Ivan Kolesar

PhD student

Publications

2022

    [PDF] [DOI] [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"
}

2017

    [Bibtex] 
    @ARTICLE {UiB2017Ivan,
author = "Kolesar, Ivan",
title = "Partial Spatiotemporal Abstraction for Comparative Visualization of Molecular Processes",
journal = "Universitetet i Bergen",
year = "2017"
}
    [PDF] [DOI] [YT] [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 possible—even  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] 
    @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"
}

2014

    [PDF] [VID] [Bibtex] 
    @INPROCEEDINGS {Kolesar-2014-IPT,
author = "Ivan Kolesar and Julius Parulek and Ivan Viola and Stefan Bruckner and Anne-Kristin Stavrum and Helwig Hauser",
title = "Illustrating Polymerization using Three-level Model Fusion",
booktitle = "Proceedings of IEEE BioVis 2014",
year = "2014",
month = "aug",
abstract = "Research in cell biology is steadily contributing new knowledge about  many different aspects of physiological processes like polymerization,  both with respect to the involved molecular structures as well as  their related function. Illustrations of the spatio-temporal development  of such processes are not only used in biomedical education, but  also can serve scientists as an additional platform for in-silico  experiments. In this paper, we contribute a new, three-level modeling  approach to illustrate physiological processes from the class of  polymerization at different time scales. We integrate physical and  empirical modeling, according to which approach suits the different  involved levels of detail best, and we additionally enable a simple  form of interactive steering while the process is illustrated. We  demonstrate the suitability of our approach in the context of several  polymerization processes and report from a first evaluation with  domain experts.",
pdf = "pdfs/Kolesar-2014-IPT.pdf",
vid = "vids/Kolesar14Polymers.mp4",
images = "images/Kolesar-2014-IPT.jpg",
thumbnails = "images/Kolesar-2014-IPT.png",
keywords = "biochemical visualization, L-system modeling, multi-agent modeling, visualization of physiology, polymerization",
owner = "bruckner",
project = "physioillustration",
timestamp = "2014.12.29"
}
    [PDF] [DOI] [YT] [Bibtex] 
    @ARTICLE {Kolesar-2014-IIP,
author = "Ivan Kolesar and Julius Parulek and Ivan Viola and Stefan Bruckner and Anne-Kristin Stavrum and Helwig Hauser",
title = "Interactively Illustrating Polymerization using Three-level Model Fusion",
journal = "BMC Bioinformatics",
year = "2014",
volume = "15",
pages = "345",
month = "oct",
abstract = "Research in cell biology is steadily contributing new knowledge about  many aspects of physiological processes, both with respect to the  involved molecular structures as well as their related function.  Illustrations of the spatio-temporal development of such processes  are not only used in biomedical education, but also can serve scientists  as an additional platform for in-silico experiments. Results In this  paper, we contribute a new, three-level modeling approach to illustrate  physiological processes from the class of polymerization at different  time scales. We integrate physical and empirical modeling, according  to which approach best suits the different involved levels of detail,  and we additionally enable a form of interactive steering, while  the process is illustrated. We demonstrate the suitability of our  approach in the context of several polymerization processes and report  from a first evaluation with domain experts. Conclusion We conclude  that our approach provides a new, hybrid modeling approach for illustrating  the process of emergence in physiology, embedded in a densely filled  environment. Our approach of a complementary fusion of three systems  combines the strong points from the different modeling approaches  and is capable to bridge different spatial and temporal scales.",
pdf = "pdfs/Kolesar-2014-IIP.pdf",
images = "images/Kolesar-2014-IIP.jpg",
thumbnails = "images/Kolesar-2014-IIP.png",
youtube = "https://www.youtube.com/watch?v=iMl5nDicmhg",
doi = "10.1186/1471-2105-15-345",
keywords = "biochemical visualization, L-system modeling, multi-agent modeling, visualization of physiology, polymerization",
owner = "bruckner",
project = "physioillustration",
timestamp = "2014.12.29",
url = "http://www.ii.uib.no/vis/projects/physioillustration/research/interactive-molecular-illustration.html"
}

2013

    [Bibtex] 
    @MISC {Kolesar13HumanPhysiology,
author = "Ivan Kolesar",
title = "Approaches for Visualizing Human Physiology",
howpublished = "Presentation in the VisBio 2013",
month = "September",
year = "2013",
abstract = "Physiology is scientific study of function in living systems. All in all, we presents several visual abstractions used to communicate physiological processes through different functional human systems in different scales from molecules to whole human body. However there are still several challenges for visualizing multi-scale physiological processes.",
images = "images/no_thumb.png",
thumbnails = "images/Kolesar13HumanPhysiology.jpg",
location = "Bergen, Norway",
project = "physioillustration"
}