present a model for comparative visualization that supports the design of according ensemble visualization solutions by partial automation. We focus on applications, where the user is interested in preserving selected spatial data characteristics of the data as much as possibleâeven when many ensemble members should be jointly studied using comparative visualization. In our model, we separate the design challenge into a minimal set of user-specified parameters and an optimization component for the automatic configuration of the remaining design variables. We provide an illustrated formal description of our model and exemplify our approach in the context of several application examples from different domains in order to demonstrate its generality within the class of comparative visualization problems for spatial data ensembles.",
pdf = "pdfs/Kolesar-2017-FCC.pdf",
images = "images/Kolesar-2017-FCC.jpg",
thumbnails = "images/Kolesar-2017-FCC.png",
youtube = "https://www.youtube.com/watch?v=_zk67fmryok",
doi = "10.1109/TVCG.2016.2598870",
event = "IEEE SciVis 2016",
keywords = "visualization models, integrating spatial and non-spatial data visualization, design methodologies",
location = "Baltimore, USA",
project = "physioillustration"
}2016
[Bibtex] @ARTICLE {Michael2016Visual,
author = "Michael Krone and Barbora Kozlikova and Norbert Lindow and Marc Baaden and Daniel Baum, and Julius Parulek and Hans-Christian Hege and Ivan Viola",
title = "Visual Analysis of Biomolecular Cavities: State of the Art",
journal = "Computer Graphics Forum",
year = "2016",
abstract = "In this report we review and structure the branch of molecular visualization that is concerned with the visual analysis of cavities in macromolecular protein structures. First the necessary background, the domain terminology, and the goals of analytical reasoning are introduced. Based on a comprehensive collection of relevant research works, we present a novel classification for cavity detection approaches and structure them into four distinct classes: grid-based, Voronoi-based, surface-based, and probe-based methods. The subclasses are then formed by their combinations. We match these approaches with corresponding visualization technologies starting with direct 3D visualization, followed with non-spatial visualization techniques that for example abstract the interactions between structures into a relational graph, straighten the cavity of interest to see its profile in one view, or aggregate the time sequence into a single contour plot. We also discuss the current state of methods for the visual analysis of cavities in dynamic data such as molecular dynamics simulations. Finally, we give an overview of the most common tools that are actively developed and used in the structural biology and biochemistry research. Our report is concluded by an outlook on future challenges in the field.",
images = "images/STARcavities2016.png",
thumbnails = "images/STARcavities2016.png",
publisher = "The Eurographics Association and John Wiley \& Sons Ltd.",
issn = "1467-8659",
doi = "10.1111/cgf.12928",
project = "physioillustration"
}@INPROCEEDINGS {Kolesar2016VCBM,
author = "Ivan Kolesar and Jan By\v{s}ka and Julius Parulek and Helwig Hauser and Barbora Kozl\'{i}kov\'{a}",
title = "Unfolding and Interactive Exploration of Protein Tunnels andtheir Dynamics",
booktitle = "Eurographics Workshop on Visual Computing for Biology and Medicine",
year = "2016",
pages = "1--10",
month = "sep",
abstract = "The presence of tunnels in protein structures substantially influences their reactivity with other molecules. Therefore, studying their properties and changes over time has been in the scope of biochemists for decades. In this paper we introduce a novel approach for comparative visualization and exploration of ensembles of tunnels. Our goal is to overcome occlusion problems present in traditional tunnel representations while providing users a quick way to navigate through the input dataset to identify potentially interesting tunnels. First, we unfold the input tunnels to a 2D representation enabling to observe the mutual position of amino acids forming the tunnel surface and the amount of surface they influence. These 2D images are subsequently described by image moments commonly used in image processing. This way we are able to detect similarities and outliers in the dataset, which are visualized as clusters in a scatterplot graph. The same coloring scheme is used in the linked bar chart enabling to detect the position of the cluster members over time. These views provide a way to select a subset of potentially interesting tunnels that can be further explored in detail using the 2D unfolded view and also traditional 3D representation. The usability of our approach is demonstrated on case studies conducted by the domain experts.",
images = "images/Kolesar-2016-VCBM.png",
thumbnails = "images/Kolesar-2016-VCBM-thumbnail.jpg",
proceedings = "Proceedings of Eurographics Workshop on Visual Computing in Biology and Medicine",
keywords = "unfolding, storytelling, game visualization",
location = "Bergen, Norway",
project = "physioillustration"
}2015
[Bibtex] @INPROCEEDINGS {eurovisstar20151112,
author = "Kozlikova, Barbora and Krone, Michael and Lindow, Norbert and Falk, Martin and Baaden, Marc and Baum, Daniel and Viola, Ivan and Parulek, Julius and Hege, Hans-Christian",
title = "Visualization of Biomolecular Structures: State of the Art",
booktitle = "Eurographics Conference on Visualization (EuroVis) - STARs",
year = "2015",
editor = "R. Borgo and F. Ganovelli and I. Viola",
volume = "-",
publisher = "The Eurographics Association",
abstract = "Structural properties of molecules are of primary concern in many fields. This report provides a comprehensiveoverview on techniques that have been developed in the fields of molecular graphics and visualization with a focuson applications in structural biology. The field heavily relies on computerized geometric and visual representationsof three-dimensional, complex, large, and time-varying molecular structures. The report presents a taxonomy thatdemonstrates which areas of molecular visualization have already been extensively investigated and where the fieldis currently heading. It discusses visualizations for molecular structures, strategies for efficient display regardingimage quality and frame rate, covers different aspects of level of detail, and reviews visualizations illustrating thedynamic aspects of molecular simulation data. The report concludes with an outlook on promising and importantresearch topics to enable further success in advancing the knowledge about interaction of molecular structures.",
images = "images/molvis_star.png",
thumbnails = "images/molvis_star.png",
proceedings = "Eurographics Conference on Visualization (EuroVis) - STARs",
doi = "10.2312/eurovisstar.20151112",
journal = "-",
number = "-",
keywords = "-",
project = "physioillustration"
}@INPROCEEDINGS {cellVIEW_2015,
author = "Mathieu Le Muzic and Ludovic Autin and Julius Parulek and Ivan Viola",
title = "cellVIEW: a Tool for Illustrative and Multi-Scale Rendering of Large Biomolecular Datasets",
booktitle = "EG Workshop on Visual Computing for Biology and Medicine",
year = "2015",
month = "sep",
abstract = "In this article we introduce cellVIEW, a new system to interactively visualize large biomolecular datasets on the atomic level. Our tool is unique and has been specifically designed to match the ambitions of our domain experts to model and interactively visualize structures comprised of several billions atom. The cellVIEW system integrates acceleration techniques to allow for real-time graphics performance of 60 Hz display rate on datasets representing large viruses and bacterial organisms. Inspired by the work of scientific illustrators, we propose a level-of-detail scheme which purpose is two-fold: accelerating the rendering and reducing visual clutter. The main part of our datasets is made out of macromolecules, but it also comprises nucleic acids strands which are stored as sets of control points. For that specific case, we extend our rendering method to support the dynamic generation of DNA strands directly on the GPU. It is noteworthy that our tool has been directly implemented inside a game engine. We chose to rely on a third party engine to reduce software development work-load and to make bleeding-edge graphics techniques more accessible to the end-users. To our knowledge cellVIEW is the only suitable solution for interactive visualization of large bimolecular landscapes on the atomic level and is freely available to use and extend.",
images = "images/cellview2015.png",
thumbnails = "images/cellview2015.png",
proceedings = "Proceedings of Eurographics Workshop on Visual Computing in Biology and Medicine",
project = "physioillustration"
}@INPROCEEDINGS {7156384,
author = "Le Muzic, Mathieu and Waldner, Manuela and Parulek, Julius and Viola, Ivan",
title = "Illustrative Timelapse: A technique for illustrative visualization of particle-based simulations",
booktitle = "Visualization Symposium (PacificVis), 2015 IEEE Pacific",
year = "2015",
pages = "247-254",
month = "April",
abstract = "Animated movies are a popular way to communicate complex phenomena in cell biology to the broadaudience. Animation artists apply sophisticated illustration techniques to communicate a story, while trying to maintain a realistic representation of a complex dynamic environment. Since suchhand-crafted animations are time-consuming and cost-intensive to create, our goal is to formalizeillustration techniques used by artists to facilitate the automatic creation of visualizations generated from mesoscale particle-based molecular simulations. Our technique Illustrative Timelapse supports visual exploration of complex biochemical processes in dynamic environments by(1) seamless temporal zooming to observe phenomena in different temporal resolutions, (2) visualabstraction of molecular trajectories to ensure that observers are able to visually follow themain actors, (3) increased visual focus on events of interest, and (4) lens effects to preserve arealistic representation of the environment in the context. Results from a first user studyindicate that visual abstraction of trajectories improves the ability to follow a story and isalso appreciated by users. Lens effects increased the perceived amount of molecular motion in theenvironment while trading off traceability of individual molecules.",
images = "images/illustrative_timelapse.png",
thumbnails = "images/illustrative_timelapse.png",
proceedings = "Proceedings of IEEE Pacific Visualization",
keywords = "Biological system modeling;Data models;Data visualization;Lenses;Trajectory;Videos;Visualization;I.3.7[COMPUTER GRAPHICS]: Three-Dimensional Graphics and Realismââ¬âAnimation;I.6.3 [SIMULATION AND MODELING]: Applicationsââ¬â",
doi = "10.1109/PACIFICVIS.2015.7156384",
project = "physioillustration"
}2014
@MISC {Kingman14GenomeMaking,
author = "Pina Kingman",
title = "Our Resilient Genome: The Making of a Science Film",
howpublished = "Presentation in the EG VCBM workshop 2014",
month = "September",
year = "2014",
abstract = "Every single human cell has to fix 10,000 to 20,000 lesions in its DNA every day. Our cells are constantly exposed to many different types of threats that damage our genome. These lesions could cause mutations in our DNA, potentially leading to cancer and other diseases. With such continuous onslaught, how can our cells possibly protect our DNA from damage and mutations? This presentation will showcase the first public screening of a short film about DNA repair, which blends computer graphics and biology to communicate exciting up-and-coming research. This film was developed in conjunction with the Department of Informatics and the Department of Molecular Biology at the University of Bergen, and the Institute of Computer Graphics and Algorithms at the Vienna University of Technology. Along with a discussion on the visualisation process, I will also talk about the intersection between film and science that helps us communicate complex information.",
images = "images/no_thumb.png",
thumbnails = "images/no_thumb.png",
location = "Wien, Austria",
project = "physioillustration"
}@MISC {LeMusic14Temporal,
author = "Mathieu Le Muzic and Julius Parulek and Manuela Waldner and Ivan Viola",
title = "Illustrative Visualization of Biochemical Processes Featuring Multiple Temporal Scales",
howpublished = "Poster presented at the EG VCBM workshop 2014",
month = "September",
year = "2014",
pdf = "pdfs/LeMusic14Temporal.pdf",
images = "images/LeMuzic14Temporal.png",
thumbnails = "images/LeMuzic14Temporal_thumb.png",
location = "Wien, Austria",
project = "physioillustration"
}![[VID]](https://vis.uib.no/wp-content/papercite-data/images/video.png)