Liver tumor segmentation from computed tomography images using multiscale residual dilated encoder-decoder network
Bindu Madhavi Tummala
School of Computer Science and Engineering, VIT-AP University, Amaravati, Andhra Pradesh, India
Search for more papers by this authorCorresponding Author
Soubhagya Sankar Barpanda
School of Computer Science and Engineering, VIT-AP University, Amaravati, Andhra Pradesh, India
Correspondence
Soubhagya Sankar Barpanda, School of Computer Science and Engineering, VIT-AP University, Amaravati, Andhra Pradesh, India.
Email: [email protected]
Search for more papers by this authorBindu Madhavi Tummala
School of Computer Science and Engineering, VIT-AP University, Amaravati, Andhra Pradesh, India
Search for more papers by this authorCorresponding Author
Soubhagya Sankar Barpanda
School of Computer Science and Engineering, VIT-AP University, Amaravati, Andhra Pradesh, India
Correspondence
Soubhagya Sankar Barpanda, School of Computer Science and Engineering, VIT-AP University, Amaravati, Andhra Pradesh, India.
Email: [email protected]
Search for more papers by this authorAbstract
In this paper, an encoder-decoder-based architecture, which segments liver tumors with a two-step training process is proposed. Accurate liver tumor segmentation from CT images is still a major problem that impacts the diagnosis process. Heterogeneous densities, shapes, and unclear boundaries make tumor extraction challenging. First, the proposed network segments the liver, and then tumors are extracted from the liver ROIs. We have scaled down the images into different resolutions at each scale and applied normal convolutions along with the dilations and residual connections to capture broad conceptual information without data loss. MDICE, a combined loss function is used to enhance the learning capability and the 3D-IRCADb1 dataset is considered for training and testing because of its tumor complexities. The segmentation quality metrics DICE, MDICE are analyzed on the 3D-IRCADb1 dataset and obtained 0.98 and 0.65 accuracies per case for liver and tumor segmentation respectively, and found improvement over U-Net and other variants.
Open Research
DATA AVAILABILITY STATEMENT
Data sharing is not applicable to this article as no new data were created or analyzed in this study.
REFERENCES
- 1https://www.cancer.org/cancer/liver-cancer/causes-risks-prevention/risk-factors.html, American cancer Society.
- 2Li F. Automatic segmentation of liver tumor in ct images with deep convolutional neural networks. J Comput Commun. 2015; 3(11): 146.
10.4236/jcc.2015.311023 Google Scholar
- 3Moghbel SM. Review of liver segmentation and computer assisted detection/diagnosis methods in computed tomography. Artif Intell Rev. 2018; 50(4): 497-537.
- 4Deng X, Du G. Editorial: 3D segmentation in the clinic: a grand challenge II-liver tumor segmentation. Paper presented at: The MIDAS Journal - Grand Challenge Liver Tumor Segmentation (MICCAI Workshop); 2008:1-4.
- 5Wong LD. A semi-automated method for liver tumor segmentation based on 2d region growing with knowledge-based constraints. Paper presented at: MICCAI Workshop, Berlin: Springer-Verlag Berlin Heidelberg; 2008.
- 6Yan J, Schwartz LH, Zhao B. Semiautomatic segmentation of liver metastases on volumetric CT images. Med Phys. 2015 Nov; 42(11): 6283-6293. https://doi.org/10.1118/1.4932365
- 7Massoptier L, Casciaro S. A new fully automatic and robust algorithm for fast segmentation of liver tissue and tumors from ct scans. Eur Radiol. 2008; 18(8): 1658.
- 8Yim PJ, Foran DJ. Volumetry of hepatic metastases in computed tomography using the watershed and active contour algorithms: Proceedings of the 16th IEEE Symposium Computer-Based Medical Systems; 2003.
- 9Park SA, Seo K-S, Park J-A. Automatic hepatic tumor segmentation using statistical optimal threshold: International Conference on Computational Science; Springer; 2005.
- 10Summers RM, Linguraru MG, Richbourg WJ, Watt JM, Pamulapati V. Liver and tumor segmentation and analysis from ct of diseased patients via a generic affine invariant shape parameterization and graph cuts. In: Yoshida H, Sakas G, Linguraru MG, eds. Abdominal imaging. Computational and clinical applications. ABD-MICCAI 2011. Lecture Notes in Computer Science. Vol: 7029, Berlin, Heidelberg: Springer; 2011: 198-206. https://doi.org/10.1007/978-3-642-28557-8_25.
- 11Zheng Z, Zhang X, Xu H, Liang W, Zheng S, Shi Y. A unified level set framework combining hybrid algorithms for liver and liver tumor segmentation in CT images. BioMed Research International. 2018; 2018: 1–26. http://doi.org/10.1155/2018/3815346.
- 12Zhou J, Xiong W, Tian Q, et al. Semi-automatic segmentation of 3D liver tumors from CT scans using voxel classification and propagational learning. Paper presented at: MICCAI Workshop. Vol. 41; 2008.
- 13Huang W, Li N, Lin Z, et al. Liver tumor detection and segmentation using kernel-based extreme learning machine. Paper presented at: 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC, IEEE; 2013:3662-3665.
- 14Huang W, Yang Y, Lin Z, et al. Random feature subspace ensemble based extreme learning machine for liver tumor detection and segmentation. Paper presented at: 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Chicago, IL, IEEE; 2014:4675-4678.
- 15Vorontsov E. Metastatic liver tumor segmentation using texture-based omni-directional deformable surface models. In: H Oshida, J Näppi, S Saini, eds. Abdominal Imaging. Computational and Clinical Applications. ABD-MICCAI 2014. Lecture Notes in Computer Science. Cham: Springer; 2014: 74-83.
10.1007/978-3-319-13692-9_7 Google Scholar
- 16Alirr OI, Rahni AAA, Golkar E. An automated liver tumour segmentation from abdominal CT scans for hepatic surgical planning. International Journal of Computer Assisted Radiology and Surgery. 2018; 13(8): 1169–1176. http://doi.org/10.1007/s11548-018-1801-z.
- 17Ben-Cohen A, Diamant I, Klang E, Amitai M, Greenspan H. Fully Convolutional Network for Liver Segmentation and Lesions Detection. In: Carneiro G, et al., eds. Deep Learning and Data Labeling for Medical Applications. DLMIA 2016, LABELS. Lecture Notes in Computer Science. 2016;2016:10008. https://doi.org/10.1007/978-3-319-46976-8_9.
10.1007/978-3-319-46976-8_9 Google Scholar
- 18Ronneberger O, Fischer P, Brox T. U-Net: convolutional networks for biomedical image segmentation. In: N Navab, J Hornegger, W Wells, A Frangi, eds. Medical Image Computing and Computer-Assisted Intervention – MICCAI 2015. MICCAI 2015. Lecture Notes in Computer Science. Vol 9351. Cham: Springer; 2015.
10.1007/978-3-319-24574-4_28 Google Scholar
- 19Li X, Chen H, Qi X, Dou Q, Fu CW, Heng PA. H-DenseUNet: hybrid densely connected UNet for liver and tumor segmentation from CT volumes. IEEE Trans Med Imaging. 2018; 37(12): 2663-2674. https://doi.org/10.1109/TMI.2018.2845918
- 20Christ E, Ettlinger F, Grün F, et al. Automatic liver and tumor segmentation of CT and MRI volumes using cascaded fully convolutional neural networks. arXiv Preprint arXiv:1702.05970; 2017:415-423.
- 21Sun C, Guo S, Zhang H. Automatic segmentation of liver tumors from multiphase contrast-enhanced ct images based on FCNs. Artif Intell Med. 2017; 83: 58-66.
- 22Han X. Automatic liver lesion segmentation using a deep convolutional neural network method. arXiv Preprint arXiv:170407239; 2017.
- 23Albishri AA, Shah SJH, Lee Y. CU-Net: Cascaded U-Net model for automated liver and lesion segmentation and summarization. Paper presented at: IEEE International Conference on Bioinformatics and Biomedicine (BIBM); 2019:1416-1423. https://doi.org/10.1109/BIBM47256.2019.8983266.
- 24Li W, Jia F, Hu Q. Automatic segmentation of liver tumor in CT images with deep convolutional neural networks. J Comput Commun. 2015; 3: 146-151. https://doi.org/10.4236/jcc.2015.311023
10.4236/jcc.2015.311023 Google Scholar
- 25Wu W, Wu S, Zhou Z, Zhang R, Zhang Y. 3D liver tumor segmentation in CT images using improved fuzzy C-means and graph cuts. BioMed Res Int. 2017; 11:2017. https://doi.org/10.1155/2017/5207685
- 26Liao M, Zhao YQ, Liu XY, et al. Automatic liver segmentation from abdominal CT volumes using graph cuts and border marching. Comput Methods Programs Biomed. 2017; 143: 1-12. https://doi.org/10.1016/j.cmpb.2017.02.015
- 27Chlebus G, Schenk A, Moltz JH, et al. Automatic liver tumor segmentation in CT with fully convolutional neural networks and object-based postprocessing. Sci Rep. 2018; 8:15497.
- 28Li Y, Zhao YQ, Zhang F, et al. Liver segmentation from abdominal CT volumes based on level set and sparse shape composition. Comput Methods Programs Biomed. 2020 Oct; 195:105533.
- 29Meng L, Tian Y, Bu S. Liver tumor segmentation based on 3D convolutional neural network with dual scale. J Appl Clin Med Phys. 2020; 21: 144-157. https://doi.org/10.1002/acm2.12784
- 30Alirr OI. Deep learning and level set approach for liver and tumor segmentation from CT scans. J Appl Clin Med Phys. 2020; 21: 200-209. https://doi.org/10.1002/acm2.13003
- 31 sliver07, https://sliver07.grand-challenge.org/
- 32 IRCAD, https://www.ircad.fr/research/3dircadb/.
- 33 Competitions, https://competitions.codalab.org/competitions/17094
- 34Renard F. Variability and reproducibility in deep learning for medical image segmentation. Sci Rep. 2020; 10(13724).
- 35 Radiopaedia, https://radiopaedia.org/articles/hounsfield_unit?lang=gb
- 36Reza A. Realization of the contrast limited adaptive histogram equalization (CLAHE) for real-time image enhancement. VLSI Signal Process. 2004; 38: 35-44.
- 37 Albumentations, https://albumentations.ai/docs/introduction/imageaugmentation/.
- 38Badrinarayanan V, Kendall A, Cipolla R. SegNet: a deep convolutional encoder-decoder architecture for image segmentation. IEEE Trans Pattern Anal Mach Intell. 2017; 39(12): 2481-2495. https://doi.org/10.1109/TPAMI.2016.2644615
- 39Almotairi S, Kareem G, Aouf M, Almutairi B, Salem MA. Liver tumor segmentation in CT scans using modified SegNet. Sensors (Basel). 2020; 20(5):1516. https://doi.org/10.3390/s20051516
10.3390/s20051516 Google Scholar
- 40Holschneider RTM. A Real-Time Algorithm for Signal Analysis with the Help of the Wavelet Transform. Germany: Springer; 1990.
10.1007/978-3-642-75988-8_28 Google Scholar
- 41Yu F, Koltun V. Multi-scale context aggregation by dilated convolutions; 2015. https://arxiv.org/abs/1511.07122.
- 42He K, Zhang X, Ren S, Sun J. Spatial pyramid pooling in deep convolutional networks for visual recognition. Paper presented at: European Conference on Computer Vision; Springer; 2014:346-361.
- 43Liu Y, Qi N, Zhu Q, Li W. CR-U-net: cascaded U-net with residual mapping for liver segmentation in CT images. Paper presented at: IEEE Visual Communications and Image Processing (VCIP); 2019:1-4. https://doi.org/10.1109/VCIP47243.2019.8966072.