Welcome to visit Journal of Shaanxi Normal University(Natural Science Edition)!

COVIDSeg: the lightweight segmentation model for the lung CT images of COVID-19 patients

  • XIE Juanying ,
  • XIA Qin
Expand
  • School of Computer Science, Shaanxi Normal University, Xi'an 710119, Shaanxi, China

Received date: 2021-10-07

  Online published: 2022-05-10

Abstract

COVID-19 has severely been threatening human being. The computer aided automatic segmentation of lung CT (computed tomography) images is an important way to help medicine doctors to make fast and accurate diagnostic decisions. Therefore, a lightweight model referred to as COVIDSeg is proposed in this paper for segmenting the lung CT images of COVID-19 patients. This model adopts encoder-decoder structure. The squeeze and extend channel attention block (SECA) and the residual multi-scale channel attention block (RMSCA) are proposed to compose the main components of the encoder subnetwork. The dual-path structure is proposed to connect each module of the encoder network. The features are transferred layer by layer along the path, and features from different layers interact between pathways, so that the feature information can be transferred and expressed between different layers. The feature aggregation module is used as the main component of the decoder network, so as to realize the multipath decoder via multiscale feature decoding. This COVIDSeg model is tested on four public COVID-19 CT image datasets. The experimental results show that the proposed lightweight model COVIDSeg for segmenting the COVID-19 CT images outperforms the current main medical image segmentation models in terms of several popular metrics, and it is so far the best model for segmenting the lung CT images of COVID-19 patients. Furthermore, the ablation experiment was carried out to test the influence over the COVIDSeg model performance from its main modules. The experimental results show that the proposed SECA module and RMSCA module are effective to advance the performance of the COVIDSeg model.The segmentation results are visualized for this COVIDSeg model for the lung CT images of COVID-19 patients, and it is found that the segmentation results are basically identical to the real Mask of the images.

Cite this article

XIE Juanying , XIA Qin . COVIDSeg: the lightweight segmentation model for the lung CT images of COVID-19 patients[J]. Journal of Shaanxi Normal University(Natural Science Edition), 2022 , 50(3) : 65 -78 . DOI: 10.15983/j.cnki.jsnu.2022108

References

[1] CUCINOTTA D,VANELLI M. WHO declares COVID-19 a pandemic[J]. Acta Bio-Medica:Atenei Parmensis,2020,91(1):157-160.
[2] CHAN J F W,YUAN S F,KOK K H,et al. A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission:a study of a family cluster[J]. The Lancet,2020,395(10223):514-523.
[3] ZHU N,ZHANG D Y,WANG W L,et al. A novel coronavirus from patients with pneumonia in China,2019[J]. The New England Journal of Medicine,2020,382(8):727-733.
[4] 中华人民共和国国家卫生健康委员会. 新型冠状病毒肺炎诊疗方案(试行第七版)[EB/OL].[2021-03-03]. http://www.nhc.gov.cn.
National Health Commission of the People's Republic of China.Diagnosis and treatment protocol for COVID-19(trial version 7)[EB/OL].[2021-03-03]. http://www.nhc.gov.cn.
[5] KANNE J P,LITTLE B P,CHUNG J H,et al. Essentials for radiologists on COVID-19:an update-radiology scientific expert panel[J]. Radiology,2020,296(2):E113-E114.
[6] SHI H S,HAN X Y,JIANG N C,et al. Radiological findings from 81 patients with COVID-19 pneumonia in Wuhan,China:a descriptive study[J]. The Lancet Infectious Diseases,2020,20(4):425-434.
[7] KANNE J P. Chest CT findings in 2019 novel coronavirus (2019-nCoV) infections from Wuhan,China:key points for the radiologist[J]. Radiology,2020,295(1):16-17.
[8] 方旭,边云,刘芳,等.计算机断层扫描对新型冠状病毒肺炎的诊断要点及临床意义[J].第二军医大学学报,2020,41(6):588-591.
FANG X,BIAN Y,LIU F,et al.Computed tomography in coronavirus disease 2019:diagnosis and clinical significance[J].Academic Journal of Second Military Medical University,2020,41(6):588-591.
[9] PENG S T,CHEN W,SUN J W,et al. Multi-scale 3D U-Nets:an approach to automatic segmentation of brain tumor[J]. International Journal of Imaging Systems and Technology,2020,30(1):5-17.
[10] HU H G,GUAN Q,CHEN S Y,et al. Detection and recognition for life state of cell cancer using two-stage cascade CNNs[J]. IEEE/ACM Transactions on Computational Biology and Bioinformatics,2020,17(3):887-898.
[11] XIE J Y,LIU R,LUTTRELL J,et al. Deep learning based analysis of histopathological images of breast cancer[J]. Frontiers in Genetics,2019,10:80.
[12] XIE J Y,PENG Y. The head and neck tumor segmentation using NNU-Net with spatial and channel ‘squeeze & excitation’ blocks[M]//Head and Neck Tumor Segmentation.Cham:Springer,2021:28-36.
[13] RAJAMANI K T,SIEBERT H,HEINRICH M P. Dynamic deformable attention network (DDANet) for COVID-19 lesions semantic segmentation[J]. Journal of Biomedical Informatics,2021,119:103816.
[14] BUDAK Ü,ÇIBUK M,CÖMERT Z,et al. Efficient COVID-19 segmentation from CT slices exploiting semantic segmentation with integrated attention mechanism[J]. Journal of Digital Imaging,2021,34(2):263-272.
[15] BADRINARAYANAN V,KENDALL A,CIPOLLA R. SegNet:a deep convolutional encoder-decoder architecture for image segmentation[J]. IEEE Transactions on Pattern Analysis and Machine Intelligence,2017,39(12):2481-2495.
[16] KUMAR SINGH V,ABDEL-NASSER M,PANDEY N,et al. LungINFseg:segmenting COVID-19 infected regions in lung CT images based on a receptive-field-aware deep learning framework[J]. Diagnostics (Basel,Switzerland),2021,11(2):158.
[17] FAN D P,ZHOU T,JI G P,et al. Inf-Net:automatic COVID-19 lung infection segmentation from CT images[J]. IEEE Transactions on Medical Imaging,2020,39(8):2626-2637.
[18] RAZAVIAN A S,AZIZPOUR H,SULLIVAN J,et al. CNN features off-the-shelf:an astounding baseline for recognition[C]//2014 IEEE Conference on Computer Vision and Pattern Recognition Workshops.Columbus,USA: IEEE,2014:512-519.
[19] SHELHAMER E,LONG J,DARRELL T. Fully convolutional networks for semantic segmentation[J]. IEEE Transactions on Pattern Analysis and Machine Intelligence,2017,39(4):640-651.
[20] RONNEBERGER O,FISCHER P,BROX T. U-Net:convolutional networks for biomedical image segmentation[C]//Medical Image Computing and Computer-Assisted Intervention.Munich,Germany:MICCAI,2015:234-241.
[21] ZHOU Z W,SIDDIQUEE M M R,TAJBAKHSH N,et al. UNet++:a nested U-Net architecture for medical image segmentation[C]//Deep Learning in Medical Image Analysis and Multimodal Learning for Clinical Decision Support.Granada,Spain:MICCAI,2018:3-11.
[22] OKTAY O,SCHLEMPER J,FOLGOC L L,et al. Attention U-Net:learning where to look for the pancreas[EB/OL].[2021-04-11]. https://arxiv.org/abs/1804.03999.
[23] CORBETTA M, SHULMAN G L. Control of goal-directed and stimulus-driven attention in the brain[J]. Nature Reviews Neuroscience, 2002, 3(3): 201-215.
[24] HU J,SHEN L,SUN G. Squeeze-and-excitation networks[C]//2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition.Salt Lake City,USA:IEEE,2018:7132-7141.
[25] WANG Q L,WU B G,ZHU P F,et al. ECA-Net:efficient channel attention for deep convolutional neural networks[C]//2020 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR).Seattle,USA:IEEE,2020:11531-11539.
[26] CAO Y,XU J R,LIN S,et al. GCNet:non-local networks meet squeeze-excitation networks and beyond[C]//2019 IEEE/CVF International Conference on Computer Vision Workshop (ICCVW).Seoul,South Korea:IEEE,2019:1971-1980.
[27] FU J,LIU J,TIAN H J,et al. Dual attention network for scene segmentation[C]//2019 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR).Long Beach,USA:IEEE,2019:3141-3149.
[28] SCHRAUDOLPH N. Accelerated gradient descent by factor-centering decomposition[J]. Technical Report/IDSIA, 1998, 98:1-10.
[29] RAIKO T, VALPOLA H, LECUN Y.Deep learning made easier by linear transformations in perceptrons[C]//Artificial Intelligence and Statistics.Canary Island,Spain:JMLR,2012: 924-932.
[30] SRIVASTAVA R K,GREFF K,SCHMIDHUBER J. Training very deep networks[EB/OL].[2015-07-22].https://arxiv.org/abs/1507.06228.
[31] HE K M,ZHANG X Y,REN S Q,et al. Deep residual learning for image recognition[C]//2016 IEEE Conference on Computer Vision and Pattern Recognition.Las Vegas,USA:IEEE,2016:770-778.
[32] HUANG G,LIU Z,VAN DER MAATEN L,et al. Densely connected convolutional networks[C]//2017 IEEE Conference on Computer Vision and Pattern Recognition.Honolulu,USA:IEEE,2017:2261-2269.
[33] SZEGEDY C,LIU W,JIA Y Q,et al. Going deeper with convolutions[C]//2015 IEEE Conference on Computer Vision and Pattern Recognition.Boston,USA:IEEE,2015:1-9.
[34] CHEN L C,PAPANDREOU G,SCHROFF F,et al. Rethinking atrous convolution for semantic image segmentation[EB/OL].[2021-06-17].https://arxiv.org/abs/1706.05587.
[35] ZHAO H S,SHI J P,QI X J,et al. Pyramid scene parsing network[C]//2017 IEEE Conference on Computer Vision and Pattern Recognition.Honolulu,USA:IEEE,2017:6230-6239.
[36] CHEN C F,FAN Q F,MALLINAR N,et al. Big-little net:an efficient multi-scale feature representation for visual and speech recognition[EB/OL].[2021-07-10]. https://arxiv.org/abs/1807.03848.
[37] QIU Y, LIU Y, LI S, et al. Miniseg:an extremely minimum network for efficient covid-19 segmentation[EB/OL]. [2021-03-03].https://arxiv.org/abs/2004.09750.
[38] ZHENG C, DENG X, FU Q, et al. Deep learning-based detection for COVID-19 from chest CT using weak label[EB/OL].[2021-03-03].https://paperswithcode.com/paper/deep-learning-based-detection-for-covid-19.
[39] SHAN F, GAO Y, WANG J, et al.Lung infection quantification of COVID-19 in CT images with deep learning[EB/OL].[2021-03-10].https://arxiv.org/abs/2003/2003.04655.
[40] LI L, QIN L, XU Z, et al. Artificial intelligence distinguishes COVID-19 from community acquired pneumonia on chest CT[J]. Radiology, 2020, 296(2): E65-E72.
[41] MA J,WANG Y X,AN X L,et al.Towards data-efficient learning:a benchmark for COVID-19 CT lung and infection segmentation[EB/OL].[2021-04-27].https://arxiv. org/abs/2004.12537.
[42] WU Y H,GAO S H,MEI J,et al. JCS:an explainable COVID-19 diagnosis system by joint classification and segmentation[J]. IEEE Transactions on Image Processing:A Publication of the IEEE Signal Processing Society,2021,30:3113-3126.
[43] AMYAR A,MODZELEWSKI R,LI H,et al. Multi-task deep learning based CT imaging analysis for COVID-19 pneumonia:classification and segmentation[J]. Computers in Biology and Medicine,2020,126:104037.
[44] ZHOU T X,CANU S,RUAN S. Automatic COVID-19 CT segmentation using U-Net integrated spatial and channel attention mechanism[J]. International Journal of Imaging Systems and Technology,2021,31(1):16-27.
[45] JENSSEN H B. COVID-19 CT segmentation dataset[EB/OL]// [2021-03-03]. https://medicalsegmentation.com/covid19.
[46] MOROZOV S P,ANDREYCHENKO A E,PAVLOV N A,et al. MosMedData:chest CT scans with COVID-19 related findings dataset[EB/OL].[2021-05-13].https://arxiv.org/abs/2005.06465v1.
[47] CHEN L C,ZHU Y K,PAPANDREOU G,et al. Encoder-decoder with atrous separable convolution for semantic image segmentation[C]//Computer Vision-ECCV 2018.Munich,Germany:ECCV,2018:801-818.
[48] PASZKE A,CHAURASIA A,KIM S,et al. ENet:a deep neural network architecture for real-time semantic segmentation[EB/OL].[2021-06-07].https://arxiv.org/abs/1606.02147.
[49] MEHTA S,RASTEGARI M,CASPI A,et al. ESPNet:efficient spatial pyramid of dilated convolutions for semantic segmentation[C]//Computer Vision-ECCV 2018.Munich,Germany:ECCV,2018:561-580.
[50] WU T Y,TANG S,ZHANG R,et al. CGNet:a light-weight context guided network for semantic segmentation[J]. IEEE Transactions on Image Processing:A Publication of the IEEE Signal Processing Society,2021,30:1169-1179.
[51] LO S Y,HANG H M,CHAN S W,et al. Efficient dense modules of asymmetric convolution for real-time semantic segmentation[C]//MMAsia,19:Proceedings of the ACM Multimedia Asia.Beijing,China:ACM,2019:1-6.
Outlines

/