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Karsten Schatz

M. Sc.

Doctoral Researcher
Visualization Research Center (VISUS)
Ertl Group

Contact

Allmandring 19
70569 Stuttgart
Deutschland

Publications

Publications:

2021
1. Schatz, Karsten ; Franco Moreno, Juan José ; Schäfer, Marco ; Rose, Alexander S. ; Ferrario, Valerio ; Pleiss, Jürgen ; Vázquez, Pere-Pau ; Ertl, Thomas ; u. a.: Visual Analysis of Large-Scale Protein-Ligand Interaction Data. In: Computer Graphics Forum, Computer Graphics Forum. Bd. 40 (2021), Nr. 6, S. 394–408
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  BibTeX
  @article{schatz2021visual, abstract = {When studying protein-ligand interactions, many different factors can influence the behaviour of the protein as well as the ligands. Molecular visualisation tools typically concentrate on the movement of single ligand molecules; however, viewing only one molecule can merely provide a hint of the overall behaviour of the system. To tackle this issue, we do not focus on the visualisation of the local actions of individual ligand molecules but on the influence of a protein and their overall movement. Since the simulations required to study these problems can have millions of time steps, our presented system decouples visualisation and data preprocessing: our preprocessing pipeline aggregates the movement of ligand molecules relative to a receptor protein. For data analysis, we present a web-based visualisation application that combines multiple linked 2D and 3D views that display the previously calculated data The central view, a novel enhanced sequence diagram that shows the calculated values, is linked to a traditional surface visualisation of the protein. This results in an interactive visualisation that is independent of the size of the underlying data, since the memory footprint of the aggregated data for visualisation is constant and very low, even if the raw input consisted of several terabytes.}, author = {Schatz, Karsten and Franco Moreno, Juan José and Schäfer, Marco and Rose, Alexander S. and Ferrario, Valerio and Pleiss, Jürgen and Vázquez, Pere-Pau and Ertl, Thomas and Krone, Michael}, doi = {10.1111/cgf.14386}, journal = {Computer Graphics Forum}, number = 6, pages = {394-408}, title = {Visual Analysis of Large-Scale Protein-Ligand Interaction Data}, url = {https://onlinelibrary.wiley.com/doi/10.1111/cgf.14386}, volume = 40, year = 2021 }
  Link
  https://onlinelibrary.wiley.com/doi/10.1111/cgf.14386
2. Schatz, Karsten ; Frieß, Florian ; Schäfer, Marco ; Buchholz, Patrick C. F. ; Pleiss, Jürgen ; Ertl, Thomas ; Krone, Michael: Analyzing the similarity of protein domains by clustering Molecular Surface Maps. In: Computers & Graphics, Computers & Graphics. Bd. 99 (2021), S. 114–127
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  @article{schatz2021analyzing, abstract = {Many biochemical and biomedical applications such as protein engineering or drug design are concerned with finding functionally similar proteins, however, this remains to be a challenging task. We present a new image-based approach for identifying and visually comparing proteins with similar function that builds on the hierarchical clustering of Molecular Surface Maps. Such maps are two-dimensional representations of complex molecular surfaces and can be used to visualize the topology and different physico-chemical properties of proteins. Our method is based on the idea that visually similar maps also imply a similarity in the function of the mapped proteins. To determine map similarity, we compute descriptive feature vectors using image moments, color moments, or a Convolutional Neural Network and use them for a hierarchical clustering of the maps. We demonstrate the feasibility of our approach using two data sets: an ensemble of hand-selected proteins with known similarities used for verification and an ensemble of ketolase enzymes, where we analyzed the individual domains using our method. Our method is integrated in an interactive visualization application, which allows users to explore and analyze the results. It visualizes the hierarchical clustering and offers linked views that provide details for a comparative data analysis.}, author = {Schatz, Karsten and Frieß, Florian and Schäfer, Marco and Buchholz, Patrick C. F. and Pleiss, Jürgen and Ertl, Thomas and Krone, Michael}, doi = {10.1016/j.cag.2021.06.007}, journal = {Computers & Graphics}, pages = {114-127}, title = {Analyzing the similarity of protein domains by clustering Molecular Surface Maps}, url = {https://www.sciencedirect.com/science/article/abs/pii/S0097849321001229}, volume = 99, year = 2021 }
  Link
  https://www.sciencedirect.com/science/article/abs/pii/S0097849321001229
3. Schatz, K. ; Müller, C. ; Gralka, P. ; Heinemann, M. ; Straub, A. ; Schulz, C. ; Braun, M. ; Rau, T. ; u. a.: 2019 IEEE Scientific Visualization Contest Winner: Visual Analysis of Structure Formation in Cosmic Evolution. In: IEEE Computer Graphics and Applications (CG&A), IEEE Computer Graphics and Applications (CG&A). Bd. 41 (2021), Nr. 06, S. 101–110
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  @article{9126163, abstract = {Simulations of cosmic evolution are a means to explain the formation of the universe as we see it today. The resulting data of such simulations comprise numerous physical quantities, which turns their analysis into a complex task. Here, we analyze such high-dimensional and time-varying particle data using various visualization techniques from the fields of particle visualization, flow visualization, volume visualization, and information visualization. Our approach employs specialized filters to extract and highlight the development of so-called active galactic nuclei and filament structures formed by the particles. Additionally, we calculate X-ray emission of the evolving structures in a pre-processing step to complement visual analysis. Our approach is integrated into a single visual analytics framework to allow for analysis of star formation at interactive frame rates. Finally, we lay out the methodological aspects of our work that led to success at the 2019 IEEE SciVis Contest.}, author = {Schatz, K. and Müller, C. and Gralka, P. and Heinemann, M. and Straub, A. and Schulz, C. and Braun, M. and Rau, T. and Becher, M. and Frey, S. and Reina, G. and Sedlmair, M. and Weiskopf, D. and Ertl, T. and Diehl, P. and Marcello, D. and Frank, J. and Müller, T.}, doi = {10.1109/MCG.2020.3004613}, issn = {1558-1756}, journal = {IEEE Computer Graphics and Applications (CG&A)}, month = {11}, number = 06, pages = {101-110}, title = {2019 IEEE Scientific Visualization Contest Winner: Visual Analysis of Structure Formation in Cosmic Evolution}, url = {https://ieeexplore.ieee.org/document/9126163}, volume = 41, year = 2021 }
  Link
  https://ieeexplore.ieee.org/document/9126163
2020
1. Schatz, Karsten ; Frieß, Florian ; Schäfer, Marco ; Ertl, Thomas ; Krone, Michael: Analyzing Protein Similarity by Clustering Molecular Surface Maps. In: Eurographics Workshop on Visual Computing for Biology and Medicine, Eurographics Workshop on Visual Computing for Biology and Medicine, 2020, S. 103–114
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  @inproceedings{schatz2020analyzing, author = {Schatz, Karsten and Frieß, Florian and Schäfer, Marco and Ertl, Thomas and Krone, Michael}, booktitle = {Eurographics Workshop on Visual Computing for Biology and Medicine}, doi = {10.2312/vcbm.20201177}, pages = {103-114}, title = {Analyzing Protein Similarity by Clustering Molecular Surface Maps}, year = 2020 }
2019
1. Schatz, Karsten ; Krone, Michael ; Pleiss, Jürgen ; Ertl, Thomas: Interactive visualization of biomolecules’ dynamic and complex properties. In: Holm, C. ; Ertl, T. ; Schmauder, S. ; Kästner, J. ; Groß, J. (Hrsg.) The European Physical Journal (Special Topics), The European Physical Journal (Special Topics). Bd. 227: Particle Methods in Natural Science and Engineering (2019), Nr. 14, S. 1725--1739
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  @article{schatz2019interactive, abstract = {In this paper, we review the advances in molecular visualization over the last 12 years and put the development of the community in context with our own efforts in the DFG Collaborative Research Center (CRC) 716. This includes advances in the field of molecular surface computation and rendering, interactive extraction of protein cavities, and comparative visualization for biomolecules. Our main focus was on the development of methods that assist the interactive and explorative visual analysis of large, dynamic molecular data sets on single desktop computers. To meet this goal, we often developed GPU-accelerated algorithms, which is in line with the general research direction of the field. Over the last years, we made seminal contributions to the field of molecular visualization, which partially still constitute the state of the art development or provided the basis for follow-up works}, author = {Schatz, Karsten and Krone, Michael and Pleiss, Jürgen and Ertl, Thomas}, doi = {https://doi.org/10.1140/epjst/e2019-800162-y}, editor = {Holm, C. and Ertl, T. and Schmauder, S. and Kästner, J. and Groß, J.}, journal = {The European Physical Journal (Special Topics)}, number = 14, pages = {1725--1739}, title = {Interactive visualization of biomolecules' dynamic and complex properties}, url = {https://epjst.epj.org/articles/epjst/abs/2019/02/epjst1800162/epjst1800162.html}, volume = {227: Particle Methods in Natural Science and Engineering}, year = 2019 }
  Link
  https://epjst.epj.org/articles/epjst/abs/2019/02/epjst1800162/epjst1800162.html
2. Miao, Haichao ; Klein, Tobias ; Kouřil, David ; Mindek, Peter ; Schatz, Karsten ; Gröller, Meister Eduard ; Kozlíková, Barbora ; Isenberg, Tobias ; u. a.: Multiscale Molecular Visualization. In: Wright, P. (Hrsg.) Journal of Molecular Biology, Journal of Molecular Biology. Bd. 431 (2019), Nr. 6, S. 1049–1070
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  @article{miao2018multiscale, author = {Miao, Haichao and Klein, Tobias and Kouřil, David and Mindek, Peter and Schatz, Karsten and Gröller, Meister Eduard and Kozlíková, Barbora and Isenberg, Tobias and Viola, Ivan}, doi = {https://doi.org/10.1016/j.jmb.2018.09.004}, editor = {Wright, Peter}, journal = {Journal of Molecular Biology}, month = {03}, number = 6, pages = {1049-1070}, title = {Multiscale Molecular Visualization}, url = {https://www.sciencedirect.com/science/article/pii/S0022283618310490?dgcid=coauthor}, volume = 431, year = 2019 }
  Link
  https://www.sciencedirect.com/science/article/pii/S0022283618310490?dgcid=coauthor
3. Schatz, Karsten ; Krone, Michael ; Bauer, Tabea L. ; Ferrario, Valerio ; Pleiss, Jürgen ; Ertl, Thomas: Molecular Sombreros: Abstract Visualization of Binding Sites within Proteins. In: Eurographics Workshop on Visual Computing for Biology and Medicine, Eurographics Workshop on Visual Computing for Biology and Medicine : The Eurographics Association, 2019 — ISBN 978-3-03868-081-9, S. 225–237
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  @inproceedings{schatz2019molecular, abstract = {We present a novel abstract visualization for the binding sites of proteins. Binding sites play an essential role in enzymatic reactions and are, thus, often investigated in structural biology. They are typically located within cavities. The shape and properties of the cavity influence whether and how easily a substrate can reach the active site where the reaction is triggered. Molecular surface visualizations can help to analyze the accessibility of binding sites, but are typically prone to visual clutter. Our novel abstract visualization shows the cavity containing the binding site as well as the surface region directly surrounding the cavity entrance in a simplified manner. The resulting visualization resembles a hat, where the brim depicts the surrounding surface region and the crown the cavity. Hence, we dubbed our abstraction Molecular Sombrero, using the Spanish term for 'hat'. Our abstraction is less cluttered than traditional molecular surface visualizations. It highlights important parameters, like cavity diameter, by mapping them to the shape of the sombrero. The visual abstraction also facilitates an easy side-by-side comparison of different data sets. We show the applicability of our Molecular Sombreros to different real-world use cases.}, author = {Schatz, Karsten and Krone, Michael and Bauer, Tabea L. and Ferrario, Valerio and Pleiss, Jürgen and Ertl, Thomas}, booktitle = {Eurographics Workshop on Visual Computing for Biology and Medicine}, doi = {10.2312/vcbm.20191248}, isbn = {978-3-03868-081-9}, issn = {2070-5786}, pages = {225-237}, publisher = {The Eurographics Association}, title = {Molecular Sombreros: Abstract Visualization of Binding Sites within Proteins}, url = {https://doi.org/10.2312/vcbm.20191248}, year = 2019 }
  Link
  https://doi.org/10.2312/vcbm.20191248
4. Gralka, Patrick ; Becher, Michael ; Braun, Matthias ; Frieß, Florian ; Müller, Christoph ; Rau, Tobias ; Schatz, Karsten ; Schulz, Christoph ; u. a.: MegaMol -- a comprehensive prototyping framework for visualizations. In: The European Physical Journal (Special Topics), The European Physical Journal (Special Topics). Bd. 227: Particle Methods in Natural Science and Engineering (2019), Nr. 14, S. 1817--1829
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  @article{Gralka2019Megamol, abstract = {We present MegaMol, a low-overhead prototyping framework for interactive visualization of large scientific data sets. We give a brief summary of related work for context and then focus on a comprehensive overview of the core architecture of the framework. This is followed by the existing and novel features and techniques in MegaMol that define its current functionality. MegaMol has originally been developed to support the visualization and analysis of particle-based data sets that, for instance, come from molecular dynamics simulations. Meanwhile, the software has evolved beyond that. New algorithms and techniques have been implemented to handle many diverse tasks, including information visualization. Additionally, improvements have been made on the software engineering side to make MegaMol more accessible for domain scientists, like an easy-to-handle scripting interface.}, author = {Gralka, Patrick and Becher, Michael and Braun, Matthias and Frieß, Florian and Müller, Christoph and Rau, Tobias and Schatz, Karsten and Schulz, Christoph and Krone, Michael and Reina, Guido and Ertl, Thomas}, doi = {10.1140/epjst/e2019-800167-5}, issn = {1951-6401}, journal = {The European Physical Journal (Special Topics)}, number = 14, pages = {1817--1829}, title = {MegaMol -- a comprehensive prototyping framework for visualizations}, url = {https://doi.org/10.1140/epjst/e2019-800167-5}, volume = {227: Particle Methods in Natural Science and Engineering}, year = 2019 }
  Link
  https://doi.org/10.1140/epjst/e2019-800167-5
5. Schatz, Karsten ; Müller, Christoph ; Gralka, Patrick ; Heinemann, Moritz ; Straub, Alexander ; Schulz, Christoph ; Braun, Matthias ; Rau, Tobias ; u. a.: Visual Analysis of Structure Formation in Cosmic Evolution. In: 2019 IEEE Scientific Visualization Conference (SciVis), 2019 IEEE Scientific Visualization Conference (SciVis), 2019, S. 33–41
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  @inproceedings{schatz2019visual, abstract = {The IEEE SciVis 2019 Contest targets the visual analysis of structure formation in the cosmic evolution of the universe from when the universe was five million years old up to now. In our submission, we analyze high-dimensional data to get an overview, then investigate the impact of Active Galactic Nuclei (AGNs) using various visualization techniques, for instance, an adapted filament filtering method for detailed analysis and particle flow in the vicinity of filaments. Based on feedback from domain scientists on these initial visualizations, we also analyzed X-ray emissions and star formation areas. The conversion of star-forming gas to stars and the resulting increasing molecular weight of the particles could be observed.}, author = {Schatz, Karsten and Müller, Christoph and Gralka, Patrick and Heinemann, Moritz and Straub, Alexander and Schulz, Christoph and Braun, Matthias and Rau, Tobias and Becher, Michael and Diehl, Patrick and Marcello, Dominic and Frank, Juhan and Müller, Thomas and Frey, Steffen and Reina, Guido and Weiskopf, Daniel and Ertl, Thomas}, booktitle = {2019 IEEE Scientific Visualization Conference (SciVis)}, doi = {10.1109/scivis47405.2019.8968855}, pages = {33-41}, title = {Visual Analysis of Structure Formation in Cosmic Evolution}, url = {http://dx.doi.org/10.1109/scivis47405.2019.8968855}, year = 2019 }
  Link
  http://dx.doi.org/10.1109/scivis47405.2019.8968855
2018
1. Schulz, Christoph ; Schatz, Karsten ; Krone, Michael ; Braun, Matthias ; Ertl, Thomas ; Weiskopf, Daniel: Uncertainty Visualization for Secondary Structures of Proteins. In: IEEE PacificVis, IEEE PacificVis. Bd. 2018 IEEE Pacific Visualization Symposium, 2018, S. 96–105
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  @inproceedings{Schulz2018Uncertainty, author = {Schulz, Christoph and Schatz, Karsten and Krone, Michael and Braun, Matthias and Ertl, Thomas and Weiskopf, Daniel}, booktitle = {IEEE PacificVis}, doi = {10.1109/PacificVis.2018.00020}, pages = {96-105}, title = {Uncertainty Visualization for Secondary Structures of Proteins}, volume = {2018 IEEE Pacific Visualization Symposium}, year = 2018 }
2. Gralka, Patrick ; Grottel, Sebastian ; Staib, Joachim ; Schatz, Karsten ; Karch, Grzegorz Karol ; Hirschler, M. ; Krone, Michael ; Reina, Guido ; u. a.: 2016 IEEE Scientific Visualization Contest Winner: Visual and Structural Analysis of Point-based Simulation Ensembles. In: IEEE Computer Graphics & Applications, IEEE Computer Graphics & Applications. Bd. 38 (2018), Nr. 3, S. 106–117
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  @article{gralka2017sciviscontest2016, author = {Gralka, Patrick and Grottel, Sebastian and Staib, Joachim and Schatz, Karsten and Karch, Grzegorz Karol and Hirschler, M. and Krone, Michael and Reina, Guido and Gumhold, S. and Ertl, Thomas}, doi = {10.1109/MCG.2017.3301120}, journal = {IEEE Computer Graphics & Applications}, number = 3, pages = {106-117}, title = {2016 IEEE Scientific Visualization Contest Winner: Visual and Structural Analysis of Point-based Simulation Ensembles}, volume = 38, year = 2018 }
2017
1. Krone, Michael ; Schatz, Karsten ; Hieronymus, Nora ; Müller, Christoph ; Becher, Michael ; Barthelmes, Tina ; Cooper, April ; Currle, Steffen ; u. a.: From Visualization Research to Public Presentation - Design and Realization of a Scientific Exhibition. In: Proceedings of SIGRAD 2017, Proceedings of SIGRAD 2017, 2017
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  @inproceedings{krone2017sigrad, author = {Krone, Michael and Schatz, Karsten and Hieronymus, Nora and Müller, Christoph and Becher, Michael and Barthelmes, Tina and Cooper, April and Currle, Steffen and Gralka, Patrick and Hlawatsch, Marcel and Pietrzyk, Lisa and Rau, Tobias and Reina, Guido and Trefft, Rene and Ertl, Thomas}, booktitle = {Proceedings of SIGRAD 2017}, title = {From Visualization Research to Public Presentation - Design and Realization of a Scientific Exhibition}, year = 2017 }
2. Schatz, Karsten ; Krone, Michael ; Müller, Christoph ; Schneider, Jens ; Reina, Guido ; Ertl, Thomas: Visualization of Halo Topologies in Dark Matter Simulations. In: Proceedings of TopoInVis, Proceedings of TopoInVis, 2017. — Rezensiertes Abstract
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  @inproceedings{schatz17topoinvis, author = {Schatz, Karsten and Krone, Michael and Müller, Christoph and Schneider, Jens and Reina, Guido and Ertl, Thomas}, booktitle = {Proceedings of TopoInVis}, note = {Rezensiertes Abstract}, title = {Visualization of Halo Topologies in Dark Matter Simulations}, year = 2017 }
2016
1. Schatz, Karsten ; Müller, Christoph ; Krone, Michael ; Schneider, Jens ; Reina, Guido ; Ertl, Thomas: Interactive Visual Exploration of a Trillion Particles. In: IEEE (Hrsg.) ; IEEE (Hrsg.): Symposium on Large Data Analysis and Visualization (LDAV), Symposium on Large Data Analysis and Visualization (LDAV), 2016
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  @inproceedings{SchatzLDAV2016, author = {Schatz, Karsten and Müller, Christoph and Krone, Michael and Schneider, Jens and Reina, Guido and Ertl, Thomas}, booktitle = {Symposium on Large Data Analysis and Visualization (LDAV)}, editor = {IEEE}, title = {Interactive Visual Exploration of a Trillion Particles}, url = {http://dx.doi.org/10.1109/LDAV.2016.7874310}, year = 2016 }
  Link
  http://dx.doi.org/10.1109/LDAV.2016.7874310

Teaching

Excercise: "Computer Graphics" (WS 2020/2021)
Excercise: "Scientific Visualization" (SS 2020)
Excercise: "Computer Graphics" (WS 2019/2020)
Excercise: "Scientific Visualization" (SS 2019)
Advanced Seminar "Particle-based Visualization" (WS 2018/2019)
"Practical Course Visual Computing" (WS 2017/2018)
"Practical Course Visual Computing" (SS 2017)
"Practical Course Visual Computing" (WS 2016/2017)
Excercise: "Scientific Visualization" (SS 2016)

Awards

IEEE VIS 2019: Winner of IEEE SciVis Contest 2019 (K. Schatz, C. Müller, P. Gralka, M. Heinemann, A. Straub, C. Schulz, M. Braun, T. Rau, M. Becher, P. Diehl, D. Marcello, J. Frank, T. Müller, S. Frey, G. Reina, D. Weiskopf, T. Ertl: "Visual Analysis of Structure Formation in Cosmic Evolution")
IEEE VIS 2016: Winner of IEEE SciVis Contest 2016 (S. Grottel, P. Gralka, J. Staib, K. Schatz, G. K. Karch, M. Hirschler, M. Krone, G. Reina, S. Gumhold, T. Ertl: "Visual and Structural Analysis of Point-based Simulation Ensembles")

Supervised Theses and Projects

Ongoing:

Efficient Rendering Methods for Visual Analysis of Astrophysical Data (Bachelor Thesis)

Finished:

Flow Visualization of Galaxy Evolution in Astrophysical Simulations (Research Project)
Comparative Visualization of Molecular Surfaces Using Similarity-based Clustering (Bachelor Thesis)
Visualizing the Uncertainty of the Secondary Structure of Proteins (Diploma Thesis)
A framework for defining animations in scientific communication (Bachelor Thesis)
Visualize the Universe in Bricked-LOD (Research Project in cooperation with TU Dresden)

Karsten Schatz

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Publications

2021

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2020

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2019

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2018

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2017

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2016

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Karsten Schatz

Contact

Publications

2021

BibTeX

Link

BibTeX

Link

BibTeX

Link

2020

BibTeX

2019

BibTeX

Link

BibTeX

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BibTeX

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BibTeX

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BibTeX

Link

2018

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2017

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2016

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Link

Teaching

Awards

Supervised Theses and Projects

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