Abstract
Reconstructing vascular networks is a challenging task in medical image processing as automated methods have to deal with large variations in vessel shape and image quality. Recent methods have addressed this problem as constrained maximum a posteriori (MAP) inference in a graphical model, formulated over an overcomplete network graph. Manual control and adjustments are often desired in practice and strongly benefit from indicating the uncertainties in the reconstruction or presenting alternative solutions. In this paper, we examine two different methods to sample vessel network graphs, a perturbation and a Gibbs sampler, and thereby estimate marginals. We quantitatively validate the accuracy of the approximated marginals using true marginals, computed by enumeration.
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References
Lesage, D., Angelini, E., Bloch, I., Funka-Lea, G.: A review of 3D vessel lumen segmentation techniques: Models, features and extraction schemes. Med. Image Anal. 13(6), 819–845 (2009)
Türetken, E., Benmansour, F., Andres, B., Glowacki, P., Pfister, H., Fua, P.: Reconstructing curvilinear networks using path classifiers and integer programming. IEEE Trans. Pattern Anal. Mach. Intell. 38(12), 2515–2530 (2016)
Rempfler, M., Schneider, M., Ielacqua, G.D., Xiao, X., Stock, S.R., Klohs, J., Székely, G., Andres, B., Menze, B.H.: Reconstructing cerebrovascular networks under local physiological constraints by integer programming. Med. Image Anal. 25(1), 86–94 (2015)
Rempfler, M., Andres, B., Menze, B.H.: The minimum cost connected subgraph problem in medical image analysis. In: Ourselin, S., Joskowicz, L., Sabuncu, M.R., Unal, G., Wells, W. (eds.) MICCAI 2016. LNCS, vol. 9902, pp. 397–405. Springer, Cham (2016). doi:10.1007/978-3-319-46726-9_46
Payer, C., Pienn, M., Blint, Z., Shekhovtsov, A., Talakic, E., Nagy, E., Olschewski, A., Olschewski, H., Urschler, M.: Automated integer programming based separation of arteries and veins from thoracic CT images. Med. Image Anal. 34, 109–122 (2016)
Robben, D., Türetken, E., Sunaert, S., Thijs, V., Wilms, G., Fua, P., Maes, F., Suetens, P.: Simultaneous segmentation and anatomical labeling of the cerebral vasculature. Med. Image Anal. 32, 201–215 (2016)
Klohs, J., Baltes, C., Princz-Kranz, F., Ratering, D., Nitsch, R.M., Knuesel, I., Rudin, M.: Contrast-enhanced magnetic resonance microangiography reveals remodeling of the cerebral microvasculature in transgenic arca\(\beta \) mice. J. Neurosci. 32(5), 1705–1713 (2012)
Batra, D., Yadollahpour, P., Guzman-Rivera, A., Shakhnarovich, G.: Diverse M-best solutions in markov random fields. In: Fitzgibbon, A., Lazebnik, S., Perona, P., Sato, Y., Schmid, C. (eds.) ECCV 2012. LNCS, vol. 7576, pp. 1–16. Springer, Heidelberg (2012). doi:10.1007/978-3-642-33715-4_1
Kirillov, A., Savchynskyy, B., Schlesinger, D., Vetrov, D., Rother, C.: Inferring M-best diverse labelings in a single one. In: IEEE International Conference on Computer Vision (ICCV), pp. 1814–1822 (2015)
Geman, S., Geman, D.: Stochastic relaxation, Gibbs distributions, and the bayesian restoration of images. IEEE Trans. Pattern Anal. Mach. Intell. PAMI 6(6), 721–741 (1984)
Koller, D., Friedman, N.: Probabilistic Graphical Models: Principles and Techniques. MIT press (2009)
Papandreou, G., Yuille, A.L.: Perturb-and-MAP random fields: using discrete optimization to learn and sample from energy models. In: International Conference on Computer Vision 2011, pp. 193–200 (2011)
Tarlow, D., Adams, R.P., Zemel, R.S.: Randomized optimum models for structured prediction. In: Proceedings of the Fifteenth International Conference on Artificial Intelligence and Statistics, vol. 22, pp. 1221–1229 (2012)
Hazan, T., Jaakkola, T.: On the partition function and random maximum a-posteriori perturbations. In: Proceedings of the 29th International Conference on Machine Learning (ICML-12), pp. 991–998 (2012)
Hazan, T., Maji, S., Jaakkola, T.: On sampling from the gibbs distribution with random maximum a-posteriori perturbations. In: Advances in Neural Information Processing Systems, pp. 1268–1276 (2013)
Orabona, F., Hazan, T., Sarwate, A., Jaakkola, T.: On measure concentration of random maximum a-posteriori perturbations. In: International Conference on Machine Learning, pp. 432–440 (2014)
Gane, A., Hazan, T., Jaakkola, T.: Learning with maximum a-posteriori perturbation models. In: Artificial Intelligence and Statistics, pp. 247–256 (2014)
Alberts, E., Rempfler, M., Alber, G., Huber, T., Kirschke, J., Zimmer, C., Menze, B.H.: Uncertainty quantification in brain tumor segmentation using CRFs and random perturbation models. In: 2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI), pp. 428–431 (2016)
Meier, R., Knecht, U., Jungo, A., Wiest, R., Reyes, M.: Perturb-and-MPM: quantifying segmentation uncertainty in dense multi-label CRFs. CoRR abs/1703.00312 (2017). http://arxiv.org/abs/1703.00312
Liu, J.S.: Monte Carlo Strategies in Scientific Computing. Springer, New York (2001)
Mehlhorn, K., Näher, S., Sanders, P.: Engineering DFS-based graph algorithms. CoRR abs/1703.10023 (2017). http://arxiv.org/abs/1703.10023
Gumbel, E.J.: Statistical theory of extreme values and some practical applications: a series of lectures. No. 33, US Govt. Print. Office (1954)
Staal, J.J., Abramoff, M.D., Niemeijer, M., Viergever, M.A., Van Ginneken, B.: Ridge based vessel segmentation in color images of the retina. IEEE Trans. Med. Imaging 23(4), 501–509 (2004)
Sironi, A., Türetken, E., Lepetit, V., Fua, P.: Multiscale centerline detection. IEEE Trans. Pattern Anal. Mach. Intell. 1, 1–14 (2015)
Gurobi Optimization, Inc.: Gurobi Optimizer Reference Manual (2017). http://www.gurobi.com
Acknowledgements
With the support of the Technische Universität München – Institute for Advanced Study, funded by the German Excellence Initiative (and the European Union Seventh Framework Programme under grant agreement n\(^{\circ }\) 291763).
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Rempfler, M., Andres, B., Menze, B.H. (2017). Uncertainty Estimation in Vascular Networks. In: Cardoso, M., et al. Graphs in Biomedical Image Analysis, Computational Anatomy and Imaging Genetics. GRAIL MICGen MFCA 2017 2017 2017. Lecture Notes in Computer Science(), vol 10551. Springer, Cham. https://doi.org/10.1007/978-3-319-67675-3_5
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