Professor
Publications
2022
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[Bibtex] @ARTICLE {Garrison2022PhysioSTAR,
author = "Laura A. Garrison and Ivan Kolesar and Ivan Viola and Helwig Hauser and Stefan Bruckner",
title = "Trends & Opportunities in Visualization for Physiology: A Multiscale Overview",
journal = "Computer Graphics Forum",
year = "2022",
volume = "41",
number = "3",
publisher = "The Eurographics Association and John Wiley & Sons Ltd.",
pages = "609-643",
doi = "10.1111/cgf.14575",
abstract = "Combining elements of biology, chemistry, physics, and medicine, the science of human physiology is complex and multifaceted. In this report, we offer a broad and multiscale perspective on key developments and challenges in visualization for physiology. Our literature search process combined standard methods with a state-of-the-art visual analysis search tool to identify surveys and representative individual approaches for physiology. Our resulting taxonomy sorts literature on two levels. The first level categorizes literature according to organizational complexity and ranges from molecule to organ. A second level identifies any of three high-level visualization tasks within a given work: exploration, analysis, and communication. The findings of this report may be used by visualization researchers to understand the overarching trends, challenges, and opportunities in visualization for physiology and to provide a foundation for discussion and future research directions in this area. ",
images = "images/garrison-STAR-taxonomy.png",
thumbnails = "images/garrison-STAR-thumb.png",
pdf = "pdfs/Garrison_STAR_cameraready.pdf",
publisher = "The Eurographics Association and John Wiley \& Sons Ltd.",
project = "VIDI"
}2019
[Bibtex] @inproceedings {Moerth-2019-VCBM,
booktitle = "Eurographics Workshop on Visual Computing for Biology and Medicine",
editor = "KozlÃková, Barbora and Linsen, Lars and Vázquez, Pere-Pau and Lawonn, Kai and Raidou, Renata Georgia",
abstract = "Three-dimensional (3D) ultrasound imaging and visualization
is often used in medical diagnostics, especially in prenatal
screening. Screening the development of the fetus is
important to assess possible complications early on. State
of the art approaches involve taking standardized
measurements to compare them with standardized tables. The
measurements are taken in a 2D slice view, where precise
measurements can be difficult to acquire due to the fetal
pose. Performing the analysis in a 3D view would enable the
viewer to better discriminate between artefacts and
representative information. Additionally making data
comparable between different investigations and patients is
a goal in medical imaging techniques and is often achieved
by standardization. With this paper, we introduce a novel
approach to provide a standardization method for 3D
ultrasound fetus screenings. Our approach is called âThe
Vitruvian Babyâ and incorporates a complete pipeline for
standardized measuring in fetal 3D ultrasound. The input of
the method is a 3D ultrasound screening of a fetus and the
output is the fetus in a standardized T-pose. In this pose,
taking measurements is easier and comparison of different
fetuses is possible. In addition to the transformation of
the 3D ultrasound data, we create an abstract representation
of the fetus based on accurate measurements. We demonstrate
the accuracy of our approach on simulated data where the
ground truth is known.",
title = "The Vitruvian Baby: Interactive Reformation of Fetal Ultrasound Data to a T-Position",
author = "M\"{o}rth, Eric and Raidou, Renata Georgia and Viola, Ivan and Smit, Noeska",
year = "2019",
publisher = "The Eurographics Association",
ISSN = "2070-5786",
ISBN = "978-3-03868-081-9",
DOI = "10.2312/vcbm.20191245",
pdf = "pdfs/VCBM_TheVitruvianBaby_ShortPaper_201-205.pdf",
images = "images/vcbmVitruvianBaby.jpg",
thumbnails = "images/vcbmVitruvianBaby.jpg",
url = "https://diglib.eg.org/handle/10.2312/vcbm20191245",
project = {VIDI}
}@MISC {Moerth-2019-EUROVIS,
booktitle = "EuroVis 2019 - Posters",
editor = "Madeiras Pereira, João and Raidou, Renata Georgia",
title = "The Vitruvian Baby: Interactive Reformation of Fetal Ultrasound Data to a T-Position",
author = "M\"{o}rth, Eric and Raidou, Renata Georgia and Smit, Noeska and Viola, Ivan",
year = "2019",
abstract = "Three dimensional (3D) ultrasound is commonly used in prenatal screening, because it provides insight into the shape as well
as the organs of the fetus. Currently, gynecologists take standardized measurements of the fetus and check for abnormalities by
analyzing the data in a 2D slice view. The fetal pose may complicate taking precise measurements in such a view. Analyzing the
data in a 3D view would enable the viewer to better distinguish between artefacts and representative information. Standardization
in medical imaging techniques aims to make the data comparable between different investigations and patients. It is
already used in different medical applications for example in magnetic resonance imaging (MRI). With this work, we introduce
a novel approach to provide a standardization method for 3D ultrasound screenings of fetuses. The approach consists of six
steps and is called âThe Vitruvian Babyâ. The input is the data of the 3D ultrasound screening of a fetus and the output shows
the fetus in a standardized T-pose in which measurements can be made. The precision of standardized measurements compared
to the gold standard is for the finger to finger span 91,08% and for the head to toe measurement 94,05%.",
publisher = "The Eurographics Association",
howpublished = "Poster presented at the EuroVis conference 2019",
ISBN = "978-3-03868-088-8",
DOI = "10.2312/eurp.20191147",
pdf = "pdfs/EUROVIS_TheVitruvianBaby_Poster.pdf",
images = "images/EUROVISTheVitruvianBabyPoster.png",
thumbnails = "images/EUROVISTheVitruvianBabyPoster.png",
url = "https://diglib.eg.org/handle/10.2312/eurp20191147"
}2018
[Bibtex]
@ARTICLE {Furmanova2018COZOID,
author = "Furmanov{\'a}, Katar{\'\i}na and By{\v{s}}ka, Jan and Gr{\"o}ller, Eduard M and Viola, Ivan and Pale{\v{c}}ek, Jan J and Kozl{\'i}kov{\'a}, Barbora",
title = "COZOID: contact zone identifier for visual analysis of protein-protein interactions",
journal = "BMC bioinformatics",
year = "2018",
abstract = "BackgroundStudying the patterns of protein-protein interactions (PPIs) is fundamental for understanding the structure and function of protein complexes. The exploration of the vast space of possible mutual configurations of interacting proteins and their contact zones is very time consuming and requires the proteomic expert knowledge.ResultsIn this paper, we propose a novel tool containing a set of visual abstraction techniques for the guided exploration of PPI configuration space. It helps proteomic experts to select the most relevant configurations and explore their contact zones at different levels of detail. The system integrates a set of methods that follow and support the workflow of proteomics experts. The first visual abstraction method, the Matrix view, is based on customized interactive heat maps and provides the users with an overview of all possible residue-residue contacts in all PPI configurations and their interactive filtering. In this step, the user can traverse all input PPI configurations and obtain an overview of their interacting amino acids. Then, the models containing a particular pair of interacting amino acids can be selectively picked and traversed. Detailed information on the individual amino acids in the contact zones and their properties is presented in the Contact-Zone list-view. The list-view provides a comparative tool to rank the best models based on the similarity of their contacts to the template-structure contacts. All these techniques are interactively linked with other proposed methods, the Exploded view and the Open-Book view, which represent individual configurations in three-dimensional space. These representations solve the high overlap problem associated with many configurations. Using these views, the structural alignment of the best models can also be visually confirmed.ConclusionsWe developed a system for the exploration of large sets of protein-protein complexes in a fast and intuitive way. The usefulness of our system has been tested and verified on several docking structures covering the three major types of PPIs, including coiled-coil, pocket-string, and surface-surface interactions. Our case studies prove that our tool helps to analyse and filter protein-protein complexes in a fraction of the time compared to using previously available techniques.",
images = "images/cozoid.jpg",
thumbnails = "images/cozoid.jpg"
}2017
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[Bibtex] @ARTICLE {Solteszova-2017-OFS,
author = "Veronika \v{S}olt{\'e}szov{\'a} and {\AA}smund Birkeland and Sergej Stoppel and Ivan Viola and Stefan Bruckner",
title = "Output-Sensitive Filtering of Streaming Volume Data",
journal = "Computer Graphics Forum",
year = "2017",
volume = "36",
number = "1",
pages = "249--262",
month = "jan",
abstract = "Real-time volume data acquisition poses substantial challenges for the traditional visualization pipeline where data enhancement is typically seen as a pre-processing step. In the case of 4D ultrasound data, for instance, costly processing operations to reduce noise and to remove artifacts need to be executed for every frame. To enable the use of high quality filtering operations in such scenarios, we propose an output-sensitive approach to the visualization of streaming volume data. Our method evaluates the potential contribution of all voxels to the final image, allowing us to skip expensive processing operations that have little or no effect on the visualization. As filtering operations modify the data values which may affect the visibility, our main contribution is a fast scheme to predict their maximum effect on the final image. Our approach prioritizes filtering of voxels with high contribution to the final visualization based on a maximal permissible error per pixel. With zero permissible error, the optimized filtering will yield a result identical to filtering of the entire volume. We provide a thorough technical evaluation of the approach and demonstrate it on several typical scenarios that require on-the-fly processing.",
pdf = "pdfs/Solteszova-2017-OFS.pdf",
images = "images/Solteszova-2017-OFS.jpg",
thumbnails = "images/Solteszova-2017-OFS.png",
youtube = "https://www.youtube.com/watch?v=xGPs560ttp0",
doi = "10.1111/cgf.12799",
keywords = "output-sensitive processing, volume data, filtering"
}@INPROCEEDINGS {vad_viktor-2017-WVE,
author = "Viktor Vad and Jan By\v{s}ka and Adam Jur\v{c}\'{i}k and Ivan Viola and Meister Eduard Gr{\"o}ller and Helwig Hauser and Sergio M. Margues and Ji\v{r}\'{i} Damborsk\'{y} and Barbora Kozl\'{i}kov\'{a}",
title = "Watergate: Visual Exploration of Water Trajectories in Protein Dynamics",
booktitle = "Eurographics Workshop on Visual Computing for Biology and Medicine 2017",
year = "2017",
pages = "33--42",
abstract = "The function of proteins is tightly related to their interactions with other molecules. The study of such interactions often requires to track the molecules that enter or exit specific regions of the proteins. This is investigated with molecular dynamics simulations, producing the trajectories of thousands of water molecules during hundreds of thousands of time steps. To ease the exploration of such rich spatio-temporal data, we propose a novel workflow for the analysis and visualization of large sets of water-molecule trajectories. Our solution consists of a set of visualization techniques, which help biochemists to classify, cluster, and filter the trajectories and to explore the properties and behavior of selected subsets in detail. Initially, we use an interactive histogram and a time-line visualization to give an overview of all water trajectories and select the interesting ones for further investigation. Further, we depict clusters of trajectories in a novel 2D representation illustrating the flows of water molecules. These views are interactively linked with a 3D representation where we show individual paths, including their simplification, as well as extracted statistical information displayed by isosurfaces. The proposed solution has been designed in tight collaboration with experts to support specific tasks in their scientific workflows. They also conducted several case studies to evaluate the usability and effectiveness of our new solution with respect to their research scenarios. These confirmed that our proposed solution helps in analyzing water trajectories and in extracting the essential information out of the large amount of input data.",
pdf = "pdfs/Vad_Victor2017.pdf",
images = "images/Watergate.png",
thumbnails = "images/Watergate.png",
proceedings = "In Proceedings of Eurographics Workshop on Visual Computing for Biology and Medicine",
location = "September, 2017 Bremen, Germany",
url = "https://www.cg.tuwien.ac.at/research/publications/2017/vad_viktor-2017-WVE/"
}@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"
}![[VID]](https://vis.uib.no/wp-content/papercite-data/images/video.png)