Skip to main content
Top

2018 | OriginalPaper | Chapter

Bridging the Gap Between 2D and 3D Organ Segmentation with Volumetric Fusion Net

Authors : Yingda Xia, Lingxi Xie, Fengze Liu, Zhuotun Zhu, Elliot K. Fishman, Alan L. Yuille

Published in: Medical Image Computing and Computer Assisted Intervention – MICCAI 2018

Publisher: Springer International Publishing

Activate our intelligent search to find suitable subject content or patents.

search-config
loading …

Abstract

There has been a debate on whether to use 2D or 3D deep neural networks for volumetric organ segmentation. Both 2D and 3D models have their advantages and disadvantages. In this paper, we present an alternative framework, which trains 2D networks on different viewpoints for segmentation, and builds a 3D Volumetric Fusion Net (VFN) to fuse the 2D segmentation results. VFN is relatively shallow and contains much fewer parameters than most 3D networks, making our framework more efficient at integrating 3D information for segmentation. We train and test the segmentation and fusion modules individually, and propose a novel strategy, named cross-cross-augmentation, to make full use of the limited training data. We evaluate our framework on several challenging abdominal organs, and verify its superiority in segmentation accuracy and stability over existing 2D and 3D approaches.

Dont have a licence yet? Then find out more about our products and how to get one now:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

  • über 102.000 Bücher
  • über 537 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Maschinenbau + Werkstoffe
  • Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 390 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Maschinenbau + Werkstoffe




 

Jetzt Wissensvorsprung sichern!

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 340 Zeitschriften

aus folgenden Fachgebieten:

  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Versicherung + Risiko




Jetzt Wissensvorsprung sichern!

Literature
1.
go back to reference Asman, A.J., Landman, B.A.: Non-local statistical label fusion for multi-atlas segmentation. Med. Image Anal. 17(2), 194–208 (2013)CrossRef Asman, A.J., Landman, B.A.: Non-local statistical label fusion for multi-atlas segmentation. Med. Image Anal. 17(2), 194–208 (2013)CrossRef
3.
go back to reference Cai, J., Lu, L., Xie, Y., Xing, F., Yang, L.: Pancreas segmentation in MRI using graph-based decision fusion on convolutional neural networks. In: Descoteaux, M., Maier-Hein, L., Franz, A., Jannin, P., Collins, D.L., Duchesne, S. (eds.) MICCAI 2017. LNCS, vol. 10435, pp. 674–682. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-66179-7_77CrossRef Cai, J., Lu, L., Xie, Y., Xing, F., Yang, L.: Pancreas segmentation in MRI using graph-based decision fusion on convolutional neural networks. In: Descoteaux, M., Maier-Hein, L., Franz, A., Jannin, P., Collins, D.L., Duchesne, S. (eds.) MICCAI 2017. LNCS, vol. 10435, pp. 674–682. Springer, Cham (2017). https://​doi.​org/​10.​1007/​978-3-319-66179-7_​77CrossRef
4.
go back to reference 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_49CrossRef 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_​49CrossRef
5.
go back to reference He, K., Zhang, X., Ren, S., Sun, J.: Deep residual learning for image recognition. In: CVPR (2016) He, K., Zhang, X., Ren, S., Sun, J.: Deep residual learning for image recognition. In: CVPR (2016)
6.
go back to reference Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. In: NIPS (2012) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. In: NIPS (2012)
7.
go back to reference Long, J., Shelhamer, E., Darrell, T.: Fully convolutional networks for semantic segmentation. In: CVPR (2015) Long, J., Shelhamer, E., Darrell, T.: Fully convolutional networks for semantic segmentation. In: CVPR (2015)
8.
go back to reference Milletari, F., Navab, N., Ahmadi, S.A.: V-net: fully convolutional neural networks for volumetric medical image segmentation. In: 3DV (2016) Milletari, F., Navab, N., Ahmadi, S.A.: V-net: fully convolutional neural networks for volumetric medical image segmentation. In: 3DV (2016)
9.
go back to reference Roth, H.R., et al.: Deeporgan: multi-level deep convolutional networks for automated pancreas segmentation. In: MICCAI (2015) Roth, H.R., et al.: Deeporgan: multi-level deep convolutional networks for automated pancreas segmentation. In: MICCAI (2015)
10.
go back to reference Roth, H.R., Lu, L., Farag, A., Sohn, A., Summers, R.M.: Spatial aggregation of holistically-nested networks for automated pancreas segmentation. In: Ourselin, S., Joskowicz, L., Sabuncu, M.R., Unal, G., Wells, W. (eds.) MICCAI 2016. LNCS, vol. 9901, pp. 451–459. Springer, Cham (2016). https://doi.org/10.1007/978-3-319-46723-8_52CrossRef Roth, H.R., Lu, L., Farag, A., Sohn, A., Summers, R.M.: Spatial aggregation of holistically-nested networks for automated pancreas segmentation. In: Ourselin, S., Joskowicz, L., Sabuncu, M.R., Unal, G., Wells, W. (eds.) MICCAI 2016. LNCS, vol. 9901, pp. 451–459. Springer, Cham (2016). https://​doi.​org/​10.​1007/​978-3-319-46723-8_​52CrossRef
11.
go back to reference Roth, H.R., et al.: Spatial aggregation of holistically-nested convolutional neural networks for automated pancreas localization and segmentation. arXiv:1702.00045 (2017) Roth, H.R., et al.: Spatial aggregation of holistically-nested convolutional neural networks for automated pancreas localization and segmentation. arXiv:​1702.​00045 (2017)
12.
go back to reference Setio, A.A.A., et al.: Pulmonary nodule detection in CT images: false positive reduction using multi-view convolutional networks. IEEE Trans. Med. Imaging 35(5), 1160–1169 (2016)CrossRef Setio, A.A.A., et al.: Pulmonary nodule detection in CT images: false positive reduction using multi-view convolutional networks. IEEE Trans. Med. Imaging 35(5), 1160–1169 (2016)CrossRef
13.
go back to reference Su, H., Maji, S., Kalogerakis, E., Learned-Miller, E.: Multi-view convolutional neural networks for 3D shape recognition. In: Proceedings of the IEEE International Conference on Computer Vision, pp. 945–953 (2015) Su, H., Maji, S., Kalogerakis, E., Learned-Miller, E.: Multi-view convolutional neural networks for 3D shape recognition. In: Proceedings of the IEEE International Conference on Computer Vision, pp. 945–953 (2015)
14.
go back to reference Tajbakhsh, N., et al.: Convolutional neural networks for medical image analysis: full training or fine tuning? IEEE TMI 35(5), 1299–1312 (2016) Tajbakhsh, N., et al.: Convolutional neural networks for medical image analysis: full training or fine tuning? IEEE TMI 35(5), 1299–1312 (2016)
15.
go back to reference Tu, Z., Bai, X.: Auto-context and its application to high-level vision tasks and 3D brain image segmentation. IEEE TPAMI 32(10), 1744–1757 (2010)CrossRef Tu, Z., Bai, X.: Auto-context and its application to high-level vision tasks and 3D brain image segmentation. IEEE TPAMI 32(10), 1744–1757 (2010)CrossRef
17.
go back to reference Yu, Q., Xie, L., Wang, Y., Zhou, Y., Fishman, E.K., Yuille, A.L.: Recurrent saliency transformation network: incorporating multi-stage visual cues for small organ segmentation. arXiv:1709.04518 (2017) Yu, Q., Xie, L., Wang, Y., Zhou, Y., Fishman, E.K., Yuille, A.L.: Recurrent saliency transformation network: incorporating multi-stage visual cues for small organ segmentation. arXiv:​1709.​04518 (2017)
18.
go back to reference Zhou, Y., Xie, L., Shen, W., Wang, Y., Fishman, E.K., Yuille, A.L.: A fixed-point model for pancreas segmentation in abdominal CT scans. In: Descoteaux, M., Maier-Hein, L., Franz, A., Jannin, P., Collins, D.L., Duchesne, S. (eds.) MICCAI 2017. LNCS, vol. 10433, pp. 693–701. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-66182-7_79CrossRef Zhou, Y., Xie, L., Shen, W., Wang, Y., Fishman, E.K., Yuille, A.L.: A fixed-point model for pancreas segmentation in abdominal CT scans. In: Descoteaux, M., Maier-Hein, L., Franz, A., Jannin, P., Collins, D.L., Duchesne, S. (eds.) MICCAI 2017. LNCS, vol. 10433, pp. 693–701. Springer, Cham (2017). https://​doi.​org/​10.​1007/​978-3-319-66182-7_​79CrossRef
19.
go back to reference Zhu, Z., Xia, Y., Shen, W., Fishman, E.K., Yuille, A.L.: A 3D coarse-to-fine framework for automatic pancreas segmentation. arXiv:1712.00201 (2017) Zhu, Z., Xia, Y., Shen, W., Fishman, E.K., Yuille, A.L.: A 3D coarse-to-fine framework for automatic pancreas segmentation. arXiv:​1712.​00201 (2017)
Metadata
Title
Bridging the Gap Between 2D and 3D Organ Segmentation with Volumetric Fusion Net
Authors
Yingda Xia
Lingxi Xie
Fengze Liu
Zhuotun Zhu
Elliot K. Fishman
Alan L. Yuille
Copyright Year
2018
DOI
https://doi.org/10.1007/978-3-030-00937-3_51

Premium Partner