Home   >   CSC-OpenAccess Library   >    Manuscript Information
Assessment of Vascular Network Segmentation
Jack Collins, Christopher Kurcz, Curtis Lisle, Yanling Liu, Enrique Zudaire
Pages - 584 - 599     |    Revised - 31-01-2011     |    Published - 08-02-2011
Volume - 4   Issue - 6    |    Publication Date - January / February  Table of Contents
MORE INFORMATION
KEYWORDS
vessel segmentation , network comparison, quantitative analysis, segmentation quality, segmentation accuracy
ABSTRACT
We present an analysis framework to assess the quality and accuracy of vessel segmentation algorithms for three dimensional images. We generate synthetic (in silico) vessel models which act as ground truth and are constructed to embody varying morphological features. These models are transformed into images constructed under different levels of contrast, noise, and intensity. To demonstrate the use of our framework, we implemented two segmentation algorithms and compare the results to the ground truth model using several measures to quantify the accuracy and quality of segmentation. Furthermore, we collect metrics which describe the characteristics of the vessels it fails to segment. Our approach is illustrated with several examples. Funded by NCI Contract No. HHSN261200800001E.
CITED BY (3)  
1 Lang, S. (2012). The visualization of the tumor vascularization using micro computed tomography (Doctoral dissertation, University of Basel).
2 Lang, S., Müller, B., Dominietto, M. D., Cattin, P. C., Zanette, I., Weitkamp, T., & Hieber, S. E. (2012). Three-dimensional quantification of capillary networks in healthy and cancerous tissues of two mice. Microvascular research, 84(3), 314-322.
3 Almasi, S., Xu, X., Ben-Zvi, A., Lacoste, B., Gu, C., & Miller, E. L. (2015). A novel method for identifying a graph-based representation of 3-D microvascular networks from fluorescence microscopy image stacks. Medical image analysis, 20(1), 208-223.
1 Google Scholar 
2 Google Scholar 
3 CiteSeerX 
4 refSeek 
5 Socol@r  
6 Scribd 
7 WorldCat 
8 SlideShare 
9 PdfSR 
A. A. Hagberg, D. A. Schult, and P. J. Swart. “Exploring network structure, dynamics, and function usingNetworkX”. In Proceedings of the 7th Python in Science Conference, Pasadena, CA, USA, August 2008.
A. F. Frangi, R. F. Frangi, W. J. Niessen, K. L. Vincken, and M. A. Viergever. “Multiscale vesselenhancement filtering”. Medical Image Computing and Computer-Assisted Interventation, 1998.
A. N. Langville and C. D. Meyer. “Google’s PageRank and Beyond: The Science of Search Engine Rankings”.Princeton University Press, Princeton, NJ, USA, 2006.
A.Lindenmayer. “Mathematical models for cellular interactions in development i. filaments with one-sided inputs”.Journal of Theoretical Biology, 18(3):280-299, 1968.
A.Lindenmayer. “Mathematical models for cellular interactions in development ii. simple and branching filamentswith two-sided inputs”. Journal of Theoretical Biology, 18(3):300-315, 1968.
C.Kirbas and F.Quek. “A review of vessel extraction techniques and algorithms”. ACM Computing Surveys,36(2):81-121, 2004.
E. Bullitt, M. Ewend, J. Vredenburgh, A. Friedman, W. Lin, K. Wilber, D. Zeng, S. R. Aylward, and D. Reardon.“Computerized assessment of vessel morphological changes during treatment of glioblastomamultiforme: report ofa case imaged serially by MRA over four years”. Neuroimage, 47(Supplement 2):T143-151, August 2009.
F. Cassot, F. Lauwers, C. Fouard, S. Prohaska, and V. Lauwers-Cances. “A novel three-dimensional computer-assistedmethod for a quantitative study of microvascular networks of the human cerebral cortex”. Microcirculation,13:1-18, January 2006.
F. Nekka, S. Kyriacos, C. Kerrigan, and L. Cartilier. “A model of growing vascular structures”. Bulletin of Mathematical Biology, 58:409-424, May 1996.
G.Kokai, Z.Toth, and R.Vanyi. “Modelling blood vessels of the eye with parametric L-systems usingevolutionary algorithms”. In Proceedings of the Joint European Conference onArtificial Intelligence in Medicine and Medical Decision Making, Aalborg, Denmark, June 1999.
G.Rozenberg and A.Salomaa, editors. “Lindenmayer Systems: Impacts on Theoretical Computer Science,Computer Graphics, and Developmental Biology”. Springer-Verlag New York, Inc., Secaucus, NJ, USA, 2001.
H. Homann. “Implementation of a 3D thinning algorithm”. Insight Journal, 2007. http://hdl.handle.net/1926/1292.
H. Honda. “Description of the form of trees by the parameters of the tree-like body: Effects of the branching angleand the branch length on the shape of the tree-like body”. Journal of Theoretical Biology, 31(2):331-338, 1971.
J. A. Sethian. “Level Set Methods and Fast Marching Methods”. Cambridge University Press, 1999.
J. D. Hunter. “Matplotlib: A 2d graphics environment”. Computing in Science and Engineering, 9(3):90-95, 2007.
J. R. Ullmann. “An algorithm for subgraph isomorphism”. Journal of ACM, 23(1):31-42, January 1976.
K.Krissian, G.Malandain, N.Ayache, R.Vaillant, and Y.Trousset. “Model-based detection oftubular structures in 3d images”. Computer Vision and Image Understanding, 80(2):130-171, 2000.
L. Antiga, M. Piccinelli, L. Botti, B. Ene-Iordache, A. Remuzzi, and D. A. Steinman. “An image-based modeling framework for patient-specific computational hemodynamics”. Medical & Biological Engineering & Computing, 46:1097-1112, November 2008.
L. Ibanez, W. Schroeder, L. Ng, and J. Cates. “The ITK Software Guide”. Kitware, Inc., 2005.
M. A. Chaplain, S. R. McDougall, and A. R. Anderson. “Mathematical modeling of tumor-induced angiogenesis”.Annual Review of Biomedical Engineering, 8:233-257, 2006. D. Conte, P. Foggia, C.Sansone, and M. Vento. “Thirty years of graph matching in patternrecognition”. International Journal of Pattern Recognition and Artificial Intelligence, 18(3):265-298.
M. Schaap, C. T. Metz, T. van Walsum, A. G. van der Giessen, A. C. Weustink, N. R. Mollet, C. Bauer, H. Bogunovi,C. Castro, X. Deng, E. Dikici, T. O’Donnell, M. Frenay, O. Friman, M. Hernandez Hoyos, P. H. Kitslaar, K. Krissian,C. Kuhnel, M. A. Luengo-Oroz, M. Orkisz, O. Smedby, M. Styner, A. Szymczak, H. Tek, C. Wang, S. K. Warfield,S. Zambal, Y. Zhang, G. P. Krestin, and W. J. Niessen. “Standardized evaluation methodology and reference databasefor evaluating coronary artery centerline extraction algorithms”. Medical Image Analysis, 13(5):701-714, October 2009.
M. Sofka and C. V. Stewart. “Retinal vessel centerline extraction using multiscale matched filters, confidence andedge measures”. IEEE Transactions on Medical Imaging, 25(12):1531–1546, Dec 2006.
N.J.Tustison, M.Siqueira, and J.C.Gee.“N-D Linear Time Exact Signed Euclidean Distance Transform”. InsightJournal, 2006. http://hdl.handle.net/1926/171.
P. J. Yim, P. L. Choyke, and R. M. Summers. “Gray-scale skeletonization of small vessels in magnetic resonanceangiography”. IEEE Transactions on Medical Imaging, 19(6):568–576, June 2000.
P.Ramachandran. “MayaVi: A free tool for CFD data visualization”. 4th Annual CFD Symposium, AeronauticalSociety of India, 2001.
R. M. Cesar, Jr., E.Bengoetxea, I. Bloch, and P.Larrañaga. “Inexact graph matching for modelbasedrecognition: Evaluation and comparison of optimization algorithms”. Pattern Recognition, 38(11):2099-2113,2005.
R. Singh, J. Xu, and B. Berger. “Global alignment of multiple protein interaction networks with application to functionalorthology detection”. In Proceedings of the National Academy of Sciences of the United States of America. 105(35):12763-12768, September 2008.
S. Luo and Y. Zhong. “Extraction of brain vessels from magnetic resonance angiographic images: concise literaturereview, challenges, and proposals”. In Proceedings of IEEE Engineering in Medicine and Biology Society, 2:1422-1425, 2005.
S. Worz and K. Rohr. “Segmentation and quantification of human vessels using a 3-D cylindrical intensity model”.IEEE Transactionson Image Processing, 16(8):1994-2004, Aug 2007.
S.Thoreson. “An efficient solution to inexact graph matching with application to computer vision”. PhD thesis,Norwegian University of Science and Technology, 2007.
W.Palubicki, K.Horel, S.Longay, A.Runions, B. Lane, R.M?ch, and P. Prusinkiewicz. “Self-organizing tree models for image synthesis”. In Proceedings of ACM SIGGRAPH 2009, New York, NY, USA, 2009.
X. Qian, M. P. Brennan, D. P. Dione, W. L. Dobrucki, M. P. Jackowski, C. K. Breuer, A. J. Sinusas, and X. Papademetris.“A non-parametric vessel detection method for complex vascular structures”. Medical Image Analysis, 13(1):49–61, February 2009.
Y. Sato, S. Nakajima, N. Shiraga, H. Atsumi, S. Yoshida, T. Koller, G. Gerig, and R. Kikinis. “Three-dimensionalmulti-scale line filter for segmentation and visualization of curvilinear structures in medical images”. Medical Image Analysis, 2(2):143-168, 1998.
Dr. Jack Collins
- United States of America
Dr. Christopher Kurcz
SAIC-Frederick - United States of America
chris.kurcz@gmail.com
Dr. Curtis Lisle
- United States of America
Dr. Yanling Liu
- United States of America
Dr. Enrique Zudaire
- United States of America