@talk{Kouril_2017_11, title = "Challenges and advances in multi-scale biology data visualization", author = "David Kou\v{r}il", year = "2017", month = nov, event = "S&T Cooperation Austria-Czech Republic", location = "Czech Technical University", URL = "https://www.cg.tuwien.ac.at/research/publications/2017/Kouril_2017_11/", } @misc{kouril-2017-sccgposter, title = "Maya2cellVIEW: Integrated Tool for Creating Large and Complex Molecular Scenes", author = "David Kou\v{r}il and Mathieu Le Muzic and Barbora Kozlikova and Ivan Viola", year = "2017", month = may, event = "Spring Conference on Computer Graphics 2017", Conference date = "Poster presented at Spring Conference on Computer Graphics 2017 (2017-05)", URL = "https://www.cg.tuwien.ac.at/research/publications/2017/kouril-2017-sccgposter/", } @misc{mindek-2017-virtualcell, title = "The Birth of a Virtual Cell", author = "Peter Mindek and Johannes Sorger and David Kou\v{r}il and Tobias Klein and Graham Johnson and Ivan Viola", year = "2017", abstract = "In our current research project, we are working on the interactive visualization of cellular data at multiple scales. The visual story telling contest motivated us to describe the process of bringing this complex volumetric data "to life". We scripted the visual story directly within the current build of our multi-scale visualization. The entire video is therefore rendered in real time. This enabled us to directly show the steps involved in the rendering of our final visualization based on the actual data and the actual algorithms that are applied. The various effects in the video are therefore parameter variables for existing multi-scale visualization functions that change over time. The final result of our visualization was inspired by a rendering of the reference 3D model that was created by a scientific illustrator. The challenge that we overcome in our visualization was to create a rendering of the original data at stable 30 frames per second that matches the offline rendered illustration in visual quality, which helps to clarify the complex 3D arrangements of the inner components of the cell.", month = apr, note = "submitted to the Pacific Vis 2017 Storytelling Contest", URL = "https://www.cg.tuwien.ac.at/research/publications/2017/mindek-2017-virtualcell/", } @mastersthesis{kouril-2015-maya2cellview, title = "Maya2CellVIEW: 3D Package Integrated Tool for Creating Large and Complex Molecular Scenes", author = "David Kou\v{r}il", year = "2017", abstract = "Scientific illustrators communicate the cutting edge of research through their illustrations. There are numerous software tools that assist them with this job. Often they use professional modeling and animation 3D programs which are primarily used in games and movies industry. Because of that however these tools are not suitable for scientific illustration out of the box. There have been attempts to address this issue which brought tremendous results. This work focuses on visualization of structures and processes in biology, focusing mostly on the scales of nano- to micrometers. At this scale we often do not gain much by using hyper-realistic rendering style that the professional software aims for. Instead we want to employ more simplified style which helps to communicate the important story without losing much detail or scientific precision. The aim of this thesis is to push abilities of illustrators working on large scale molecular scenes. This is done by connecting two software packages—Maya and cellVIEW—combining the real-time rendering possibilities of cellVIEW and modeling and animation tools of Maya which results in more effective and efficient workflow.", month = jan, address = "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria", school = "Institute of Computer Graphics and Algorithms, Vienna University of Technology ", URL = "https://www.cg.tuwien.ac.at/research/publications/2017/kouril-2015-maya2cellview/", } @article{mindek-2017-marion, title = "Visualization Multi-Pipeline for Communicating Biology", author = "Peter Mindek and David Kou\v{r}il and Johannes Sorger and David Toloudis and Blair Lyons and Graham Johnson and Eduard Gr\"{o}ller and Ivan Viola", year = "2017", abstract = "We propose a system to facilitate biology communication by developing a pipeline to support the instructional visualization of heterogeneous biological data on heterogeneous user-devices. Discoveries and concepts in biology are typically summarized with illustrations assembled manually from the interpretation and application of heterogenous data. The creation of such illustrations is time consuming, which makes it incompatible with frequent updates to the measured data as new discoveries are made. Illustrations are typically non-interactive, and when an illustration is updated, it still has to reach the user. Our system is designed to overcome these three obstacles. It supports the integration of heterogeneous datasets, reflecting the knowledge that is gained from different data sources in biology. After pre-processing the datasets, the system transforms them into visual representations as inspired by scientific illustrations. As opposed to traditional scientific illustration these representations are generated in real-time - they are interactive. The code generating the visualizations can be embedded in various software environments. To demonstrate this, we implemented both a desktop application and a remote-rendering server in which the pipeline is embedded. The remote-rendering server supports multi-threaded rendering and it is able to handle multiple users simultaneously. This scalability to different hardware environments, including multi-GPU setups, makes our system useful for efficient public dissemination of biological discoveries. ", journal = "IEEE Transactions on Visualization and Computer Graphics", volume = "24", number = "1", keywords = "Biological visualization, remote rendering, public dissemination", URL = "https://www.cg.tuwien.ac.at/research/publications/2017/mindek-2017-marion/", }