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Visualization of Fibrous and Thread-like Data
September-October 2006 (vol. 12 no. 5)
pp. 1165-1172
Thread-like structures are becoming more common in modern volumetric data sets as our ability to image vascular and neural tissue at higher resolutions improves. The thread-like structures of neurons and micro-vessels pose a unique problem in visualization since they tend to be densely packed in small volumes of tissue. This makes it difficult for an observer to interpret useful patterns from the data or trace individual fibers. In this paper we describe several methods for dealing with large amounts of thread-like data, such as data sets collected using Knife-Edge Scanning Microscopy (KESM) and Serial Block-Face Scanning Electron Microscopy (SBF-SEM). These methods allow us to collect volumetric data from embedded samples of whole-brain tissue. The neuronal and microvascular data that we acquire consists of thin, branching structures extending over very large regions. Traditional visualization schemes are not sufficient to make sense of the large, dense, complex structures encountered. In this paper, we address three methods to allow a user to explore a fiber network effectively. We describe interactive techniques for rendering large sets of neurons using self-orienting surfaces implemented on the GPU. We also present techniques for rendering fiber networks in a way that provides useful information about flow and orientation. Third, a global illumination framework is used to create high-quality visualizations that emphasize the underlying fiber structure. Implementation details, performance, and advantages and disadvantages of each approach are discussed.
[1] 1165 K. Al-Kofahi, S. Lasek, D. Szarowski, C. Pace, G. Nagy, J. Turner, and B. Roysam, Rapid automated three-dimensional tracing of neurons from confocal image stacks. IEEE Transactions on Information Technology in Biomedicine, 6 (2): 171–186, June 2002.[2] H. Axer, G. Berks, and D. G. V. Keyserlingk, Visualization of nerve fiber orientation in gross histological sections of the human brain. Microscopy Research and Technique, 51 (5): 481–492, 2000.[3] A. Can, H. Shen, J. N. Turner, H. L. Tanenbaum, and B. Roysam, Rapid automated tracing and feature extraction from retinal fundus images using direct exploratory algorithms. IEEE Transactions on Information Technology in Biomedicine, 3 (2): 125–138, June 1999.[4] C. De Boor, A Practical Guide to Splines. Springer, 1978. de Boor.[5] W. Denk and H. Horstmann, Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure. PLoS Biology, 2 (11): e329, Nov. 2004.[6] P. Doddapaneni, Segmentation strategies for polymerized volume data sets. Master's thesis, Department of Computer Science, Texas A&M University, 2004.[7] G. E. Farin, Curves and Surfaces for CAGD: A Practical Guide. Morgan Kaufmann Publishers, San Franscisco, CA, USA, 5th edition, 2002.[8] J. T. Kajiya and T. L. Kay, Rendering fur with three dimensional textures. In SIGGRAPH '89: Proceedings of the 16th annual conference on Computer graphics and interactive techniques, pages 271–280, New York, NY, USA, 1989. ACM Press.[9] T.-Y. Kim and U. Neumann, Opacity shadow maps. In Proceedings of the 12th Eurographics Workshop on Rendering Techniques, pages 177–182, London, UK, 2001. Springer-Verlag.[10] P. Kondratieva, J. Krüger, and R. Westermann, The application of gpu particle tracing to diffusion tensor field visualization. In IEEE Visualization, page 10, 2005.[11] S. R. Marschner, H. W. Jensen, M. Cammarano, S. Worley, and P. Hanrahan, Light scattering from human hair fibers. ACM Trans. Graph., 22 (3): 780–791, 2003.[12] B. McCormick, Development of the brain tissue scanner. Technical Report 18, Department of Computer Science, Texas A&M University, College Station, TX, Mar. 2002.[13] B. McCormick, B. Busse, P. Doddapaneni, Z. Melek, and J. Keyser, Compression, segmentation, and modeling of filamentary volumetric data. In Proceedings of Symposium on Solid Modeling and Applications '04, pages 333–338, 2004.[14] NVIDIA. CG Toolkit User's Manual 1.2, January 2004.[15] C. Rössl, F. Zeilfelder, G. Nürnberger, and H.-P. Seidel, Visualization of volume data with quadratic super splines. In IEEE Visualization, pages 393–400, 2003.[16] G. Schussman and K.-L. Ma, Scalable self-orienting surfaces: A compact, texture-enhanced representation for interactive visualization of 3d vector fields. pages 1–10. IEEE, Oct. 2002.[17] C. Stoll, S. Gumhold, and H.-P. Seidel, Visualization with stylized line primitives. In IEEE Visualization, page 88, 2005.
Index Terms:
neuron visualization, GPU acceleration, global illumination, orientation filtering
Citation:
Zeki Melek, David Mayerich, Cem Yuksel, John Keyser, "Visualization of Fibrous and Thread-like Data," IEEE Transactions on Visualization and Computer Graphics, vol. 12, no. 5, pp. 1165-1172, Sept. 2006, doi:10.1109/TVCG.2006.197
