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ANT-UNet: Accurate and Noise-Tolerant Segmentation for Pathology Image Processing

Published: 31 December 2021 Publication History

Abstract

Pathology image segmentation is an essential step in early detection and diagnosis for various diseases. Due to its complex nature, precise segmentation is not a trivial task. Recently, deep learning has been proved as an effective option for pathology image processing. However, its efficiency is highly restricted by inconsistent annotation quality. In this article, we propose an accurate and noise-tolerant segmentation approach to overcome the aforementioned issues. This approach consists of two main parts: a preprocessing module for data augmentation and a new neural network architecture, ANT-UNet. Experimental results demonstrate that, even on a noisy dataset, the proposed approach can achieve more accurate segmentation with 6% to 35% accuracy improvement versus other commonly used segmentation methods. In addition, the proposed architecture is hardware friendly, which can reduce the amount of parameters to one-tenth of the original and achieve 1.7× speed-up.

References

[1]
Anant Madabhushi. 2009. Digital pathology image analysis: Opportunities and challenges. Imaging in Medicine 1, 1 (2009), 7.
[2]
Anant Madabhushi and George Lee. 2016. Image Analysis and Machine Learning in Digital Pathology: Challenges and Opportunities. 33 (2016), 170–175.
[3]
A. M. Zaitoun, H. Al Mardini, and C. O. Record. 1998. Quantitative assessment of gastric atrophy using the syntactic structure analysis. Journal of Clinical Pathology 51, 12 (1998), 895–900.
[4]
Harshita Sharma, Norman Zerbe, Iris Klempert, Olaf Hellwich, and Peter Hufnagl. 2017. Deep convolutional neural networks for automatic classification of gastric carcinoma using whole slide images in digital histopathology. Computerized Medical Imaging and Graphics 61 (2017), 2–13.
[5]
Axel Wismüller, Frank Vietze, Johannes Behrends, Anke Meyer-Baese, Maximilian Reiser, and Helge Ritter. 2004. Fully automated biomedical image segmentation by self-organized model adaptation. Neural Networks 17, 8–9 (2004), 1327–1344.
[6]
Emilio Garcia, Renato Hermoza, Cesar Beltran Castanon, Luis Cano, Miluska Castillo, and Carlos Castanneda. 2017. Automatic lymphocyte detection on gastric cancer IHC images using deep learning. In IEEE 30th International Symposium on Computer-based Medical Systems (CBMS’17), Thessaloniki, Greece. IEEE, 200–204.
[7]
Jonathan Long, Evan Shelhamer, and Trevor Darrell. 2015. Fully convolutional networks for semantic segmentation. In Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, Boston, Massachusetts, USA. IEEE, 3431–3440.
[8]
Vijay Badrinarayanan, Alex Kendall, and Roberto Cipolla. 2017. Segnet: A deep convolutional encoder-decoder architecture for image segmentation. IEEE Transactions on Pattern Analysis and Machine Intelligence 39, 12 (2017), 2481–2495.
[9]
Olaf Ronneberger, Philipp Fischer, and Thomas Brox. 2015. U-net: Convolutional networks for biomedical image segmentation. In International Conference on Medical Image Computing and Computer-assisted Intervention, Munich, Germany. Springer, 234–241.
[10]
Hengshuang Zhao, Jianping Shi, Xiaojuan Qi, Xiaogang Wang, and Jiaya Jia. 2017. Pyramid scene parsing network. In Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, Honolulu, Hawaii, USA. IEEE, 2881–2890.
[11]
Liang-Chieh Chen, George Papandreou, Florian Schroff, and Hartwig Adam. 2017. Rethinking Atrous convolution for semantic image segmentation. arXiv preprint arXiv:1706.05587
[12]
Kaiming He, Xiangyu Zhang, Shaoqing Ren, and Jian Sun. 2016. Deep residual learning for image recognition. In Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, Las Vegas, Nevada, USA. IEEE, 770–778.
[13]
Xiao Xiao, Shen Lian, Zhiming Luo, and Shaozi Li. 2018. Weighted Res-UNet for high-quality retina vessel segmentation. In 9th International Conference on Information Technology in Medicine and Education (ITME’18), Hangzhou, China. IEEE, 327–331.
[14]
Alex Krizhevsky, Ilya Sutskever, and Geoffrey E. Hinton. 2012. Imagenet classification with deep convolutional neural networks. In Advances in Neural Information Processing Systems. Morgan Kaufmann Publishers Inc., Lake Tahoe, Nevada, USA, 1097–1105.
[15]
Liang-Chieh Chen, George Papandreou, Iasonas Kokkinos, Kevin Murphy, and Alan L. Yuille. 2014. Semantic image segmentation with deep convolutional nets and fully connected CRFs. arXiv preprint arXiv:1412.7062
[16]
Liang-Chieh Chen, George Papandreou, Iasonas Kokkinos, Kevin Murphy, and Alan L. Yuille. 2017. DeepLab: Semantic image segmentation with deep convolutional nets, Atrous convolution, and fully connected CRFs. IEEE Transactions on Pattern Analysis and Machine Intelligence 40, 4 (2017), 834–848.
[17]
Liang-Chieh Chen, Yukun Zhu, George Papandreou, Florian Schroff, and Hartwig Adam. 2018. Encoder-decoder with Atrous separable convolution for semantic image segmentation. In Proceedings of the European Conference on Computer Vision (ECCV’18), Munich, Germany. Springer, 801–818.
[18]
Forrest N. Iandola, Song Han, Matthew W. Moskewicz, Khalid Ashraf, William J. Dally, and Kurt Keutzer. 2016. SqueezeNet: AlexNet-level accuracy with 50x fewer parameters and < 0.5 MB model size. arXiv preprint arXiv:1602.07360(2016).
[19]
Andrew G. Howard, Menglong Zhu, Bo Chen, Dmitry Kalenichenko, Weijun Wang, Tobias Weyand, Marco Andreetto, and Hartwig Adam. 2017. MobileNets: Efficient convolutional neural networks for mobile vision applications. arXiv preprint arXiv:1704.04861
[20]
Mark Sandler, Andrew Howard, Menglong Zhu, Andrey Zhmoginov, and Liang-Chieh Chen. 2018. MobileNetv2: Inverted residuals and linear bottlenecks. In Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition. 4510–4520.
[21]
Xiangyu Zhang, Xinyu Zhou, Mengxiao Lin, and Jian Sun. 2018. ShuffleNet: An extremely efficient convolutional neural network for mobile devices. In Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, Salt Lake City, Utah, USA. IEEE, 6848–6856.
[22]
Ningning Ma, Xiangyu Zhang, Hai-Tao Zheng, and Jian Sun. 2018. ShuffleNet v2: Practical guidelines for efficient CNN architecture design. In Proceedings of the European Conference on Computer Vision (ECCV’18), Munich, Germany. Springer, 116–131.
[23]
Barret Zoph, Vijay Vasudevan, Jonathon Shlens, and Quoc V. Le. 2018. Learning transferable architectures for scalable image recognition. In Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, Salt LakeCity, Utah, USA. IEEE, 8697–8710.
[24]
Jianing Deng, Zhiguo Shi, and Cheng Zhuo. 2019. Energy-efficient real-time UAV object detection on embedded platforms. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 39, 10 (2019), 3123–3127.
[25]
Mingxing Tan, Bo Chen, Ruoming Pang, Vijay Vasudevan, Mark Sandler, Andrew Howard, and Quoc V. Le. 2019. MnasNet: Platform-aware neural architecture search for mobile. In Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, Long Beach, CA, USA. IEEE, 2820–2828.
[26]
Andrew Howard, Mark Sandler, Grace Chu, Liang-Chieh Chen, Bo Chen, Mingxing Tan, Weijun Wang, Yukun Zhu, Ruoming Pang, Vijay Vasudevan, et al. 2019. Searching for MobileNetv3. In Proceedings of the IEEE International Conference on Computer Vision, Seoul, Korea. IEEE, 1314–1324.
[27]
Shunjie Dong, Jinlong Zhao, Maojun Zhang, Zhengxue Shi, Jianing Deng, Yiyu Shi, Mei Tian, and Cheng Zhuo. 2020. DeU-Net: Deformable U-Net for 3D cardiac MRI video segmentation. In International Conference on Medical Image Computing and Computer-Assisted Intervention, Lima, Peru. Springer, 98–107.
[28]
Zitao Zeng, Weihao Xie, Yunzhe Zhang, and Yao Lu. 2019. RIC-Unet: An improved neural network based on Unet for nuclei segmentation in histology images. IEEE Access 7 (2019), 21420–21428.
[29]
Xingang Yan, Weiwen Jiang, Yiyu Shi, and Cheng Zhuo. 2020. MS-NAS: Multi-scale neural architecture search for medical image segmentation. In International Conference on Medical Image Computing and Computer-Assisted Intervention, Lima, Peru. Springer, 388–397.
[30]
Michal Drozdzal, Eugene Vorontsov, Gabriel Chartrand, Samuel Kadoury, and Chris Pal. 2016. The importance of skip connections in biomedical image segmentation. In Deep Learning and Data Labeling for Medical Applications. Springer, 179–187.
[31]
Yufei Chen, Qinming Zhang, Tingtao Li, Hao Yu, Mei Tian, and Cheng Zhuo. 2019. ANT-UNet: Accurate and noise-tolerant segmentation for pathology image processing. In IEEE Biomedical Circuits and Systems Conference (BioCAS). IEEE, 1–4.
[32]
NVIDIA TensorRT. 2020. (2020). Retrieved December 10, 2021 from https://developer.nvidia.com/tensorrt.
[33]
Andrew Janowczyk and Anant Madabhushi. 2016. Deep learning for digital pathology image analysis: A comprehensive tutorial with selected use cases. Journal of Pathology Informatics 7 (2016).
[34]
Ilya Sutskever, James Martens, George Dahl, and Geoffrey Hinton. 2013. On the importance of initialization and momentum in deep learning. In International Conference on Machine Learning, Atlanta, USA. Omnipress, 1139–1147.
[35]
Pierre Gravel, Gilles Beaudoin, and Jacques A. De Guise. 2004. A method for modeling noise in medical images. IEEE Transactions on Medical Imaging 23, 10 (2004), 1221–1232.
[36]
Davood Karimi, Haoran Dou, Simon K. Warfield, and Ali Gholipour. 2020. Deep learning with noisy labels: Exploring techniques and remedies in medical image analysis. Medical Image Analysis 65 (2020), 101759.

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  • (2023)A Deep Learning Onion Peeling Approach to Measure Oral Epithelium Layer NumberCancers10.3390/cancers1515389115:15(3891)Online publication date: 31-Jul-2023

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Published In

cover image ACM Journal on Emerging Technologies in Computing Systems
ACM Journal on Emerging Technologies in Computing Systems  Volume 18, Issue 2
April 2022
411 pages
ISSN:1550-4832
EISSN:1550-4840
DOI:10.1145/3508462
  • Editor:
  • Ramesh Karri
Issue’s Table of Contents

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Association for Computing Machinery

New York, NY, United States

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Publication History

Published: 31 December 2021
Accepted: 01 February 2021
Revised: 01 December 2020
Received: 01 August 2020
Published in JETC Volume 18, Issue 2

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Author Tags

  1. Deep learning
  2. neural networks
  3. biomedical image segmentation
  4. lightweight network

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  • Research-article
  • Refereed

Funding Sources

  • Zhejiang Provincial Innovation Team
  • National Natural Science Foundation of China

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  • (2023)A Deep Learning Onion Peeling Approach to Measure Oral Epithelium Layer NumberCancers10.3390/cancers1515389115:15(3891)Online publication date: 31-Jul-2023

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