Visibility Equalizer Cutaway Visualization of Mesoscopic Biological Models
In scientific illustrations and visualization, cutaway views are often employed as an effective technique for occlusion management in densely packed scenes. We propose a novel method for authoring cutaway illustrations of mesoscopic biological models. In contrast to the existing cutaway algorithms,...
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| Published in: | Computer graphics forum Vol. 35; no. 3; pp. 161 - 170 |
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| Main Authors: | , , , , , |
| Format: | Journal Article |
| Language: | English |
| Published: |
England
Blackwell Publishing Ltd
01.06.2016
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| ISSN: | 0167-7055, 1467-8659 |
| Online Access: | Get full text |
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| Abstract | In scientific illustrations and visualization, cutaway views are often employed as an effective technique for occlusion management in densely packed scenes. We propose a novel method for authoring cutaway illustrations of mesoscopic biological models. In contrast to the existing cutaway algorithms, we take advantage of the specific nature of the biological models. These models consist of thousands of instances with a comparably smaller number of different types. Our method constitutes a two stage process. In the first step, clipping objects are placed in the scene, creating a cutaway visualization of the model. During this process, a hierarchical list of stacked bars inform the user about the instance visibility distribution of each individual molecular type in the scene. In the second step, the visibility of each molecular type is fine‐tuned through these bars, which at this point act as interactive visibility equalizers. An evaluation of our technique with domain experts confirmed that our equalizer‐based approach for visibility specification is valuable and effective for both, scientific and educational purposes. |
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| AbstractList | In scientific illustrations and visualization, cutaway views are often employed as an effective technique for occlusion management in densely packed scenes. We propose a novel method for authoring cutaway illustrations of mesoscopic biological models. In contrast to the existing cutaway algorithms, we take advantage of the specific nature of the biological models. These models consist of thousands of instances with a comparably smaller number of different types. Our method constitutes a two stage process. In the first step, clipping objects are placed in the scene, creating a cutaway visualization of the model. During this process, a hierarchical list of stacked bars inform the user about the instance visibility distribution of each individual molecular type in the scene. In the second step, the visibility of each molecular type is fine-tuned through these bars, which at this point act as interactive visibility equalizers. An evaluation of our technique with domain experts confirmed that our equalizer-based approach for visibility specification is valuable and effective for both, scientific and educational purposes. In scientific illustrations and visualization, cutaway views are often employed as an effective technique for occlusion management in densely packed scenes. We propose a novel method for authoring cutaway illustrations of mesoscopic biological models. In contrast to the existing cutaway algorithms, we take advantage of the specific nature of the biological models. These models consist of thousands of instances with a comparably smaller number of different types. Our method constitutes a two stage process. In the first step, clipping objects are placed in the scene, creating a cutaway visualization of the model. During this process, a hierarchical list of stacked bars inform the user about the instance visibility distribution of each individual molecular type in the scene. In the second step, the visibility of each molecular type is fine-tuned through these bars, which at this point act as interactive visibility equalizers. An evaluation of our technique with domain experts confirmed that our equalizer-based approach for visibility specification was valuable and effective for both, scientific and educational purposes.In scientific illustrations and visualization, cutaway views are often employed as an effective technique for occlusion management in densely packed scenes. We propose a novel method for authoring cutaway illustrations of mesoscopic biological models. In contrast to the existing cutaway algorithms, we take advantage of the specific nature of the biological models. These models consist of thousands of instances with a comparably smaller number of different types. Our method constitutes a two stage process. In the first step, clipping objects are placed in the scene, creating a cutaway visualization of the model. During this process, a hierarchical list of stacked bars inform the user about the instance visibility distribution of each individual molecular type in the scene. In the second step, the visibility of each molecular type is fine-tuned through these bars, which at this point act as interactive visibility equalizers. An evaluation of our technique with domain experts confirmed that our equalizer-based approach for visibility specification was valuable and effective for both, scientific and educational purposes. In scientific illustrations and visualization, cutaway views are often employed as an effective technique for occlusion management in densely packed scenes. We propose a novel method for authoring cutaway illustrations of mesoscopic biological models. In contrast to the existing cutaway algorithms, we take advantage of the specific nature of the biological models. These models consist of thousands of instances with a comparably smaller number of different types. Our method constitutes a two stage process. In the first step, clipping objects are placed in the scene, creating a cutaway visualization of the model. During this process, a hierarchical list of stacked bars inform the user about the instance visibility distribution of each individual molecular type in the scene. In the second step, the visibility of each molecular type is fine-tuned through these bars, which at this point act as interactive visibility equalizers. An evaluation of our technique with domain experts confirmed that our equalizer-based approach for visibility specification was valuable and effective for both, scientific and educational purposes. |
| Author | Mindek, P. Autin, L. Viola, I. Goodsell, D. S. Le Muzic, M. Sorger, J. |
| AuthorAffiliation | 2 VRVis Research Center, Vienna, Austria 3 The Scripps Research Institute, La Jolla, California, USA 1 TU Wien, Austria |
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| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/28344374$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1111/cgf.12370 10.1109/TVCG.2003.1207438 10.1145/2448531.2448537 10.1111/1467-8659.t01-1-00591 10.1007/BF01897116 10.1145/1111411.1111431 10.1111/cgf.12197 10.1109/TVCG.2010.35 10.1111/j.1467-8659.2012.03128.x 10.1109/TVCG.2005.62 10.1109/TVCG.2015.2467961 10.1111/j.1467-8659.2011.01930.x 10.1111/j.1467-8659.2012.03208.x 10.1109/PacificVis.2012.6183590 10.1109/TVCG.2006.124 10.1038/nmeth.3204 10.1111/1467-8659.t01-3-00700 10.1109/TVCG.2011.173 |
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| Copyright | 2016 The Author(s) Computer Graphics Forum © 2016 The Eurographics Association and John Wiley & Sons Ltd. Published by John Wiley & Sons Ltd. 2016 The Eurographics Association and John Wiley & Sons Ltd. |
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| References | Viola I.: Importance-Driven Expressive Visualization. PhD thesis, Institute of Computer Graphics and Algorithms, Vienna University of Technology, Favoritenstrasse 9-11/186, A-1040 Vienna, Austria, June 2005. 3 Falk M., Krone M., Ertl T.: Atomistic visualization of mesoscopic whole-cell simulations using ray-casted instancing. Computer Graphics Forum 32, 8 (2013), 195-206. 3 Le Muzic M., Parulek J., Stavrum A.-K., Viola I.: Illustrative visualization of molecular reactions using omniscient intelligence and passive agents. Computer Graphics Forum 33, 3 (2014), 141-150. 3 Weiskopf D., Engel K., Ertl T.: Interactive clipping techniques for texture-based volume visualization and volume shading. Visualization and Computer Graphics, IEEE Transactions on 9, 3 (July 2003), 298-312. 3 Diepstraten J., Weiskopf D., Ertl T.: Interactive cutaway illustrations. Computer Graphics Forum 22, 3 (2003), 523-532. 3 Kubisch C., Tavenrath M.: Opengl 4.4 scene rendering techniques. NVIDIA Corporation (2014). 5 Johnson G.T., Autin L., Al-Alusi M., Goodsell D.S., Sanner M.F., Olson A.J.: cellPACK: a virtual mesoscope to model and visualize structural systems biology. Nature methods 12, 1 (Jan. 2015), 85-91. 2, 4, 7 Krüger J., Schneider J., Westermann R.: Clearview: An interactive context preserving hotspot visualization technique. Visualization and Computer Graphics, IEEE Transactions on 12, 5 (Sept 2006), 941-948. 3 Lindow N., Baum D., Hege H.-C.: Interactive rendering of materials and biological structures on atomic and nanoscopic scale. Computer Graphics Forum 31, 3 (2012), 1325-1334. 3 Diepstraten J., Weiskopf D., Ertl T.: Transparency in interactive technical illustrations. Computer Graphics Forum 21, 3 (2002), 317-325. 3 Viola I., Kanitsar A., Gröller M. E: Importance-driven feature enhancement in volume visualization. Visualization and Computer Graphics, IEEE Transactions on 11, 4 (July 2005), 408-418. 3 Lawonn K., Glasser S., Vilanova A., Preim B., Isenberg T.: Occlusion-free blood flow animation with wall thickness visualization. Visualization and Computer Graphics, IEEE Transactions on 22, 1 (Jan 2016), 728-737. 3 Baer A., Gasteiger R., Cunningham D., Preim B.: Perceptual evaluation of ghosted view techniques for the exploration of vascular structures and embedded flow. Computer Graphics Forum 30, 3 (2011), 811-820. 3 Feiner S., Seligmann D.: Cutaways and ghosting: satisfying visibility constraints in dynamic 3d illustrations. The Visual Computer 8, 5-6 (1992), 292-302. 3 Ruiz M., Bardera A., Boada I., Viola I., Feixas M., Sbert M.: Automatic transfer functions based on informational divergence. Visualization and Computer Graphics, IEEE Transactions on 17, 12 (Dec 2011), 1932-1941. 3 Díaz J., Monclús E., Navazo I., Vázquez P.: Adaptive cross-sections of anatomical models. Computer Graphics Forum 31, 7 (2012), 2155-2164. 3 Correa C., Ma K.-L.: Visibility histograms and visibilitydriven transfer functions. Visualization and Computer Graphics, IEEE Transactions on 17, 2 (Feb 2011), 192-204. 3 2015; 12 1992; 8 2006; I3D 2006; 12 2012 2013; 32 2002; 21 2003; 9 2008 2011; 30 2007 2005 2015 2004 2014 2011; 17 2005; 11 2012; 31 2014; 33 2003; 22 2016; 22 Li W. (e_1_2_11_21_2) 2007 Viola I. (e_1_2_11_27_2) 2004 Viola I. (e_1_2_11_26_2) 2005 e_1_2_11_13_2 e_1_2_11_12_2 Viola I. (e_1_2_11_25_2) 2005 e_1_2_11_11_2 e_1_2_11_10_2 e_1_2_11_6_2 e_1_2_11_28_2 e_1_2_11_5_2 e_1_2_11_4_2 e_1_2_11_3_2 e_1_2_11_29_2 Kubisch C. (e_1_2_11_14_2) 2014 e_1_2_11_20_2 e_1_2_11_24_2 e_1_2_11_9_2 e_1_2_11_23_2 e_1_2_11_8_2 e_1_2_11_22_2 e_1_2_11_7_2 e_1_2_11_17_2 Burns M. (e_1_2_11_2_2) 2008 e_1_2_11_16_2 e_1_2_11_15_2 e_1_2_11_19_2 e_1_2_11_18_2 |
| References_xml | – reference: Lindow N., Baum D., Hege H.-C.: Interactive rendering of materials and biological structures on atomic and nanoscopic scale. Computer Graphics Forum 31, 3 (2012), 1325-1334. 3 – reference: Weiskopf D., Engel K., Ertl T.: Interactive clipping techniques for texture-based volume visualization and volume shading. Visualization and Computer Graphics, IEEE Transactions on 9, 3 (July 2003), 298-312. 3 – reference: Kubisch C., Tavenrath M.: Opengl 4.4 scene rendering techniques. NVIDIA Corporation (2014). 5 – reference: Krüger J., Schneider J., Westermann R.: Clearview: An interactive context preserving hotspot visualization technique. Visualization and Computer Graphics, IEEE Transactions on 12, 5 (Sept 2006), 941-948. 3 – reference: Viola I., Kanitsar A., Gröller M. E: Importance-driven feature enhancement in volume visualization. Visualization and Computer Graphics, IEEE Transactions on 11, 4 (July 2005), 408-418. 3 – reference: Falk M., Krone M., Ertl T.: Atomistic visualization of mesoscopic whole-cell simulations using ray-casted instancing. Computer Graphics Forum 32, 8 (2013), 195-206. 3 – reference: Diepstraten J., Weiskopf D., Ertl T.: Interactive cutaway illustrations. Computer Graphics Forum 22, 3 (2003), 523-532. 3 – reference: Lawonn K., Glasser S., Vilanova A., Preim B., Isenberg T.: Occlusion-free blood flow animation with wall thickness visualization. Visualization and Computer Graphics, IEEE Transactions on 22, 1 (Jan 2016), 728-737. 3 – reference: Correa C., Ma K.-L.: Visibility histograms and visibilitydriven transfer functions. Visualization and Computer Graphics, IEEE Transactions on 17, 2 (Feb 2011), 192-204. 3 – reference: Feiner S., Seligmann D.: Cutaways and ghosting: satisfying visibility constraints in dynamic 3d illustrations. The Visual Computer 8, 5-6 (1992), 292-302. 3 – reference: Viola I.: Importance-Driven Expressive Visualization. PhD thesis, Institute of Computer Graphics and Algorithms, Vienna University of Technology, Favoritenstrasse 9-11/186, A-1040 Vienna, Austria, June 2005. 3 – reference: Johnson G.T., Autin L., Al-Alusi M., Goodsell D.S., Sanner M.F., Olson A.J.: cellPACK: a virtual mesoscope to model and visualize structural systems biology. Nature methods 12, 1 (Jan. 2015), 85-91. 2, 4, 7 – reference: Díaz J., Monclús E., Navazo I., Vázquez P.: Adaptive cross-sections of anatomical models. Computer Graphics Forum 31, 7 (2012), 2155-2164. 3 – reference: Le Muzic M., Parulek J., Stavrum A.-K., Viola I.: Illustrative visualization of molecular reactions using omniscient intelligence and passive agents. Computer Graphics Forum 33, 3 (2014), 141-150. 3 – reference: Baer A., Gasteiger R., Cunningham D., Preim B.: Perceptual evaluation of ghosted view techniques for the exploration of vascular structures and embedded flow. Computer Graphics Forum 30, 3 (2011), 811-820. 3 – reference: Diepstraten J., Weiskopf D., Ertl T.: Transparency in interactive technical illustrations. Computer Graphics Forum 21, 3 (2002), 317-325. 3 – reference: Ruiz M., Bardera A., Boada I., Viola I., Feixas M., Sbert M.: Automatic transfer functions based on informational divergence. Visualization and Computer Graphics, IEEE Transactions on 17, 12 (Dec 2011), 1932-1941. 3 – volume: 12 start-page: 85 issue: 1 year: 2015 end-page: 91 article-title: cellPACK: a virtual mesoscope to model and visualize structural systems biology publication-title: Nature methods – volume: 32 start-page: 195 issue: 8 year: 2013 end-page: 206 article-title: Atomistic visualization of mesoscopic whole‐cell simulations using ray‐casted instancing publication-title: Computer Graphics Forum – volume: 22 start-page: 523 issue: 3 year: 2003 end-page: 532 article-title: Interactive cutaway illustrations publication-title: Computer Graphics Forum – year: 2005 – volume: 30 start-page: 811 issue: 3 year: 2011 end-page: 820 article-title: Perceptual evaluation of ghosted view techniques for the exploration of vascular structures and embedded flow publication-title: Computer Graphics Forum – year: 2007 – volume: 21 start-page: 317 issue: 3 year: 2002 end-page: 325 article-title: Transparency in interactive technical illustrations publication-title: Computer Graphics Forum – start-page: 139 year: 2004 end-page: 146 – start-page: 69 year: 2005 end-page: 76 – volume: 22 start-page: 728 issue: 1 year: 2016 end-page: 737 article-title: Occlusion‐free blood flow animation with wall thickness visualization publication-title: Visualization and Computer Graphics, IEEE Transactions on – volume: 11 start-page: 408 issue: 4 year: 2005 end-page: 418 article-title: Importance‐driven feature enhancement in volume visualization publication-title: Visualization and Computer Graphics, IEEE Transactions on – year: 2014 – start-page: 53 year: 2012 end-page: 60 – start-page: 185 year: 2012 end-page: 192 – volume: 8 start-page: 292 issue: 5 year: 1992 end-page: 6 302 article-title: Cutaways and ghosting: satisfying visibility constraints in dynamic 3d illustrations publication-title: The Visual Computer – start-page: 154:1 year: 2008 – volume: 12 start-page: 941 issue: 5 year: 2006 end-page: 948 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| Snippet | In scientific illustrations and visualization, cutaway views are often employed as an effective technique for occlusion management in densely packed scenes. We... |
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| SubjectTerms | Algorithms Analysis Bars Categories and Subject Descriptors (according to ACM CCS) Computer graphics Education Equalizers I.3.3 [Computer Graphics]: Picture/Image Generation-Viewing algorithms Illustrations Interactive Specifications Studies Visibility Visualization |
| Title | Visibility Equalizer Cutaway Visualization of Mesoscopic Biological Models |
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