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Contour Propagation in CT Scans with Convolutional Neural Networks

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Advanced Concepts for Intelligent Vision Systems (ACIVS 2018)

Part of the book series: Lecture Notes in Computer Science ((LNIP,volume 11182))

Abstract

Although deep convolutional neural networks (CNNs) have outperformed state-of-the-art in many medical image segmentation tasks, deep network architectures generally fail in exploiting common sense prior to drive the segmentation. In particular, the availability of a segmented (source) image observed in a CT slice that is adjacent to the slice to be segmented (or target image) has not been considered to improve the deep models segmentation accuracy. In this paper, we investigate a CNN architecture that maps a joint input, composed of the target image and the source segmentation, to a target segmentation. We observe that our solution succeeds in taking advantage of the source segmentation when it is sufficiently close to the target segmentation, without being penalized when the source is far from the target.

J. Léger and E. Brion—Contributed equally.

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Notes

  1. 1.

    https://openreggui.org/.

  2. 2.

    http://simpleelastix.github.io.

  3. 3.

    https://developer.nvidia.com/cudnn.

References

  1. Mazurowski, M.A., Buda, M., Saha, A., Bashir, M.R.: Deep learning in radiology: an overview of the concepts and a survey of the state of the art. arXiv preprint arXiv:1802.08717 (2018)

  2. Sharp, G., et al.: Vision 20/20: perspectives on automated image segmentation for radiotherapy. Med. Phys. 41(5), 050902 (2014)

    Google Scholar 

  3. Cha, K.H., et al.: Bladder cancer treatment response assessment in CT using radiomics with deep-learning. Sci. Rep. 7(1), 8738 (2017)

    Article  Google Scholar 

  4. Iglesias, J.E., Sabuncu, M.R.: Multi-atlas segmentation of biomedical images: a survey. Med. Image Anal. 24(1), 205–219 (2015)

    Article  Google Scholar 

  5. Cremers, D., Rousson, M., Deriche, R.: A review of statistical approaches to level set segmentation: integrating color, texture, motion and shape. Int. J. Comput. Vis. 72(2), 195–215 (2007)

    Article  Google Scholar 

  6. Heimann, T., Meinzer, H.P.: Statistical shape models for 3D medical image segmentation: a review. Med. Image Anal. 13(4), 543–563 (2009)

    Article  Google Scholar 

  7. Polan, D.F., Brady, S.L., Kaufman, R.A.: Tissue segmentation of computed tomography images using a random forest algorithm: a feasibility study. Phys. Med. Biol. 61(17), 6553 (2016)

    Article  Google Scholar 

  8. Luo, S., Hu, Q., He, X., Li, J., Jin, J.S., Park, M.: Automatic liver parenchyma segmentation from abdominal CT images using support vector machines. In: ICME International Conference on Complex Medical Engineering, CME 2009, pp. 1–5. IEEE (2009)

    Google Scholar 

  9. Hu, Y.C.J., Grossberg, M.D., Mageras, G.S.: Semi-automatic medical image segmentation with adaptive local statistics in conditional random fields framework. In: 30th Annual International Conference of the IEEE on Engineering in Medicine and Biology Society, EMBS 2008, pp. 3099–3102. IEEE (2008)

    Google Scholar 

  10. Tong, T., et al.: Discriminative dictionary learning for abdominal multi-organ segmentation. Med. Image Anal. 23(1), 92–104 (2015)

    Google Scholar 

  11. Gao, Y., Shao, Y., Lian, J., Wang, A.Z., Chen, R.C., Shen, D.: Accurate segmentation of CT male pelvic organs via regression-based deformable models and multi-task random forests. IEEE Trans. Med. Imaging 35(6), 1532–1543 (2016)

    Article  Google Scholar 

  12. Oda, M., et al.: Regression forest-based atlas localization and direction specific atlas generation for pancreas segmentation. In: Ourselin, S., Joskowicz, L., Sabuncu, M.R., Unal, G., Wells, W. (eds.) MICCAI 2016. LNCS, vol. 9901, pp. 556–563. Springer, Cham (2016). https://doi.org/10.1007/978-3-319-46723-8_64

    Chapter  Google Scholar 

  13. Litjens, G., et al.: A survey on deep learning in medical image analysis. Med. Image Anal. 42, 60–88 (2017)

    Google Scholar 

  14. Long, J., Shelhamer, E., Darrell, T.: Fully convolutional networks for semantic segmentation. In: Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, pp. 3431–3440 (2015)

    Google Scholar 

  15. Ronneberger, O., Fischer, P., Brox, T.: U-net: convolutional networks for biomedical image segmentation. In: Navab, N., Hornegger, J., Wells, W.M., Frangi, A.F. (eds.) MICCAI 2015. LNCS, vol. 9351, pp. 234–241. Springer, Cham (2015). https://doi.org/10.1007/978-3-319-24574-4_28

    Chapter  Google Scholar 

  16. Çiçek, Ö., Abdulkadir, A., Lienkamp, S.S., Brox, T., Ronneberger, O.: 3D U-Net: learning dense volumetric segmentation from sparse annotation. In: Ourselin, S., Joskowicz, L., Sabuncu, M.R., Unal, G., Wells, W. (eds.) MICCAI 2016. LNCS, vol. 9901, pp. 424–432. Springer, Cham (2016). https://doi.org/10.1007/978-3-319-46723-8_49

    Chapter  Google Scholar 

  17. Milletari, F., Navab, N., Ahmadi, S.A.: V-net: fully convolutional neural networks for volumetric medical image segmentation. In: 2016 Fourth International Conference on 3D Vision (3DV), pp. 565–571. IEEE (2016)

    Google Scholar 

  18. Ibragimov, B., Xing, L.: Segmentation of organs-at-risks in head and neck CT images using convolutional neural networks. Med. Phys. 44(2), 547–557 (2017)

    Article  Google Scholar 

  19. Kazemifar, S., et al.: Segmentation of the prostate and organs at risk in male pelvic CT images using deep learning. arXiv preprint arXiv:1802.09587 (2018)

  20. Roth, H.R., et al.: Hierarchical 3D fully convolutional networks for multi-organ segmentation. arXiv preprint arXiv:1704.06382 (2017)

  21. Larsson, M., Zhang, Y., Kahl, F.: Robust abdominal organ segmentation using regional convolutional neural networks. In: Sharma, P., Bianchi, F.M. (eds.) SCIA 2017. LNCS, vol. 10270, pp. 41–52. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-59129-2_4

    Chapter  Google Scholar 

  22. Milletari, F., Rothberg, A., Jia, J., Sofka, M.: Integrating statistical prior knowledge into convolutional neural networks. In: Descoteaux, M., Maier-Hein, L., Franz, A., Jannin, P., Collins, D.L., Duchesne, S. (eds.) MICCAI 2017. LNCS, vol. 10433, pp. 161–168. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-66182-7_19

    Chapter  Google Scholar 

  23. Trullo, R., Petitjean, C., Ruan, S., Dubray, B., Nie, D., Shen, D.: Segmentation of organs at risk in thoracic CT images using a sharpmask architecture and conditional random fields. In: 2017 IEEE 14th International Symposium on Biomedical Imaging (ISBI 2017), pp. 1003–1006. IEEE (2017)

    Google Scholar 

  24. Klein, S., Staring, M.: Elastix, the manual (2018). http://elastix.isi.uu.nl/download/elastix-4.9.0-manual.pdf

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Acknowledgments

Jean Léger is a Research Fellow of the Fonds de la Recherche Scientifique - FNRS, Eliott Brion’s work was supported by FEDER-RW project UserMEDIA, Umair Javaid is a Research Fellow funded by the FNRS Televie grant no. 7.4625.16, John A. Lee and Christophe De Vleeschouwer are Senior Research Associates with the Belgian F.R.S.-FNRS. We thank CHU-UCL-Namur (Dr J.-F. Daisne) as well as CHU-Charleroi (Dr N. Meert) for providing the data.

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Léger, J., Brion, E., Javaid, U., Lee, J., De Vleeschouwer, C., Macq, B. (2018). Contour Propagation in CT Scans with Convolutional Neural Networks. In: Blanc-Talon, J., Helbert, D., Philips, W., Popescu, D., Scheunders, P. (eds) Advanced Concepts for Intelligent Vision Systems. ACIVS 2018. Lecture Notes in Computer Science(), vol 11182. Springer, Cham. https://doi.org/10.1007/978-3-030-01449-0_32

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  • DOI: https://doi.org/10.1007/978-3-030-01449-0_32

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