Continuous levels-of-detail and visual abstraction for seamless molecular visualization

Computer Graphics Forum

Volumn 33, Issue 6, 2014, Pages 276-287

  Parulek, Julius ^a   Jönsson, Daniel ^b   Ropinski, Timo ^b   Bruckner, Stefan ^a   Ynnerman, Anders ^b   Viola, Ivan ^a,c  

^a UNIVERSITY OF BERGEN   (Norway)

^b LINKÖPING UNIVERSITY   (Sweden)

^c VIENNA UNIVERSITY OF TECHNOLOGY   (Austria)

Author keywords

clustering; implicit surfaces; level of detail algorithms; scientific visualization

Indexed keywords

ABSTRACTING; ATOMS; DATA VISUALIZATION; INTERPOLATION; MOLECULAR STRUCTURE; MOLECULES; PROTEINS; SPHERES; VAN DER WAALS FORCES; VISUALIZATION;

CLUSTERING; IMPLICIT SURFACES; IMPORTANCE FUNCTIONS; LEVEL OF DETAIL; LINEAR INTERPOLATION; MOLECULAR VISUALIZATION; RENDERING PERFORMANCE; SEAMLESS TRANSITION;

RENDERING (COMPUTER GRAPHICS);

EID: 84908504480     PISSN: 01677055     EISSN: 14678659     Source Type: Journal    
DOI: 10.1111/cgf.12349     Document Type: Article

References (43)

1. [And06], Andrews B.,: Introduction to 'perceptual principles in medical illustration '. In ACM SIGGRAPH 2006 Courses (New York, NY, USA, 2006), SIGGRAPH '06, ACM.
2. [BDST04], Bajaj C., Djeu P., Siddavanahalli V., Thane A.,: Texmol: Interactive visual exploration of large flexible multi-component molecular complexes. In Proceedings of IEEE Visualization 2004 (Austin, TX, USA, 2004), pp. 243-250.
3. [BHH13], Bittner J., Hapala M., Havran V.,: Fast insertion-based optimization of bounding volume hierarchies. Computer Graphics Forum 32, 1 (2013), 85-100.
4. [Bli82], Blinn J.,: A generalization of algebraic surface drawing. ACM Transactions on Graphics 1 (1982), 235-256.
5. [Car84], Carpenter L.,: The a -buffer, an antialiased hidden surface method. SIGGRAPH Computer Graphics 18, 3 (January 1984), 103-108.
6. [CG07], Cipriano G., Gleicher M.,: Molecular surface abstraction. IEEE Transactions on Visualization and Computer Graphics 13, 6 (2007), 1608-1615.
7. [DG11], Dias S. E., Gomes A. J.,: Graphics processing unit-based triangulations of blinn molecular surfaces. Concurrency and Computation: Practice and Experience 23, 17 (2011), 2280-2291.
8. [DVRH07], Daae Lampe O., Viola I., Reuter N., Hauser H.,: Two-level approach to efficient visualization of protein dynamics. IEEE Transactions on Visualization and Computer Graphics 13, 6 (2007), 1616-1623.
9. [FAW10], Fraedrich R., Auer S., Westermann R.,: Efficient high-quality volume rendering of SPH data. IEEE Transactions on Visualization and Computer Graphics 16, 6 (2010), 1533-1540.
10. [FD07], Frey B. J., Dueck D.,: Clustering by passing messages between data points. Science 315 (2007), 972-976.
11. [FKE12], Falk M., Krone M., Ertl T.,: Atomistic visualization of mesoscopic whole-cell simulations. In EG Workshop on Visual Computing for Biology and Medicine (Norrköping, Sweden, 2012).
12. [FSG 11], Frey S., Schlomer T., Grottel S., Dachsbacher C., Deussen O., Ertl T.,: Loose capacity-constrained representatives for the qualitative visual analysis in molecular dynamics. In IEEE Pacific Visualization Symposium (Hong Kong, China, 2011), pp. 51-58.
13. [Goo09], Goodsell D.,: The Machinery of Life. Springer, New York, 2009.
14. [GP95], Grant J. A., Pickup B. T.,: A Gaussian description of molecular shape. The Journal of Physical Chemistry 99, 11 (March 1995), 3503-3510.
15. [GRDE10], Grottel S., Reina G., Dachsbacher C., Ertl T.,: Coherent culling and shading for large molecular dynamics visualization. Computer Graphics Forum 29, 3 (2010), 953-962.
16. [Har94], Hart J. C.,: Sphere tracing: A geometric method for the antialiased ray tracing of implicit surfaces. The Visual Computer 12 (1994), 527-545.
17. [KBE09], Krone M., Bidmon K., Ertl T.,: Interactive visualization of molecular surface dynamics. IEEE Transactions on Visualization and Computer Graphics 15, 6 (2009), 1391-1398.
18. [KFR11], Krone M., Falk M., Rehm S.,: Interactive exploration of protein cavities. Computer Graphics Forum 30, 3 (2011), 673-682.
19. [KOK06], Kanai T., Ohtake Y., Kase K.,: Hierarchical error-driven approximation of implicit surfaces from polygonal meshes. In Proceedings of the Eurographics Symposium on Geometry Processing 2006 (Sardinia, Italy, 2006), pp. 21-30.
20. [KSES12], Krone M., Stone J., Ertl T., Schulten K.,: Fast visualization of Gaussian density surfaces for molecular dynamics and particle system trajectories. In Proceedings of EuroVis 2012 Short Papers (Vienna, Austria, 2012), pp. 67-71.
21. [KSW06], Kruger J., Schneider J., Westermann R.,: Clearview: An interactive context preserving hotspot visualization technique. IEEE Transactions on Visualization and Computer Graphics 12, 5 (September-October 2006), 941-948.
22. [KWTM03], Kindlmann G., Whitaker R., Tasdizen T., Moller T.,: Curvature-based transfer functions for direct volume rendering: Methods and applications. In Proceedings of the 14th IEEE Visualization 2003 (VIS'03) (Washington, DC, USA, 2003), VIS '03, IEEE Computer Society.
23. [LBPH10], Lindow N., Baum D., Prohaska S., Hege H.-C.,: Accelerated visualization of dynamic molecular surfaces. Computer Graphics Forum 29, 3 (2010), 943-952.
24. [LCD06], Luft T., Colditz C., Deussen O.,: Image enhancement by unsharp masking the depth buffer. ACM Transactions on Graphics 25, 3 (July 2006), 1206-1213.
25. [Llo82], Lloyd S.,: Least squares quantization in PCM. IEEE Transactions on Information Theory 28, 2 (1982), 129-137.
26. [LPK06], Lee J., Park S., Kim J.-I.,: View-dependent rendering of large-scale molecular models using level of detail. In Proceedings of the International Conference on Hybrid Information Technology 2006 (Cheju Island, Korea, 2006), pp. 691-698.
27. [LVvdZ 11], Lueks W., Viola I., van der Zwan M., Bekker H., Isenberg T.,: Spatially continuous change of abstraction in molecular visualization. In Abstracts of 1st IEEE Symposium on Biological Data Visualization (BioVis 2011, Providence, RI, USA, 2011), M. Meyer, and, C. Nielsen, (Eds.), IEEE Computer Society.
28. [LWC 02], Luebke D., Watson B., Cohen J. D., Reddy M., Varshney A.,: Level of Detail for 3D Graphics. Elsevier Science Inc., New York, NY, 2002.
29. [Mül13], Müllner D.,: fastcluster: Fast hierarchical, agglomerative clustering routines for r and python. Journal of Statistical Software 53, 9 (5 2013), 1-18.
30. [PB13], Parulek J., Brambilla A.,: Fast blending scheme for molecular surface representation. IEEE Transactions on Visualization and Computer Graphics 19 (December 2013), 2653-2662.
31. [PRV13], Parulek J., Ropinski T., Viola I.,: Seamless abstraction of molecular surfaces. In Proceedings of the 29th Spring Conference on Computer Graphics (Comenius University, Bratislava, Slovakia, 2013), pp. 120-127.
32. [PV12], Parulek J., Viola I.,: Implicit representation of molecular surfaces. In Proceedings of the IEEE Pacific Visualization Symposium (PacificVis 2012) (Songdo, Korea, March 2012), pp. 217-224.
33. [Ric72], Ricci A.,: A constructive geometry for computer graphics. The Computer Journal 16, 2 (1972), 157-160.
34. [Ric77], Richards F. M.,: Areas, volumes, packing, and protein structure. Annual Review of Biophysics and Bioengineering 6, 1 (1977), 151-176.
35. [SBG00], Sprenger T. C., Brunella R., Gross M.,: H-blob: A hierarchical visual clustering method using implicit surfaces. In Proceedings of IEEE Visualization 2000 (Salt Lake City, Utah, USA, 2000), pp. 61-68.
36. [SI12], Szecsi L., Illes D.,: Real-Time Metaball Ray Casting with Fragment Lists (2012)., C Andujar, and, E Puppo, (Eds.), Eurographics Association, Cagliari, Sardinia, Italy, pp. 93-96.
37. [SKNV04], Sharma A., Kalia R. K., Nakano A., Vashishta P.,: Scalable and portable visualization of large atomistic datasets. Computer Physics Communications 163, 1 (2004), 53-64.
38. [SP98], Savchenko V., Pasko A.,: Transformation of functionally defined shapes by extended space mappings. The Visual Computer 14, 5-6 (1998), 257-270.
39. [TCM06], Tarini M., Cignoni P., Montani C.,: Ambient occlusion and edge cueing for enhancing real time molecular visualization. IEEE Transactions on Visualization and Computer Graphics 12, 5 (2006), 1237-1244.
40. [TO99], Turk G., O'Brien J. F.,: Shape transformation using variational implicit functions. Computer Graphics 33, Annual Conference Series (1999), 335-342.
41. [VBW94], Varshney A., Brooks Jr, F. P., Wright W. V.,: Computing smooth molecular surfaces. IEEE Computer Graphics Applications 14 (September 1994), 19-25.
42. [vdZLBI11], van der Zwan M., Lueks W., Bekker H., Isenberg T.,: Illustrative molecular visualization with continuous abstraction. Computer Graphics Forum 30, 3 (2011), 683-690.
43. [Web09], Weber J. R.,: ProteinShader: Illustrative rendering of macromolecules. BMC Structural Biology 9, 1 (2009), 1-19.