HyperLabels: Browsing of Dense and Hierarchical Molecular 3D Models

dc.contributor.authorKouřil, David
dc.contributor.authorIsenberg, Tobias
dc.contributor.authorKozlikova, Barbora
dc.contributor.authorMeyer, Miriah
dc.contributor.authorGroeller, Eduard
dc.contributor.authorViola, Ivan
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.contributor.departmentComputer Science Program
dc.contributor.departmentVisual Computing Center (VCC)
dc.contributor.institutionInstitute of Visual Computing & Human-Centered Technology, TU Wien, 27259 Wien, Wien Austria 1040
dc.contributor.institutionAVIZ, INRIA, Saclay, Ile-de-France France
dc.contributor.institutionFaculty of Informatics, Masaryk University, Brno, South Moravian Region Czech Republic
dc.contributor.institutionSchool of Computing, University of Utah, Salt Lake City, Utah United States 84112
dc.contributor.institutionInstitute of Computer Graphics and Algorithms, Vienna University of Technology, A-1040 Vienna, Austria Austria A-1040
dc.date.accessioned2020-02-25T07:37:56Z
dc.date.available2020-02-25T07:37:56Z
dc.date.issued2020-02-24
dc.date.published-online2020-02-24
dc.date.published-print2020
dc.date.submitted2019-10-11
dc.description.abstractWe present a method for the browsing of hierarchical 3D models in which we combine the typical navigation of hierarchical structures in a 2D environment---using clicks on nodes, links, or icons---with a 3D spatial data visualization. Our approach is motivated by large molecular models, for which the traditional single-scale navigational metaphors are not suitable. Multi-scale phenomena, e.g., in astronomy or geography, are complex to navigate due to their large data spaces and multi-level organization. Models from structural biology are in addition also densely crowded in space and scale. Cutaways are needed to show individual model subparts. The camera has to support exploration on the level of a whole virus, as well as on the level of a small molecule. We address these challenges by employing HyperLabels: active labels that---in addition to their annotational role---also support user interaction. Clicks on HyperLabels select the next structure to be explored. Then, we adjust the visualization to showcase the inner composition of the selected subpart and enable further exploration. Finally, we use a breadcrumbs panel for orientation and as a mechanism to traverse upwards in the model hierarchy. We demonstrate our concept of hierarchical 3D model browsing using two exemplary models from meso-scale biology.
dc.description.sponsorshipThis work was funded through the ILLUSTRARE grant by both the Austrian Science Fund (FWF; I 2953-N31) and the French National Research Agency (ANR; ANR-16-CE91-0011-01). This work was also funded under the ILLVISATION grant by WWTF (VRG11-010). The research was further supported by the King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR), under award numbers OSR-2019-CPF-4108 and BAS/1/1680-01-01. This paper was partly written in collaboration with the VRVis Competence Center. We thank Nanographics GmbH (nanographics.at) for providing the Marion Software Framework. We also thank Haichao Miao for his help with the video as well as the anonymous reviewers and the associate editor for their comments to improve the article
dc.eprint.versionPublisher's Version/PDF
dc.identifier.citationKouril, D., Isenberg, T., Kozlikova, B., Meyer, M., Groeller, E., & Viola, I. (2020). HyperLabels: Browsing of Dense and Hierarchical Molecular 3D Models. IEEE Transactions on Visualization and Computer Graphics, 1–1. doi:10.1109/tvcg.2020.2975583
dc.identifier.doi10.1109/TVCG.2020.2975583
dc.identifier.journalIEEE Transactions on Visualization and Computer Graphics
dc.identifier.urihttp://hdl.handle.net/10754/661679
dc.publisherInstitute of Electrical and Electronics Engineers (IEEE)
dc.relation.urlhttps://ieeexplore.ieee.org/document/9007694/
dc.relation.urlhttps://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=9007694
dc.rightsThis article is open access.
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectScientific visualization
dc.subjectnavigation
dc.subject3D molecular data
dc.subjectmulti-scale data
dc.subjecthierarchical data
dc.subjectHyperLabels
dc.titleHyperLabels: Browsing of Dense and Hierarchical Molecular 3D Models
dc.typeArticle
display.details.left<span><h5>License</h5>https://creativecommons.org/licenses/by/4.0/<br><br><h5>Type</h5>Article<br><br><h5>Authors</h5><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Kouřil, David,equals">Kouřil, David</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Isenberg, Tobias,equals">Isenberg, Tobias</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Kozlikova, Barbora,equals">Kozlikova, Barbora</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Meyer, Miriah,equals">Meyer, Miriah</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Groeller, Eduard,equals">Groeller, Eduard</a><br><a href="https://repository.kaust.edu.sa/search?query=orcid.id:0000-0003-4248-6574&spc.sf=dc.date.issued&spc.sd=DESC">Viola, Ivan</a> <a href="https://orcid.org/0000-0003-4248-6574" target="_blank"><img src="https://repository.kaust.edu.sa/server/api/core/bitstreams/82a625b4-ed4b-40c8-865a-d6a5225a26a4/content" width="16" height="16"/></a><br><br><h5>KAUST Department</h5><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.department=Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division,equals">Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.department=Computer Science Program,equals">Computer Science Program</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.department=Visual Computing Center (VCC),equals">Visual Computing Center (VCC)</a><br><br><h5>KAUST Grant Number</h5>BAS/1/1680-01-01<br><br><h5>Online Publication Date</h5>2020-02-24<br><br><h5>Print Publication Date</h5>2020<br><br><h5>Date</h5>2020-02-24<br><br><h5>Submitted Date</h5>2019-10-11</span>
display.details.right<span><h5>Abstract</h5>We present a method for the browsing of hierarchical 3D models in which we combine the typical navigation of hierarchical structures in a 2D environment---using clicks on nodes, links, or icons---with a 3D spatial data visualization. Our approach is motivated by large molecular models, for which the traditional single-scale navigational metaphors are not suitable. Multi-scale phenomena, e.g., in astronomy or geography, are complex to navigate due to their large data spaces and multi-level organization. Models from structural biology are in addition also densely crowded in space and scale. Cutaways are needed to show individual model subparts. The camera has to support exploration on the level of a whole virus, as well as on the level of a small molecule. We address these challenges by employing HyperLabels: active labels that---in addition to their annotational role---also support user interaction. Clicks on HyperLabels select the next structure to be explored. Then, we adjust the visualization to showcase the inner composition of the selected subpart and enable further exploration. Finally, we use a breadcrumbs panel for orientation and as a mechanism to traverse upwards in the model hierarchy. We demonstrate our concept of hierarchical 3D model browsing using two exemplary models from meso-scale biology.<br><br><h5>Citation</h5>Kouril, D., Isenberg, T., Kozlikova, B., Meyer, M., Groeller, E., & Viola, I. (2020). HyperLabels: Browsing of Dense and Hierarchical Molecular 3D Models. IEEE Transactions on Visualization and Computer Graphics, 1–1. doi:10.1109/tvcg.2020.2975583<br><br><h5>Acknowledgements</h5>This work was funded through the ILLUSTRARE grant by both the Austrian Science Fund (FWF; I 2953-N31) and the French National Research Agency (ANR; ANR-16-CE91-0011-01). This work was also funded under the ILLVISATION grant by WWTF (VRG11-010). The research was further supported by the King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR), under award numbers OSR-2019-CPF-4108 and BAS/1/1680-01-01. This paper was partly written in collaboration with the VRVis Competence Center. We thank Nanographics GmbH (nanographics.at) for providing the Marion Software Framework. We also thank Haichao Miao for his help with the video as well as the anonymous reviewers and the associate editor for their comments to improve the article<br><br><h5>Publisher</h5><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.publisher=Institute of Electrical and Electronics Engineers (IEEE),equals">Institute of Electrical and Electronics Engineers (IEEE)</a><br><br><h5>Journal</h5><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.journal=IEEE Transactions on Visualization and Computer Graphics,equals">IEEE Transactions on Visualization and Computer Graphics</a><br><br><h5>DOI</h5><a href="https://doi.org/10.1109/TVCG.2020.2975583">10.1109/TVCG.2020.2975583</a><br><br><h5>Additional Links</h5>https://ieeexplore.ieee.org/document/9007694/https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=9007694</span>
kaust.acknowledged.supportUnitOffice of Sponsored Research (OSR)
kaust.grant.numberBAS/1/1680-01-01
kaust.personViola, Ivan
orcid.id0000-0003-4248-6574
refterms.dateFOA2020-02-25T07:39:52Z
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