Nothing Special   »   [go: up one dir, main page]

skip to main content
10.1145/3364836.3364894acmotherconferencesArticle/Chapter ViewAbstractPublication PagesisicdmConference Proceedingsconference-collections
research-article

Fixed-Point Deformable U-Net for Pancreas CT Segmentation

Published: 24 August 2019 Publication History

Abstract

Delineating pancreas region is of great importance for medical image analysis, but challenging due to imbalance of labelling data, background distractions and high anatomical variability. In this work, we propose a fixed-point deformable U-Net, namely fixedpoint DUNet, which exploits the essential local features of pancreas with a U-shape architecture in an end-to-end manner for the segmentation of pancreas CT images. Inspired by the recently introduced deformable convolutional networks ([1], [2]), we integrate the deformable convolution into the proposed neural network, i.e. DUNet, with upsampling operators to increase the output resolution, which is designed to extract context information and enable precise localization by combining low-level feature maps with high-level ones. DUNet is capable of capturing the pancreas region at various shapes and scales by adaptively adjusting the receptive fields according to pancreas' scales and shapes. Meanwhile, we propose a new loss function based on the generalized dice coefficient to address the class imbalance of pancreas. Experiments showed the proposed method outperformed state-of-the-art methods for automatically segmenting pancreas CT images in terms of accuracy and reliability.

References

[1]
Dai, J., Qi, H., Xiong, Y., Li, Y., Zhang, G., Hu, H., Wei, Y. 2015. Deformable Convolutional Networks. International Conference on Computer Vision, 764--773.
[2]
Xizhou Zhu, Han Hu, Stephen Lin, Jifeng Dai. 2018. Deformable ConvNets v2: More Deformable, Better Results. arXiv preprint arXiv:1811.11168v2.
[3]
Krizhevsky, A., Sutskever, I., and Hinton, G. 2012. ImageNet Classification with Deep Convolutional Neural Networks. Advances in Neural Information Processing Systems.
[4]
Simonyan, K., Zisserman, A. 2015. Very Deep Convolutional Networks for Large-Scale Image Recognition. International Conference on Learning Representations.
[5]
Havaei, M., Davy, A., Warde-Farley, D., Biard, A., Courville, A., Bengio, Y., Pal, C., Jodoin, P., Larochelle, H. 2017. Brain Tumor Segmentation with Deep Neural Networks. Medical Image Analysis, 35, 18--31.
[6]
Zhou, Y., Xie, L., Fishman, E., Yuille, A. 2017. Deep Supervision for Pancreatic Cyst Segmentation in Abdominal CT Scans. International Conference on Medical Image Computing and Computer-Assisted Intervention.
[7]
Roth, H., Lu, L., Farag, A., Shin, H., Liu, J., Turkbey, E., Summers, R. 2015. DeepOrgan: Multi-level Deep Convolutional Networks for Automated Pancreas Segmentation. International Conference on Medical Image Computing and Computer- Assisted Intervention.
[8]
Robin, W., Chengwen, C., Kazunari, M., Michitaka, F., Kensaku, M., Daniel, R. 2013. Automated Abdominal Multi-organ Segmentation with Subject Specific Atlas Generation. IEEE Transactions on Medical Imaging, 32, 9, 1723--1730.
[9]
Zhou, Y., Xie, L., Shen, W., Wang, Y., Fishman, E. K., Yuille, A. L. 2017. A Fixed-Point Model for Pancreas Segmentation in Abdominal CT Scans. International Conference on Medical Image Computing and Computer- Assisted Intervention, 693--701.
[10]
Yu, Q., Xie, L., Wang, Y., Zhou, Y., Fishman, E. K., Yuille, A. L. 2018. Recurrent Saliency Transformation Network: Incorporating Multi-Stage Visual Cues for Small Organ Segmentation. IEEE Conference on Computer Vision and Pattern Recognition, 8280--8289.
[11]
Zhu, Z., Xia, Y., Shen, W., Fishman, E., Yuille, A. L. 2018. A 3D Coarse-to-Fine Framework for Volumetric Medical Image Segmentation. International Conference on 3D Vision, 682--690.
[12]
Xia, Y., Xie, L., Liu, F., Zhu, Z., Fishman, E. K., Yuille, A. L. 2018. Bridging the Gap Between 2D and 3D Organ Segmentation with Volumetric Fusion Net. International Conference on Medical Image Computing and Computer- Assisted Intervention, 445--453.
[13]
Ronneberger, O., Fischer, P., Brox, T. 2015. U-Net: Convolutional Networks for Biomedical Image Segmentation. International Conference on Medical Image Computing and Computer-Assisted Intervention, 234--241.
[14]
Kamnitsas, K., Bai, W., Ferrante, E., McDonagh, S., Sinclair, M., Pawlowski, N., Rajchl, M., Lee, M., Kainz, B., Rueckert, D., Glocker, B. 2018. Ensembles of multiple models and architectures for robust brain tumour segmentation. In: Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries, 450--462.
[15]
Roth, H.R., Lu, L., Lay, N., Harrison, A.P., Farag, A., Sohn, A., Summers, R.M. 2018. Spatial aggregation of holisticallynested convolutional neural networks for automated pancreas localization and segmentation. Medical Image Analysis, 45, 94--107.
[16]
Yijun Liu, Shuang Liu. 2018. U-NET for pancreas segmentation in abdominal CT scans. ISBI Challenge.
[17]
Qiangguo Jin, Zhaopeng Meng, Tuan D.Pham, Qi Chen, Leyi Wei, Ran Su. 2018. DUNet: A deformable network for retinal vessel segmentation. arXiv preprint arXiv:1811.01206v1.
[18]
Yunze Man, Yangsibo Huang, Junyi Feng, Xi Li, Fei Wu. 2019. Deep Q Learning Driven Pancreas Segmentation with Geometry-Aware U-Net. IEEE, Transactions on Medical Imaging, DOI 10.1109/TMI.2019.2911588.
[19]
Ioffe, S., Szegedy, C. 2015. Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shift. International Conference on Machine Learning, 448--456.
[20]
Milletari, F., Navab, N., Ahmadi, S. 2016. V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation. International Conference on 3D Vision, 565--571.
[21]
Lin, T. Y., Goyal, P., Girshick, R., He, K. M., Dollar, P. 2018. Focal Loss for Dense Object Detection. IEEE Transactions on Pattern Analysis and Machine Intelligence.
[22]
Nabila Abraham, Naimul Mefraz Khan. 2018. A Novel Focal Tversky Loss Function with Improved Attention U-Net for Lesion Segmentation. arXiv: 1810.07842v1.
[23]
F. Chollet and others, Keras. GitHub. [Online]. Available: https: //github.com/keras- team/keras.
[24]
M. Abadi, A. Agarwal, P. Barham, E. Brevdo, Z. Chen, C. Citro, G. S. Corrado, A. Davis, J. Dean, M. Devin et al. 2015. "TensorFlow: Large-Scale Machine Learning on Heterogeneous Distributed Systems." arXiv preprint arXiv:1603.04467.

Cited By

View all
  • (2024)State-of-the-Art and Challenges in Pancreatic CT Segmentation: A Systematic Review of U-Net and Its VariantsIEEE Access10.1109/ACCESS.2024.339259512(78726-78742)Online publication date: 2024
  • (2024) DMGM: deformable-mechanism based cervical cancer staging via MRI multi-sequence * Physics in Medicine & Biology10.1088/1361-6560/ad4c5069:11(115044)Online publication date: 30-May-2024
  • (2022)Learning a Discriminative Feature Attention Network for pancreas CT segmentationApplied Mathematics-A Journal of Chinese Universities10.1007/s11766-022-4346-437:1(73-90)Online publication date: 17-Mar-2022

Index Terms

  1. Fixed-Point Deformable U-Net for Pancreas CT Segmentation

    Recommendations

    Comments

    Please enable JavaScript to view thecomments powered by Disqus.

    Information & Contributors

    Information

    Published In

    cover image ACM Other conferences
    ISICDM 2019: Proceedings of the Third International Symposium on Image Computing and Digital Medicine
    August 2019
    370 pages
    ISBN:9781450372626
    DOI:10.1145/3364836
    Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

    In-Cooperation

    • Xidian University

    Publisher

    Association for Computing Machinery

    New York, NY, United States

    Publication History

    Published: 24 August 2019

    Permissions

    Request permissions for this article.

    Check for updates

    Author Tags

    1. Pancreas CT image segmentation
    2. deep neural networks
    3. deformable U-Net
    4. medical image segmentation

    Qualifiers

    • Research-article
    • Research
    • Refereed limited

    Conference

    ISICDM 2019

    Contributors

    Other Metrics

    Bibliometrics & Citations

    Bibliometrics

    Article Metrics

    • Downloads (Last 12 months)10
    • Downloads (Last 6 weeks)1
    Reflects downloads up to 25 Nov 2024

    Other Metrics

    Citations

    Cited By

    View all
    • (2024)State-of-the-Art and Challenges in Pancreatic CT Segmentation: A Systematic Review of U-Net and Its VariantsIEEE Access10.1109/ACCESS.2024.339259512(78726-78742)Online publication date: 2024
    • (2024) DMGM: deformable-mechanism based cervical cancer staging via MRI multi-sequence * Physics in Medicine & Biology10.1088/1361-6560/ad4c5069:11(115044)Online publication date: 30-May-2024
    • (2022)Learning a Discriminative Feature Attention Network for pancreas CT segmentationApplied Mathematics-A Journal of Chinese Universities10.1007/s11766-022-4346-437:1(73-90)Online publication date: 17-Mar-2022

    View Options

    Login options

    View options

    PDF

    View or Download as a PDF file.

    PDF

    eReader

    View online with eReader.

    eReader

    Media

    Figures

    Other

    Tables

    Share

    Share

    Share this Publication link

    Share on social media