@article{Alharbi_2021, title = "Nanotilus: Generator of Immersive Guided-Tours in Crowded 3D Environments", author = "Ruwayda Alharbi and Ondrej Strnad and Laura R. Luidolt and Manuela Waldner and David Kou\v{r}il and Ciril Bohak and Tobias Klein and Eduard Gr\"{o}ller and Ivan Viola", year = "2021", abstract = "Immersive virtual reality environments are gaining popularity for studying and exploring crowded three-dimensional structures. When reaching very high structural densities, the natural depiction of the scene produces impenetrable clutter and requires visibility and occlusion management strategies for exploration and orientation. Strategies developed to address the crowdedness in desktop applications, however, inhibit the feeling of immersion. They result in nonimmersive, desktop-style outside-in viewing in virtual reality. This paper proposesNanotilus---a new visibility and guidance approach for very dense environments that generates an endoscopic inside-out experience instead of outside-in viewing, preserving the immersive aspect of virtual reality. The approach consists of two novel, tightly coupled mechanisms that control scene sparsification simultaneously with camera path planning. The sparsification strategy is localized around the camera and is realized as a multiscale, multishell, variety-preserving technique. When Nanotilus dives into the structures to capture internal details residing on multiple scales, it guides the camera using depth-based path planning. In addition to sparsification and path planning, we complete the tour generation with an animation controller, textual annotation, and text-to-visualization conversion. We demonstrate the generated guided tours on mesoscopic biological models -- SARS-CoV-2 and HIV viruses. We evaluate the Nanotilus experience with a baseline outside-in sparsification and navigational technique in a formal user study with 29 participants. While users can maintain a better overview using the outside-in sparsification, the study confirms our hypothesis that Nanotilus leads to stronger engagement and immersion.", month = dec, doi = "10.1109/TVCG.2021.3133592", journal = "IEEE Transactions on Visualization and Computer Graphics", pages = "1--16", URL = "https://www.cg.tuwien.ac.at/research/publications/2021/Alharbi_2021/", } @article{wu-2021-vi, title = "Visualization working group at TU Wien: Visibile Facimus Quod Ceteri Non Possunt", author = "Hsiang-Yun Wu and Aleksandr Amirkhanov and Nicolas Grossmann and Tobias Klein and David Kou\v{r}il and Haichao Miao and Laura R. Luidolt and Peter Mindek and Renata Raidou and Ivan Viola and Manuela Waldner and Eduard Gr\"{o}ller", year = "2021", abstract = "Building-up and running a university-based research group is a multi-faceted undertaking. The visualization working group at TU Wien (vis-group) has been internationally active over more than 25 years. The group has been acting in a competitive scientific setting where sometimes contradicting multiple objectives require trade-offs and optimizations. Research-wise the group has been performing basic and applied research in visualization and visual computing. Teaching-wise the group has been involved in undergraduate and graduate lecturing in (medical) visualization and computer graphics. To be scientifically competitive requires to constantly expose the group and its members to a strong international competition at the highest level. This necessitates to shield the members against the ensuing pressures and demands and provide (emotional) support and encouragement. Internally, the vis-group has developed a unique professional and social interaction culture: work and celebrate, hard and together. This has crystallized into a nested, recursive, and triangular organization model, which concretizes what it takes to make a research group successful. The key elements are the creative and competent vis-group members who collaboratively strive for (scientific) excellence in a socially enjoyable environment.", month = mar, doi = "https://doi.org/10.1016/j.visinf.2021.02.003", journal = "Visual Informatics", volume = "5", pages = "76--84", URL = "https://www.cg.tuwien.ac.at/research/publications/2021/wu-2021-vi/", } @article{nguyen_2020-covid, title = "Modeling in the Time of COVID-19: Statistical and Rule-based Mesoscale Models", author = "Ngan Nguyen and Ondrej Strnad and Tobias Klein and Ruwayda Alharbi and Peter Wonka and Martina Maritan and Peter Mindek and Ludovic Autin and David Goodsell and Ivan Viola", year = "2020", abstract = "We present a new technique for rapid modeling and construction of scientifically accurate mesoscale biological models. Resulting 3D models are based on few 2D microscopy scans and the latest knowledge about the biological entity represented as a set of geometric relationships. Our new technique is based on statistical and rule-based modeling approaches that are rapid to author, fast to construct, and easy to revise. From a few 2D microscopy scans, we learn statistical properties of various structural aspects, such as the outer membrane shape, spatial properties and distribution characteristics of the macromolecular elements on the membrane. This information is utilized in 3D model construction. Once all imaging evidence is incorporated in the model, additional information can be incorporated by interactively defining rules that spatially characterize the rest of the biological entity, such as mutual interactions among macromolecules, their distances and orientations to other structures. These rules are defined through an intuitive 3D interactive visualization and modeling feedback loop. We demonstrate the utility of our approach on a use case of the modeling procedure of the SARS-CoV-2 virus particle ultrastructure. Its first complete atomistic model, which we present here, can steer biological research to new promising directions in fighting spread of the virus.", journal = "IEEE Transactions on Visualization and Computer Graphics", URL = "https://www.cg.tuwien.ac.at/research/publications/2020/nguyen_2020-covid/", } @phdthesis{klein_2019_PHD, title = "Instant Construction of Atomistic Models for Visualization in Integrative Cell Biology", author = "Tobias Klein", year = "2019", abstract = "AbstractComputational models have advanced research of integrative cell biology in variousways. Especially in the biological mesoscale, the scale between atoms and cellularenvironments, computational models improve the understanding and qualitative anal-ysis. The mesoscale is an important range, since it represents the range of scalesthat are not fully accessible to a single experimental technique. Complex molecularassemblies within this scale have been visualized with x-ray crystallography, thoughonly in isolation. Mesoscale models shows how molecules are assembled into morecomplex subcelluar environments that orchestrate the processes of life. The skillfulcombination of the results of imaging and experimental techniques provides a glimpseof the processes, which are happening here. Only recently, biologists have startedto unify the various sources of information. They have begun to computationallyassemble and subsequently visualize complex environments, such as viruses or bacteria.Currently, we live in an opportune time for researching integrative structural biologydue to several factors. First and foremost, the wealth of data, driven through sourceslike online databases, makes structural information about biological entities publiclyavailable. In addition to that, the progress of parallel processors builds the foundationto instantly construct and render large mesoscale environments in atomistic detail.Finally, new scientific advances in visualization allow the efficient rendering of complexbiological phenomena with millions of structural units.In this cumulative thesis, we propose several novel techniques that facilitate the instantconstruction of mesoscale structures. The common methodological strategy of thesetechniques and insight from this thesis is “compute instead of store”. This approacheliminates the storage and memory management complexity, and enables instantchanges of the constructed models. Combined, our techniques are capable of instantlyconstructing large-scale biological environments using the basic structural buildingblocks of cells. These building blocks are mainly nucleic acids, lipids, and solubleproteins. For the generation of long linear polymers formed by nucleic acids, wepropose a parallel construction technique that makes use of a midpoint displacementalgorithm. The efficient generation of lipid membranes is realized through a texturesynthesis approach that makes use of the Wang tiling concept. For the population ofsoluble proteins, we present a staged algorithm, whereby each stage is processed inparallel. We have integrated the instant construction approach into a visual environmentin order to improve several aspects. First, it allows immediate feedback on the createdix structures and the results of parameter changes. Additionally, the integration ofconstruction in visualization builds the foundation for visualization systems that striveto construct large-scale environments on-the-fly. Lastly, it advances the qualitativeanalysis of biological mesoscale environments, where a multitude of synthesized modelsis required. In order to disseminate the physiology of biological mesoscale models,we propose a novel concept that simplifies the creation of multi-scale proceduralanimations. ", month = nov, 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 ", URL = "https://www.cg.tuwien.ac.at/research/publications/2019/klein_2019_PHD/", } @article{klein_2019_PGG, title = "Parallel Generation and Visualization of Bacterial Genome Structures", author = "Tobias Klein and Peter Mindek and Ludovic Autin and David Goodsell and Arthur Olson and Eduard Gr\"{o}ller and Ivan Viola", year = "2019", abstract = "Visualization of biological mesoscale models provides a glimpse at the inner workings of living cells. One of the most complex components of these models is DNA, which is of fundamental importance for all forms of life. Modeling the 3D structure of genomes has previously only been attempted by sequential approaches. We present the first parallel approach for the instant construction of DNA structures. Traditionally, such structures are generated with algorithms like random walk, which have inherent sequential constraints. These algorithms result in the desired structure, are easy to control, and simple to formulate. Their execution, however, is very time-consuming, as they are not designed to exploit parallelism. We propose an approach to parallelize the process, facilitating an implementation on the GPU.", month = nov, journal = "Computer Graphics Forum", volume = "38", number = "7", doi = "10.1111/cgf.13816", pages = "57--68", URL = "https://www.cg.tuwien.ac.at/research/publications/2019/klein_2019_PGG/", } @misc{mindek-2019-mci, title = "Microtubule Catastrophe", author = "Peter Mindek and Tobias Klein and Ludovic Autin and Theresia Gschwandtner", year = "2019", abstract = "This is a procedural model of microtubule dynamics. It is rendered in real-time in the Marion molecular visualization framework. The image shows the "catastrophe" event, i.e., a sudden switch between the growth and rapid shortening of a microtubule, a filament which is a part of cytoskeleton. In the background, molecules of proteins cell cytoplasm proteins are visible. ", month = sep, note = "VCBM 2019, Image Contest Jury's Award", keywords = "molecular visualization, microtubules, biology", URL = "https://www.cg.tuwien.ac.at/research/publications/2019/mindek-2019-mci/", } @article{klein_2019_PMP, title = "Multi-Scale Procedural Animations of Microtubule Dynamics Based on Measured Data", author = "Tobias Klein and Ivan Viola and Eduard Gr\"{o}ller and Peter Mindek", year = "2019", abstract = "Biologists often use computer graphics to visualize structures, which due to physical limitations are not possible to imagewith a microscope. One example for such structures are microtubules, which are present in every eukaryotic cell. They are part ofthe cytoskeleton maintaining the shape of the cell and playing a key role in the cell division. In this paper, we propose a scientifically-accurate multi-scale procedural model of microtubule dynamics as a novel application scenario for procedural animation, which cangenerate visualizations of their overall shape, molecular structure, as well as animations of the dynamic behaviour of their growth anddisassembly. The model is spanning from tens of micrometers down to atomic resolution. All the aspects of the model are driven byscientific data. The advantage over a traditional, manual animation approach is that when the underlying data change, for instance dueto new evidence, the model can be recreated immediately. The procedural animation concept is presented in its generic form, withseveral novel extensions, facilitating an easy translation to other domains with emergent multi-scale behavior.", month = aug, journal = "IEEE Transactions on Visualization and Computer Graphics", volume = "26", number = "1", doi = "10.1109/TVCG.2019.2934612", pages = "622--632", URL = "https://www.cg.tuwien.ac.at/research/publications/2019/klein_2019_PMP/", } @article{Miao_2019, title = "Multiscale Molecular Visualization", author = "Haichao Miao and Tobias Klein and David Kou\v{r}il and Peter Mindek and Karsten Schatz and Eduard Gr\"{o}ller and Barbora Kozlikova and Tobias Isenberg and Ivan Viola", year = "2019", abstract = "We provide a high-level survey of multiscale molecular visualization techniques, with a focus on application-domain questions, challenges, and tasks. We provide a general introduction to molecular visualization basicsand describe a number of domain-specific tasks that drive this work. These tasks, in turn, serve as the generalstructure of the following survey. First, we discuss methods that support the visual analysis of moleculardynamics simulations. We discuss, in particular, visual abstraction and temporal aggregation. In the secondpart, we survey multiscale approaches that support the design, analysis, and manipulation of DNAnanostructures and related concepts for abstraction, scale transition, scale-dependent modeling, andnavigation of the resulting abstraction spaces. In the third part of the survey, we showcase approaches thatsupport interactive exploration within large structural biology assemblies up to the size of bacterial cells.We describe fundamental rendering techniques as well as approaches for element instantiation, visibilitymanagement, visual guidance, camera control, and support of depth perception. We close the survey with abrief listing of important tools that implement many of the discussed approaches and a conclusion thatprovides some research challenges in the field.", month = jan, doi = "10.1016/j.jmb.2018.09.004.", journal = "Journal of Molecular Biology", number = "31", volume = "6", pages = "1049--1070", keywords = "molecular visualization, molecular dynamics, modelitics, DNA nanotechnology, visual abstraction", URL = "https://www.cg.tuwien.ac.at/research/publications/2019/Miao_2019/", } @misc{klein_2019_MSA_Poster, title = "A Multi-Scale Animation Framework for Biological Fibrous Structures", author = "Tobias Klein and Ivan Viola and Peter Mindek", year = "2019", abstract = "Fibrous structures are ubiquitous in cell biology and play essential structural and functional roles in the life cycle of a cell. They are long polymers, such as DNA carrying genetic information, or filaments forming the cytoskeleton, crucial for cell division and maintaining the cell shape. In order to disseminate new findings of such structures to peers or a general audience, animated 3D models of these structures have to be created, as they are too small to be imaged with microscopes. However, this is a tedious task carried out by scientific animators, who manually create expressive visual representations of biological phenomena. In this work, we present a novel concept which simplifies the process of animating multi-scale procedural models of biological fibrous structures. In contrast with existing work in the domain of molecular visualization, our approach can also capture dynamics, which are important to show when communicating biological processes.", event = "EuroVis 2019", doi = "https://doi.org/10.2312/eurp.20191149", Conference date = "Poster presented at EuroVis 2019 ()", URL = "https://www.cg.tuwien.ac.at/research/publications/2019/klein_2019_MSA_Poster/", } @article{koch_bernhard_2018-1, title = "Semantic Screen-Space Occlusion for Multiscale Molecular Visualization", author = "Thomas Bernhard Koch and David Kou\v{r}il and Tobias Klein and Peter Mindek and Ivan Viola", year = "2018", abstract = "Visual clutter is a major problem in large biological data visualization. It is often addressed through the means of level of detail schemes coupled with an appropriate coloring of the visualized structures. Ambient occlusion and shadows are often used to improve the depth perception. However, when used excessively, these techniques are sources of visual clutter themselves. In this paper we present a new approach to screen-space illumination algorithms suitable for use in illustrative visualization. The illumination effect can be controlled so that desired levels of semantic scene organization cast shadows while other remain flat. This way the illumination design can be parameterized to keep visual clutter, originating from illumination, to a minimum, while also guiding the user in a multiscale model exploration. We achieve this by selectively applying occlusion shading based on the inherent semantics of the visualized hierarchically-organized data. The technique is in principle generally applicable to any hierarchically organized 3D scene and has been demonstrated on an exemplary scene from integrative structural biology. ", month = sep, journal = "Eurographics Workshop on Visual Computing for Biology and Medicine", URL = "https://www.cg.tuwien.ac.at/research/publications/2018/koch_bernhard_2018-1/", } @article{klein_2017_IM, title = "Instant Construction and Visualization of Crowded Biological Environments", author = "Tobias Klein and Ludovic Autin and Barbora Kozlikova and David Goodsell and Arthur Olson and Eduard Gr\"{o}ller and Ivan Viola", year = "2018", abstract = "We present the first approach to integrative structural modeling of the biological mesoscale within an interactive visual environment. These complex models can comprise up to millions of molecules with defined atomic structures, locations, and interactions. Their construction has previously been attempted only within a non-visual and non-interactive environment. Our solution unites the modeling and visualization aspect, enabling interactive construction of atomic resolution mesoscale models of large portions of a cell. We present a novel set of GPU algorithms that build the basis for the rapid construction of complex biological structures. These structures consist of multiple membrane-enclosed compartments including both soluble molecules and fibrous structures. The compartments are defined using volume voxelization of triangulated meshes. For membranes, we present an extension of the Wang Tile concept that populates the bilayer with individual lipids. Soluble molecules are populated within compartments using the Halton sequence for their distribution. Fibrous structures, such as RNA or actin filaments, are created by self-avoiding random walks. Resulting overlaps of molecules are resolved by a forced-based system. Our approach opens new possibilities to the world of interactive construction of cellular compartments. We demonstrate its effectiveness by showcasing scenes of different scale and complexity that comprise blood plasma, mycoplasma, and HIV.", journal = "IEEE Transactions on Visualization and Computer Graphics", doi = "10.1109/TVCG.2017.2744258", URL = "https://www.cg.tuwien.ac.at/research/publications/2018/klein_2017_IM/", } @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/", } @inproceedings{sorger-2016-fowardabstraction, title = "Illustrative Transitions in Molecular Visualization via Forward and Inverse Abstraction Transform", author = "Johannes Sorger and Peter Mindek and Tobias Klein and Graham Johnson and Ivan Viola", year = "2016", abstract = "A challenging problem in biology is the incompleteness of acquired information when visualizing biological phenomena. Structural biology generates detailed models of viruses or bacteria at different development stages, while the processes that relate one stage to another are often not clear. Similarly, the entire life cycle of a biological entity might be available as a quantitative model, while only one structural model is available. If the relation between two models is specified at a lower level of detail than the actual models themselves, the two models cannot be interpolated correctly. We propose a method that deals with the visualization of incomplete data information in the developmental or evolutionary states of biological mesoscale models, such as viruses or microorganisms. The central tool in our approach is visual abstraction. Instead of directly interpolating between two models that show different states of an organism, we gradually forward transform the models into a level of visual abstraction that matches the level of detail of the modeled relation between them. At this level, the models can be interpolated without conveying false information. After the interpolation to the new state, we apply the inverse transformation to the model’'s original level of abstraction. To show the flexibility of our approach, we demonstrate our method on the basis of molecular data, in particular data of the HIV virion and the mycoplasma bacterium.", month = sep, organization = "Eurographics", location = "Bergen", editor = "S. Bruckner, B. Preim, and A. Vilanova", booktitle = "Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM)", pages = "21--30", keywords = "I.3.3 [Computer Graphics]: Picture/Image Generation-Display algorithms", URL = "https://www.cg.tuwien.ac.at/research/publications/2016/sorger-2016-fowardabstraction/", } @misc{klein-2016-WCL, title = "Towards Interactive Visual Exploration of Parallel Programs using a Domain-Specific Language", author = "Tobias Klein and Stefan Bruckner and Eduard Gr\"{o}ller and Markus Hadwiger and Peter Rautek", year = "2016", abstract = "The use of GPUs and the massively parallel computing paradigm have become wide-spread. We describe a framework for the interactive visualization and visual analysis of the run-time behavior of massively parallel programs, especially OpenCL kernels. This facilitates understanding a program's function and structure, finding the causes of possible slowdowns, locating program bugs, and interactively exploring and visually comparing different code variants in order to improve performance and correctness. Our approach enables very specific, user-centered analysis, both in terms of the recording of the run-time behavior and the visualization itself. Instead of having to manually write instrumented code to record data, simple code annotations tell the source-to-source compiler which code instrumentation to generate automatically. The visualization part of our framework then enables the interactive analysis of kernel run-time behavior in a way that can be very specific to a particular problem or optimization goal, such as analyzing the causes of memory bank conflicts or understanding an entire parallel algorithm.", month = apr, publisher = "ACM", location = "Vienna, Austria", event = "4th International Workshop on OpenCL (IWOCL '16)", Conference date = "Poster presented at 4th International Workshop on OpenCL (IWOCL '16) ()", URL = "https://www.cg.tuwien.ac.at/research/publications/2016/klein-2016-WCL/", } @mastersthesis{Klein_Tobias_2015TIV, title = "Towards Interactive Visual Exploration of Parallel Programs using a Domain-specific Language", author = "Tobias Klein", year = "2015", abstract = "The utilization of GPUs and the massively parallel computing paradigm have become increasingly prominent in many research domains. Recent developments of platforms, such as OpenCL and CUDA, enable the usage of heterogeneous parallel computing in a wide-spread field. However, the efficient utilization of parallel hardware requires profound knowledge of parallel programming and the hardware itself. Our approach presents a domain-specific language that facilitates fast prototyping of parallel programs, and a visual explorer which reveals their execution behavior. With the aid of our visualizations, interactions with the hardware become visible, supporting the comprehensibility of the program and its utilization of the hardware components. Furthermore, we aggregate behavior that leads to common issues in parallel programming and present it in a clearly structured view to the user. We augment the standard methods for debugging and profiling by a visual approach that enables a more problem-specific, fine-grained way of analyzing parallel code. Our framework parses all program code and user-specified annotations in order to enable automatic, yet configurable code instrumentation. The resulting recordings are directly linked to interactive visualizations created with the well-known D3 (data-driven documents) framework. To demonstrate our approach, we present two case studies about the visual analysis of memory bank conflicts and branch divergence. They investigate different parallel reduction implementations and a common image processing example (all from the NVIDIA OpenCL SDK). We show that our visualizations provide immediate visual insight in the execution behavior of the program and that the performance influence of the implementations is directly reflected visually.", month = nov, 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/2015/Klein_Tobias_2015TIV/", } @article{wu-2021, title = "Visualization working group at TU Wien: Visible Facimus Quod Ceteri Non Possunt", author = "Hsiang-Yun Wu and Aleksandr Amirkhanov and Nicolas Grossmann and Tobias Klein and David Kou\v{r}il and Haichao Miao and Laura R. Luidolt and Peter Mindek and Renata Raidou and Ivan Viola and Manuela Waldner and Eduard Gr\"{o}ller", abstract = "Building-up and running a university-based research group is a multi-faceted undertaking. The visualization working group at TU Wien (vis-group) has been internationally active over more than 25 years. The group has been acting in a competitive scientific setting where sometimes contradicting multiple objectives require trade-offs and optimizations. Research-wise the group has been performing basic and applied research in visualization and visual computing. Teaching-wise the group has been involved in undergraduate and graduate lecturing in (medical) visualization and computer graphics. To be scientifically competitive requires to constantly expose the group and its members to a strong international competition at the highest level. This necessitates to shield the members against the ensuing pressures and demands and provide (emotional) support and encouragement. Internally, the vis-group has developed a unique professional and social interaction culture: work and celebrate, hard and together. This has crystallized into a nested, recursive, and triangular organization model, which concretizes what it takes to make a research group successful. The key elements are the creative and competent vis-group members who collaboratively strive for (scientific) excellence in a socially enjoyable environment.", doi = "https://doi.org/10.1016/j.visinf.2021.02.003", journal = "Visual Informatics", volume = "5", pages = "76--84", URL = "https://www.cg.tuwien.ac.at/research/publications/ongoing/wu-2021/", }