| | This Article | |
| |
| |
| | Share | |
| |
| |
| | Bibliographic References | |
| |
| |
| | Add to: | |
| |
 Digg
 Furl
 Spurl
 Blink
 Simpy
 Google
 Del.icio.us
 Y!MyWeb
| |
| | Search | |
| |
| |
| | |
Visualization of Cellular and Microvascular Relationships
November/December 2008 (vol. 14 no. 6)
pp. 1611-1618
Understanding the structure of microvasculature structures and their relationship to cells in biological tissue is an important and complex problem. Brain microvasculature in particular is known to play an important role in chronic diseases. However, these networks are only visible at the microscopic level and can span large volumes of tissue. Due to recent advances in microscopy, large volumes of data can be imaged at the resolution necessary to reconstruct these structures. Due to the dense and complex nature of microscopy data sets, it is important to limit the amount of information displayed. In this paper, we describe methods for encoding the unique structure of microvascular data, allowing researchers to selectively explore microvascular anatomy. We also identify the queries most useful to researchers studying microvascular and cellular relationships. By associating cellular structures with our microvascular framework, we allow researchers to explore interesting anatomical relationships in dense and complex data sets.
[1] 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: 171–186, 2002.
[2] F. Aurenhammer, Voronoi diagrams: A survey of a fundamental geometric data structure. ACM Computing Surveys (CSUR), 23: 345–405, 1991.
[3] G. D. Battista, P. Eades, R. Tamassia, and I. G. Tollis, Graph Drawing: Algorithms for the Visualization of Graphs. Prentice Hall PTR Upper Saddle River, NJ, USA, 1998.
[4] J. Bloomenthal and K. Shoemake, Convolution surfaces. Proceedings of the 18th Annual Conference on Computer Graphics and Interactive Techniques, pages 251–256, 1991.
[5] J. A. Bondy and U. S. R. Murty, Graph Theory with Applications. Elsevier Science Ltd., 1976.
[6] J. Bresenham, Algorithm for computer control of a digital plotter. IBM Systems Journal, 4: 25–30, 1965.
[7] A. D'Souza, Automated Counting of Cell Bodies Using Nissl Stained Cross-Sectional Images. Master's thesis, Texas A&M University, 2007.
[8] G. Gerig, T. Roller, G. Szekely, C. Brechbuhler, and O. Kubler, Symbolic description of 3-D structures applied to cerebral vessel tree obtained from MR angiography volume data, volume 687 of Lecture Notes in Computer Science, pages 94–111. Springer Berlin, 1993.
[9] K. E. Hoff III, T. Culver, J. Keyser, M. Lin, and D. Manocha, Fast computation of generalized voronoi diagrams using graphics hardware. In Proceedings of the 26th Annual Conference on Computer Graphics and Interactive Techniques, pages 277–286, 1999.
[10] C. Kirbas and F. Quek, A review of vessel extraction techniques and algorithms. ACM Computing Surveys, 36: 81–121, 2004.
[11] G. Li, T. Liu, J. Nie, L. Guo, J. Chen, J. Zhu, W. Xia, A. Mara, S. Holley, and S. Wong, Segmentation of touching cell nuclei using gradient flow tracking. Journal of Microscopy, 231: 47–58, 2008.
[12] W. E. Lorensen and H. E. Cline, Marching cubes: A high resolution 3d surface construction algorithm. In Proceedings of the 14th Annual Conference on Computer Graphics and Interactive Techniques, pages 163–169, 1987.
[13] Y. Masutani, T. Schiemann, and K. H. Hohne, Vascular shape segmentation and structure extraction using a shape-based region-growing model. Proceedings of the 1st International Conference on Medical Image Computing and Computer-Assisted Intervention, pages 1242–1249, 1998.
[14] D. Mayerich, L. C. Abbott, and B. H. McCormick, Knife-edge scanning microscopy for imaging and reconstruction of three-dimensional anatomical structures of the mouse brain. Journal of Microscopy, 231: 134–143, June 2008.
[15] D. Mayerich and J. Keyser, Filament tracking and encoding for complex biological networks. Proceedings of the ACM Solid and Physical Modeling Symposium, pages 353–358, 2008.
[16] D. Mayerich, B. H. McCormick, and J. Keyser, Noise and artifact removal in knife-edge scanning microscopy. Proceedings of the 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, pages 556–559, 2007.
[17] A. Mazziotti, A. Cavallari, and J. Belghiti, Techniques in Liver Surgery. Greenwich Medical Media, 1997.
[18] B. McCormick, B. Busse, P. Doddapaneni, Z. Melek, and J. Keyser, Compression, segmentation, and modeling of filamentary volumetric data. In Proceedings of the 9th ACM Symposium on Solid Modeling and Applications, pages 333–338, 2004.
[19] D. P. Mccullough, P. R. Gudla, K. Meaburn, A. Kumar, M. Kuehn, and S. J. Lockett, 3d segmentation of whole cells and cell nuclei in tissue using dynamic programming. Proceedings of the 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, pages 276–279, 2007.
[20] Z. Melek, D. M. Mayerich, C. Yuksel, and J. Keyser, Visualization of fibrous and thread-like data. IEEE Transactions on Visualization and Computer Graphics, 12: 1165–1172, 2006.
[21] K. D. Micheva and S. J. Smith, Array tomography: A new tool for imaging the molecular architecture and ultrastructure of neural circuits. Neuron, 55: 25–36, 2007.
[22] Nielsen and Museth, Dynamic tubular grid: An efficient data structure and algorithms for high resolution level sets. Journal of Scientific Computing, 26: 261–299, 2006.
[23] N. Niki, Y. Kawata, H. Satoh, and T. Kumazaki, 3d imaging of blood vessels using x-ray rotational angiographic system. In IEEE Nuclear Science Symposium and Medical Imaging Conference, volume 3, pages 1873–1877.
[24] A. Okabe, B. Boots, and K. Sugihara, Spatial Tessellations: Concepts and Applications of Voronoi Diagrams. John Wiley & Sons, Inc. New York, NY, USA, 1992.
[25] S. J. Osher and R. P. Fedkiw, Level Set Methods and Dynamic Implicit Surfaces. Springer, 2002.
[26] V. Petrovic, J. Fallon, and F. Kuester, Visualizing whole-brain dti tractography with gpu-based tuboids and lod management. Transactions on Visualization and Computer Graphics, 13: 1488–1495, 2007.
[27] A. Pommert, K. H. Hohne, B. Pflesser, E. Richter, M. Riemer, T. Schiemann, R. Schubert, U. Schumacher, and U. Tiede, Creating a high-resolution spatial/symbolic model of the inner organs based on the visible human. Medical Image Analysis, 5: 221–228, 2001.
[28] A. Puig, D. Tost, and I. Navazo, An interactive cerebral blood vessel exploration system. Proceedings of the 8th Conference on Visualization '97, pages 433–436, 1997.
[29] Y. Sato, S. Nakajima, N. Shiraga, H. Atsumi, S. Yoshida, T. Koller, G. Gerig, and R. Kikinis, Three-dimensional multi-scale line filter for segmentation and visualization of curvilinear structures in medical images. Medical Image Analysis, 2: 143–168, 1998.
[30] P. Schroder and G. Stoll, Data parallel volume rendering as line drawing. In Proceedings of the 1992 Workshop on Volume Visualization, pages 25–32, 1992.
[31] J. A. Sethian, Level Set Methods and Fast Marching Methods: Evolving Interfaces in Computational Geometry, Fluid Mechanics, Computer Vision, and Materials Science. Cambridge University Press, 1999.
[32] C. Stoll, S. Gumhold, and H.-P. Seidel, Visualization with stylized line primitives. In Proceedings of the 16th Conference on Visualization 2005, pages 695–702, 2005.
[33] T. Tozaki, Y. Kawata, N. Niki, H. Ohmatsu, K. Eguchi, and N. Moriyama, Three-dimensional analysis of lung areas using thin slice ct images. In Proceedings of SPIE, volume 2709, pages 1–11, 1996.
[34] H. Zhao, A fast sweeping method for eikonal equations. Mathematics of Computation, 74: 603–627, 2004.
[35] B. Zlokovic, The blood-brain barrier in health and chronic neurodegenerative disorders. Neuron, 57: 178–201, 2008.
Index Terms:
Index Terms—vascular, microscopy, fibers, cells, complex data
Citation:
David Mayerich, Louise Abbott, John Keyser, "Visualization of Cellular and Microvascular Relationships," IEEE Transactions on Visualization and Computer Graphics, vol. 14, no. 6, pp. 1611-1618, Nov./Dec. 2008, doi:10.1109/TVCG.2008.179
