Skip to main content

SGNet: Structure-Aware Graph-Based Network for Airway Semantic Segmentation

  • Conference paper
  • First Online:

Part of the book series: Lecture Notes in Computer Science ((LNIP,volume 12901))

Abstract

Airway semantic segmentation, which refers to segmenting airway from background and dividing it into anatomical segments, provides clinically valuable information for lung lobe analysis, pulmonary lesion localization, and comparison between different patients. It is technically challenging due to the complicated tree-like structure, individual variations, and severe class imbalance. We propose a structure-aware graph-based network (SGNet) for airway semantic segmentation directly from chest CT scans. The proposed framework consists of a feature extractor combining a multi-task U-Net with a structure-aware GCN, and an inference module comprised of two convolutional layers. The multi-task U-Net is trained to regress bifurcation landmark heatmaps, binary and semantic segmentation maps simultaneously, providing initial predictions for graph construction. By introducing irregular edges connecting voxels with the sampled points around corresponding bifurcation landmarks, the two-layer GCN incorporates the structural prior explicitly. Experiments on both public and private datasets demonstrate that the SGNet achieves superior and robust performance, even on subjects affected by severe pulmonary diseases.

This work was supported in part by the National Natural Science Foundation of China under Grants 82071921.

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

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   139.99
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

Learn about institutional subscriptions

Notes

  1. 1.

    Annotations are available at https://cloud.tsinghua.edu.cn/d/43bbc05fb9714f71a56f/

References

  1. van Ginneken, B., Baggerman, W., van Rikxoort, E.M.: Robust segmentation and anatomical labeling of the airway tree from thoracic CT scans. In: Metaxas, D., Axel, L., Fichtinger, G., Székely, G. (eds.) MICCAI 2008. LNCS, vol. 5241, pp. 219–226. Springer, Heidelberg (2008). https://doi.org/10.1007/978-3-540-85988-8_27

    Chapter  Google Scholar 

  2. Tschirren, J., McLennan, G., Palágyi, K., et al.: Matching and anatomical labeling of human airway tree. IEEE T-MI 24(12), 1540–1547 (2005)

    Google Scholar 

  3. 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 

  4. 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 

  5. Qin, Y., et al.: AirwayNet: a voxel-connectivity aware approach for accurate airway segmentation using convolutional neural networks. In: Shen, D., et al. (eds.) MICCAI 2019. LNCS, vol. 11769, pp. 212–220. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-32226-7_24

    Chapter  Google Scholar 

  6. Qin, Y., Gu, Y., Zheng, H., et al.: AirwayNet-SE: a simple-yet-effective approach to improve airway segmentation using context scale fusion. In: ISBI (2020)

    Google Scholar 

  7. Qin, Y., et al.: Learning bronchiole-sensitive airway segmentation CNNs by feature recalibration and attention distillation. In: Martel, A.L., et al. (eds.) MICCAI 2020. LNCS, vol. 12261, pp. 221–231. Springer, Cham (2020). https://doi.org/10.1007/978-3-030-59710-8_22

    Chapter  Google Scholar 

  8. Charbonnier, J.P., Van Rikxoort, E.M., Setio, A.A., et al.: Improving airway segmentation in computed tomography using leak detection with convolutional networks. MedIA 36, 52–60 (2017)

    Google Scholar 

  9. Meng, Q., Roth, H.R., Kitasaka, T., Oda, M., Ueno, J., Mori, K.: Tracking and segmentation of the airways in chest CT using a fully convolutional network. In: Descoteaux, M., Maier-Hein, L., Franz, A., Jannin, P., Collins, D.L., Duchesne, S. (eds.) MICCAI 2017. LNCS, vol. 10434, pp. 198–207. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-66185-8_23

    Chapter  Google Scholar 

  10. Yun, J., Park, J., Yu, D., et al.: Improvement of fully automated airway segmentation on volumetric computed tomographic images using a 2.5 dimensional convolutional neural net. MedIA 51, 13–20 (2019)

    Google Scholar 

  11. Wang, C., et al.: Tubular structure segmentation using spatial fully connected network with radial distance loss for 3D medical images. In: Shen, D., et al. (eds.) MICCAI 2019. LNCS, vol. 11769, pp. 348–356. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-32226-7_39

    Chapter  Google Scholar 

  12. Zhao, T., Yin, Z., Wang, J., Gao, D., Chen, Y., Mao, Y.: Bronchus segmentation and classification by neural networks and linear programming. In: Shen, D., et al. (eds.) MICCAI 2019. LNCS, vol. 11769, pp. 230–239. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-32226-7_26

    Chapter  Google Scholar 

  13. Gu, S., Wang, Z., Siegfried, J.M., et al.: Automated lobe-based airway labeling. Int. J. Biomed. Imaging 2012 (2012)

    Google Scholar 

  14. Feragen, A.: A hierarchical scheme for geodesic anatomical labeling of airway trees. In: Ayache, N., Delingette, H., Golland, P., Mori, K. (eds.) MICCAI 2012. LNCS, vol. 7512, pp. 147–155. Springer, Heidelberg (2012). https://doi.org/10.1007/978-3-642-33454-2_19

    Chapter  Google Scholar 

  15. Wu, D., et al.: Automated anatomical labeling of coronary arteries via bidirectional tree LSTMs. Int. J. Comput. Assist. Radiol. Surg. 14(2), 271–280 (2018). https://doi.org/10.1007/s11548-018-1884-6

    Article  Google Scholar 

  16. Yang, H., Zhen, X., Chi, Y., et al.: CPR-GCN: conditional partial-residual graph convolutional network in automated anatomical labeling of coronary arteries. In: CVPR (2020)

    Google Scholar 

  17. Cao, Q., et al.: Automatic identification of coronary tree anatomy in coronary computed tomography angiography. Int. J. Cardiovasc. Imaging 33(11), 1809–1819 (2017). https://doi.org/10.1007/s10554-017-1169-0

    Article  Google Scholar 

  18. Robben, D., Türetken, E., Sunaert, S., et al.: Simultaneous segmentation and anatomical labeling of the cerebral vasculature. MedIA 32, 201–215 (2016)

    Google Scholar 

  19. Matsuzaki, T., Oda, M., Kitasaka, T., et al.: Automated anatomical labeling of abdominal arteries and hepatic portal system extracted from abdominal CT volumes. MedIA 20(1), 152–161 (2015)

    Google Scholar 

  20. Kipf, T.N., Welling, M.: Semi-supervised classification with graph convolutional networks. In: ICLR (2017)

    Google Scholar 

  21. Selvan, R., Kipf, T., Welling, M., et al.: Extraction of airways using graph neural networks. In: MIDL (2018)

    Google Scholar 

  22. Selvan, R., Kipf, T., Welling, M., et al.: Graph refinement based airway extraction using mean-field networks and graph neural networks. MedIA 64, 101751 (2020)

    Google Scholar 

  23. Shin, S.Y., Lee, S., Yun, I.D., et al.: Deep vessel segmentation by learning graphical connectivity. MedIA 58, 101556 (2019)

    Google Scholar 

  24. Juarez, A.G.U., Selvan, R., Saghir, Z., de Bruijne, M.: A joint 3D unet-graph neural network-based method for airway segmentation from chest CTs. In: MLMI (2019)

    Google Scholar 

  25. Yao, L., Jiang, P., Xue, Z., et al.: Graph convolutional network based point cloud for head and neck vessel labeling. In: MLMI (2020)

    Google Scholar 

  26. Payer, C., Štern, D., Bischof, H., Urschler, M.: Regressing heatmaps for multiple landmark localization using CNNs. In: Ourselin, S., Joskowicz, L., Sabuncu, M.R., Unal, G., Wells, W. (eds.) MICCAI 2016. LNCS, vol. 9901, pp. 230–238. Springer, Cham (2016). https://doi.org/10.1007/978-3-319-46723-8_27

    Chapter  Google Scholar 

  27. Milletari, F., Navab, N., Ahmadi, S.A.: V-net: fully convolutional neural networks for volumetric medical image segmentation. In: 3DV (2016)

    Google Scholar 

  28. Armato, I.I.I., Samuel, G., et al.: The lung image database consortium (LIDC) and image database resource initiative (IDRI): a completed reference database of lung nodules on CT scans. Med. Phys. 38(2), 915–931 (2011)

    Article  Google Scholar 

  29. Lo, P., Ginneken, B.V., Reinhardt, J.M., et al.: Extraction of airways from CT (EXACT’09). IEEE T-MI 31(11), 2093–2107 (2012)

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Jianjiang Feng .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2021 Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Tan, Z., Feng, J., Zhou, J. (2021). SGNet: Structure-Aware Graph-Based Network for Airway Semantic Segmentation. In: de Bruijne, M., et al. Medical Image Computing and Computer Assisted Intervention – MICCAI 2021. MICCAI 2021. Lecture Notes in Computer Science(), vol 12901. Springer, Cham. https://doi.org/10.1007/978-3-030-87193-2_15

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-87193-2_15

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-87192-5

  • Online ISBN: 978-3-030-87193-2

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics