Skip to main content

Efficient 3D Depthwise and Separable Convolutions with Dilation for Brain Tumor Segmentation

  • Conference paper
  • First Online:
AI 2019: Advances in Artificial Intelligence (AI 2019)

Abstract

In this paper, we propose a 3D convolutional neural network targeting at the segmentation of brain tumor. There are different types of brain tumors and our focus is one common type named glioma. The proposed network is efficient and balances the tradeoff between the number of parameters and accuracy of segmentation. It consists of Anisotropic Block, Dilated Parallel Residual Block, and Feature Refinement Module. The Anisotropic Block applies anisotropic convolutional kernels on different branches. In addition, the Dilated Parallel Residual Block incorporates 3D depthwise and separable convolutions to reduce the amount of required parameters dramatically, while multiscale dilated convolutions enlarge the receptive field. The Feature Refinement Module prevents global contextual information loss. Our method is evaluated on the BRATS 2017 dataset. The results show that our method achieved competitive performance among all compared methods, with a reduced number of parameters. The ablation study also proves that each individual block or module is effective.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Bakas, S., et al.: Advancing the Cancer Genome Atlas glioma MRI collections with expert segmentation labels and radiomic features. Sci. Data 4, 170117 (2017)

    Article  Google Scholar 

  2. Chen, L.C., Papandreou, G., Kokkinos, I., Murphy, K., Yuille, A.L.: DeepLab: semantic image segmentation with deep convolutional nets, atrous convolution, and fully connected CRFs. IEEE Trans. Pattern Anal. Mach. Intell. 40(4), 834–848 (2018)

    Article  Google Scholar 

  3. 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 

  4. Havaei, M., et al.: Brain tumor segmentation with deep neural networks. Med. Image Anal. 35, 18–31 (2017)

    Article  Google Scholar 

  5. Jia, H., et al.: 3D APA-Net: 3D adversarial pyramid anisotropic convolutional network for prostate segmentation in mr images. IEEE Trans. Med. Imag. (2019)

    Google Scholar 

  6. Li, W., Wang, G., Fidon, L., Ourselin, S., Cardoso, M.J., Vercauteren, T.: On the compactness, efficiency, and representation of 3D convolutional networks: brain parcellation as a pretext task. In: Niethammer, M., et al. (eds.) IPMI 2017. LNCS, vol. 10265, pp. 348–360. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-59050-9_28

    Chapter  Google Scholar 

  7. Liu, D., et al.: Densely connected large kernel convolutional network for semantic membrane segmentation in microscopy images. In: 2018 25th IEEE International Conference on Image Processing (ICIP), pp. 2461–2465. IEEE (2018)

    Google Scholar 

  8. Liu, D., Zhang, D., Song, Y., Zhang, F., O’Donnell, L.J., Cai, W.: 3D large kernel anisotropic network for brain tumor segmentation. In: Cheng, L., Leung, A.C.S., Ozawa, S. (eds.) ICONIP 2018. LNCS, vol. 11307, pp. 444–454. Springer, Cham (2018). https://doi.org/10.1007/978-3-030-04239-4_40

    Chapter  Google Scholar 

  9. Ma, J., Yang, X.: Automatic brain tumor segmentation by exploring the multi-modality complementary information and cascaded 3D lightweight CNNs. In: Crimi, A., Bakas, S., Kuijf, H., Keyvan, F., Reyes, M., van Walsum, T. (eds.) BrainLes 2018. LNCS, vol. 11384, pp. 25–36. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-11726-9_3

    Chapter  Google Scholar 

  10. Menze, B.H., et al.: The multimodal brain tumor image segmentation benchmark (BRATS). IEEE Trans. Med. Imag. 34(10), 1993–2024 (2015)

    Article  Google Scholar 

  11. Milletari, F., Navab, N., Ahmadi, S.A.: V-Net: fully convolutional neural networks for volumetric medical image segmentation. In: 3D Vision, pp. 565–571 (2016)

    Google Scholar 

  12. Pereira, S., Pinto, A., Alves, V., Silva, C.A.: Brain tumor segmentation using convolutional neural networks in MRI images. IEEE Trans. Med. Imag. 35(5), 1240–1251 (2016)

    Article  Google Scholar 

  13. Sandler, M., Howard, A., Zhu, M., Zhmoginov, A., Chen, L.C.: MobileNetV2: inverted residuals and linear bottlenecks. In: CVPR (2018)

    Google Scholar 

  14. Subbanna, N.K., Precup, D., Collins, D.L., Arbel, T.: Hierarchical probabilistic gabor and MRF segmentation of brain tumours in MRI volumes. In: Mori, K., Sakuma, I., Sato, Y., Barillot, C., Navab, N. (eds.) MICCAI 2013. LNCS, vol. 8149, pp. 751–758. Springer, Heidelberg (2013). https://doi.org/10.1007/978-3-642-40811-3_94

    Chapter  Google Scholar 

  15. Wang, H., et al.: Segmenting neuronal structure in 3D optical microscope images via knowledge distillation with teacher-student network. In: 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019), pp. 228–231. IEEE (2019)

    Google Scholar 

  16. Wen, P.Y., et al.: Updated response assessment criteria for high-grade gliomas: response assessment in neuro-oncology working group. J. Clin. Oncol. 28(11), 1963–1972 (2010)

    Article  Google Scholar 

  17. Wu, Y., et al.: Vessel-Net: retinal vessel segmentation under multi-path supervision. In: Shen, D., et al. (eds.) MICCAI 2019. Lecture Notes in Computer Science, vol. 11764, pp. 264–272. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-32239-7_30

    Chapter  Google Scholar 

  18. Yu, C., Wang, J., Peng, C., Gao, C., Yu, G., Sang, N.: BiSeNet: bilateral segmentation network for real-time semantic segmentation. In: Ferrari, V., Hebert, M., Sminchisescu, C., Weiss, Y. (eds.) ECCV 2018. LNCS, vol. 11217, pp. 334–349. Springer, Cham (2018). https://doi.org/10.1007/978-3-030-01261-8_20

    Chapter  Google Scholar 

  19. Zhang, C., et al.: MS-GAN: GAN-based semantic segmentation of multiple sclerosis lesions in brain magnetic resonance imaging. In: 2018 Digital Image Computing: Techniques and Applications (DICTA), pp. 1–8. IEEE (2018)

    Google Scholar 

  20. Zhang, D., et al.: Panoptic segmentation with an end-to-end cell R-CNN for pathology image analysis. In: Frangi, A.F., Schnabel, J.A., Davatzikos, C., Alberola-López, C., Fichtinger, G. (eds.) MICCAI 2018. LNCS, vol. 11071, pp. 237–244. Springer, Cham (2018). https://doi.org/10.1007/978-3-030-00934-2_27

    Chapter  Google Scholar 

  21. Zhao, H., Shi, J., Qi, X., Wang, X., Jia, J.: Pyramid scene parsing network. In: CVPR, pp. 6230–6239 (2017)

    Google Scholar 

  22. Zhao, X., et al.: A deep learning model integrating FCNNs and CRFs for brain tumor segmentation. Med. Image Anal. 43, 98–111 (2018)

    Article  Google Scholar 

  23. Zhou, C., Ding, C., Lu, Z., Wang, X., Tao, D.: One-pass multi-task convolutional neural networks for efficient brain tumor segmentation. In: Frangi, A.F., Schnabel, J.A., Davatzikos, C., Alberola-López, C., Fichtinger, G. (eds.) MICCAI 2018. LNCS, vol. 11072, pp. 637–645. Springer, Cham (2018). https://doi.org/10.1007/978-3-030-00931-1_73

    Chapter  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Yang Song .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Zhang, D. et al. (2019). Efficient 3D Depthwise and Separable Convolutions with Dilation for Brain Tumor Segmentation. In: Liu, J., Bailey, J. (eds) AI 2019: Advances in Artificial Intelligence. AI 2019. Lecture Notes in Computer Science(), vol 11919. Springer, Cham. https://doi.org/10.1007/978-3-030-35288-2_45

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-35288-2_45

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-35287-5

  • Online ISBN: 978-3-030-35288-2

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics