Abstract
We present an interactive approach for identifying skeletons (i.e. centerlines) in intensity volumes, such as those produced by biomedical imaging. While skeletons are very useful for a range of image analysis tasks, it is extremely difficult to obtain skeletons with correct connectivity and shape from noisy inputs using automatic skeletonization methods. In this paper we explore how easy-to-supply user inputs, such as simple mouse clicking and scribbling, can guide the creation of satisfactory skeletons. Our contributions include formulating the task of drawing 3D centerlines given 2D user inputs as a constrained optimization problem, solving this problem on a discrete graph using a shortest-path algorithm, building a graphical interface for interactive skeletonization and testing it on a range of biomedical data.
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Abeysinghe, S.S., Baker, M., Chiu, W., Ju, T.: Segmentation-free skeletonization of grayscale volumes for shape understanding. In: Shape Modeling and Applications. IEEE International Conference on SMI 2008, pp. 63–71 (2008)
Abeysinghe, S.S., Coleman, R., Marsh, M., Ruths, T., Baker, M., Chiu, W., Ju, T.: Gorgon—an interactive molecular modeling system. http://www.cs.wustl.edu/~ssa1/gorgon/
Armstrong, C.J., Price, B.L., Barrett, W.A.: Interactive segmentation of image volumes with live surface. Comput. Graph. 31(2), 212–229 (2007)
Barrett, W.A., Mortensen, E.N.: Interactive live-wire boundary extraction. Med. Image Anal. 1(4), 331–341 (1997)
Boykov, Y., Funka-Lea, G.: Graph cuts and efficient n–d image segmentation. Int. J. Comput. Vis. 70(2), 109–131 (2006)
Chiu, W., Baker, M., Jiang, W., Dougherty, M., Schmid, M.: Electron cryomicroscopy of biological machines at subnanometer resolution. Structure (Camb.) 13, 363–372 (2005)
Cohen, L.D., Kimmel, R.: Global minimum for active contour models: A minimal path approach. Int. J. Comput. Vis. 24(1), 57–78 (1997)
Cornea, N.D., Min, P.: Curve-skeleton properties, applications, and algorithms. IEEE Trans. Vis. Comput. Graph. 13(3), 530–548 (2007)
Deschamps, T., Cohen, L.D.: Minimal paths in 3d images and application to virtual endoscopy. In: ECCV ’00: Proceedings of the 6th European Conference on Computer Vision—Part II, pp. 543–557. Springer, London (2000)
Eberly, D., Gardner, R., Morse, B., Pizer, S., Scharlach, C.: Ridges for image analysis. J. Math. Imaging Vis. 4(4), 353–373 (1994)
Falcao, A., Udupa, J., Miyazawa, F.: An ultra-fast user-steered image segmentation paradigm: live wire on the fly. IEEE Trans. Med. Imaging 19(1), 55–62 (2000)
Furst, J.D., Pizer, S.M., Eberly, D.H.: Marching cores: A method for extracting cores from 3d medical images. In: MMBIA ’96: Proceedings of the 1996 Workshop on Mathematical Methods in Biomedical Image Analysis (MMBIA ’96), p. 124. IEEE Computer Society, Washington (1996)
Jiang, W., Baker, M.L., Jakana, J., Weigele, P.R., King, J., Chiu, W.: Backbone structure of the infectious 15 virus capsid revealed by electron cryomicroscopy. Nature 451, 1130–1134 (2008)
Ju, T., Baker, M., Chiu, W.: Computing a family of skeletons of volumetric models for shape description. Comput. Aided Des. 39(5), 352–360 (2007)
Krissian, K., Malandain, G., Ayache, N., Vaillant, R., Trousset, Y.: Model-based detection of tubular structures in 3d images. Comput. Vis. Image Underst. 80(2), 130–171 (2000)
Krissian, K., Vaillant, R., Trousset, Y., Malandain, G., Ayache., N.: Automatic and accurate measurement of a cross-sectional area of vessels in 3d x-ray angiography images. In: Proc. of SPIE 2000 (2000)
Krissian, K., Kikinis, R., Westin, C.F.: Algorithms for extracting vessel centerlines. Tech. Rep. 0003, Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Laboratory of Mathematics in Imaging (2004)
Metz, C.T., Schaap, M., van Walsum, T., van der Giessen, A., Weustink, A., Mollet, N., Krestin, G., Niessen, W.: 2008 MICCAI workshop: 3d segmentation in the clinic: A grand challenge II—coronary artery tracking. http://hdl.handle.net/10380/1399
Mortensen, E.N., Barrett, W.A.: Intelligent scissors for image composition. In: SIGGRAPH ’95: Proceedings of the 22nd Annual Conference on Computer Graphics and Interactive Techniques, pp. 191–198. ACM, New York (1995)
Nathan, A., Lee, S.L., Marquez, J., Ju, T., Pryse, K., Elson, E., Genin, G.M.: Active and passive responses of myofibroblasts in response to mechanical stretching in 3d culture. In: Proceedings of the ASME 2008 Summer Bioengineering Conference (SBC2008) (2008)
Poon, M., Hamarneh, G., Abugharbieh, R.: Efficient interactive 3d livewire segmentation of complex objects with arbitrary topology. Comput. Med. Imaging Graph. 32(8), 639–650 (2008)
Reniers, D., van Wijk, J., Telea, A.: Computing multiscale curve and surface skeletons of genus 0 shapes using a global importance measure. IEEE Trans. Vis. Comput. Graph. 14(2), 355–368 (2008)
Selle, D., Preim, B., Schenk, A., Peitgen, H.: Analysis of vasculature for liver surgical planning. IEEE Trans. Med. Imaging 21(11), 1344–1357 (2002)
Siddiqi, K., Pizer, S. (eds.): Medial Representations: Mathematics, Algorithms and Applications. Springer, Berlin (2008)
Weickert, J.: Anisotropic Diffusion in Image Processing. Teubner, Leipzig (1998)
Whitaker, R.T., Breen, D.E., Museth, K., Soni, N.: A framework for level set segmentation of volume datasets. In: Volume Graphics (2001)
Wong, C.J., Rice, R.L., Baker, N.A., Ju, T., Lohman, T.M.: Probing 3′-ssdna loop formation in E. coli recbcd/recbc-dna complexes using non-natural DNA: A model for “chi” recognition complexes. J. Mol. Biol. 362(1), 26–43 (2006)
Yim, P., Choyke, P., Summers, R.: Gray-scale skeletonization of small vessels in magnetic resonance angiography. IEEE Trans. Med. Imaging 19(6), 568–576 (2000)
Yu, Z., Bajaj, C.: A structure tensor approach for 3d image skeletonization: Applications in protein secondary structure analysis. Image Processing, 2006 IEEE International Conference, pp. 2513–2516 (8–11 Oct. 2006)
Yushkevich, P., Piven, J., Hazlett, H., Smith, R., Ho, S., Gee, J.: User-guided 3d active contour segmentation of anatomical structures: significantly improved efficiency and reliability. NeuroImage 31, 1116–1128 (2006)
Zhang, H., Maslov, K., Stoica, G., Wang, L.: Functional photoacoustic microscopy for high-resolution and noninvasive in vivo imaging. Nat. Biotechnol. 24, 848–851 (2006)
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Abeysinghe, S.S., Ju, T. Interactive skeletonization of intensity volumes. Vis Comput 25, 627–635 (2009). https://doi.org/10.1007/s00371-009-0325-5
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DOI: https://doi.org/10.1007/s00371-009-0325-5