MRU-NET: A U-Shaped Network for Retinal Vessel Segmentation
Abstract
:1. Introduction
- In MRU-Net, we add a multi-scale feature fusion module in the transition phase between the encoder and decoder and extract the feature information with different granularities using multi-scale dilated convolutions, so as to improve the model’s understanding of context information and to improve the model’s segmentation ability for microvessels.
- In MRU-Net, we add a feature balance module in the skip connection between the encoder and decoder to solve the problem of possible semantic gaps between low-dimensional features in the encoder and high-dimensional features in the decoder.
2. Proposed Method
- Data preprocessing: The original retinal blood vessel image cannot be effectively segmented due to factors such as uneven illumination, low noise, and low contrast. Therefore, image preprocessing is required before training to ensure the maximum possible increase in contrast between the retinal blood vessels and the background, thereby effectively improving the segmentation effect.
- Data expansion: Supervised segmentation training requires manual segmentation of images as labels, so data acquisition is difficult, resulting in insufficient training data for deep learning training. To solve this problem, we randomly divided each preprocessed image data into many smaller image blocks to achieve the purpose of expanding the data set.
- Model training: The image block is divided into a training set and validation set according to the ratio of 9:1. The training set is used as the input of U-Net model, and the corresponding gold standard image block is used as the label. The gradient descent method is used to train the model. According to the training effect of the training set and validation set, the model is continuously optimized until the model reaches the optimum.
- Effect test: Firstly, preprocess the test data in the same way; secondly, orderly segment the test image; then, input the segmented image blocks into the trained U-Net model to obtain the corresponding segmentation results; and finally, the segmentation results of each image block are combined to obtain a complete retinal blood vessel segmentation image.
2.1. Image Preprocessing
2.1.1. Data Set
2.1.2. Image Enhancement
- Through the contrast experiment, the green channel of the retinal blood vessel image has a higher contrast, so the fundus blood vessel image of the green channel is selected for experiments.
- The green channel image is processed for data standardization, and the conversion formula is as follows:
- Limited contrast histogram (CLAHE) is used to equalize the normalized image, thereby increasing the contrast between the blood vessel and the background image and making the image easier to segment.
- Gamma adaptive correction is performed according to different pixel characteristics of blood vessels and background images, thereby suppressing uneven light and centerline reflection in the fundus image, and the gamma value was set to 1.2.
2.1.3. Image Expansion
2.2. MRU-Net Structure
2.2.1. Encoder–Decoder Structure
2.2.2. Feature Fusion Module
2.2.3. Res-Dilated Block
2.2.4. Loss Function
3. Experiment
3.1. Evaluation Indicators
- Sensitivity (SE): The ratio of the total number of correctly segmented blood vessel pixels to the total number of manually segmented blood vessel pixels.
- Accuracy (ACC): The ratio of the total number of correctly segmented blood vessels and background pixels to the pixels of the entire image.
- precision: The ratio of the actual blood vessel pixels in the segmented blood vessel pixels.
- F1 value: The result of combining sensitivity and precision. When the F1 value is high, the method is more effective.
- Area Under Curve (AUC): The area under the receiver operating characteristic (ROC) curve. The larger the value, the better the segmentation effect.Among them, , , , and respectively represent true positive, true negative, false positive, and false negative.
3.2. Experimental Results
3.2.1. Subjective Assessment Results
3.2.2. Indicator Evalution Results
4. Discussion
5. Conclusions
Author Contributions
Funding
Conflicts of Interest
References
- Dash, J.; Bhoi, N. Retinal Blood Vessel Extraction Using Morphological Operators and Kirsch’s Template. In Soft Computing and Signal Processing; Springer: Berlin/Heidelberg, Germany, 2019; pp. 603–611. [Google Scholar]
- Zhang, J.; Dashtbozorg, B.; Bekkers, E.; Pluim, J.P.; Duits, R.; ter Haar Romeny, B.M. Robust retinal vessel segmentation via locally adaptive derivative frames in orientation scores. IEEE Trans. Med. Imaging 2016, 35, 2631–2644. [Google Scholar] [CrossRef] [Green Version]
- Ben Abdallah, M.; Malek, J.; Azar, A.T.; Montesinos, P.; Belmabrouk, H.; Esclarín Monreal, J.; Krissian, K. Automatic extraction of blood vessels in the retinal vascular tree using multiscale medialness. Int. J. Biomed. Imaging 2015, 2015. [Google Scholar] [CrossRef] [Green Version]
- Orlando, J.I.; Prokofyeva, E.; Blaschko, M.B. A discriminatively trained fully connected conditional random field model for blood vessel segmentation in fundus images. IEEE Trans. Biomed. Eng. 2016, 64, 16–27. [Google Scholar] [CrossRef] [Green Version]
- Wang, X.; Chen, D.; Luo, L. Retinal blood vessels segmentation based on multi-classifier fusion. In Proceedings of the 2018 Chinese Control And Decision Conference (CCDC), Shenyang, China, 9–11 June 2018; pp. 3542–3546. [Google Scholar]
- Gu, Z.; Cheng, J.; Fu, H.; Zhou, K.; Hao, H.; Zhao, Y.; Zhang, T.; Gao, S.; Liu, J. CE-Net: Context encoder network for 2D medical image segmentation. IEEE Trans. Med. Imaging 2019, 38, 2281–2292. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Zhou, Z.; Siddiquee, M.M.R.; Tajbakhsh, N.; Liang, J. Unet++: Redesigning skip connections to exploit multiscale features in image segmentation. IEEE Trans. Med. Imaging 2019, 39, 1856–1867. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Soomro, T.A.; Afifi, A.J.; Shah, A.A.; Soomro, S.; Baloch, G.A.; Zheng, L.; Yin, M.; Gao, J. Impact of Image Enhancement Technique on CNN Model for Retinal Blood Vessels Segmentation. IEEE Access 2019, 7, 158183–158197. [Google Scholar] [CrossRef]
- Kumawat, S.; Raman, S. Local phase U-Net for fundus image segmentation. In Proceedings of the ICASSP 2019—2019 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Brighton, UK, 12–17 May 2019; pp. 1209–1213. [Google Scholar]
- Tamim, N.; Elshrkawey, M.; Abdel Azim, G.; Nassar, H. Retinal Blood Vessel Segmentation Using Hybrid Features and Multi-Layer Perceptron Neural Networks. Symmetry 2020, 12, 894. [Google Scholar] [CrossRef]
- Cheng, Y.; Ma, M.; Zhang, L.; Jin, C.; Ma, L.; Zhou, Y. Retinal blood vessel segmentation based on Densely Connected U-Net. Math. Biosci. Eng. 2020, 17, 3088. [Google Scholar] [CrossRef]
- Francia, G.A.; Pedraza, C.; Aceves, M.; Tovar-Arriaga, S. Chaining a U-Net With a Residual U-Net for Retinal Blood Vessels Segmentation. IEEE Access 2020, 8, 38493–38500. [Google Scholar] [CrossRef]
- Xiuqin, P.; Zhang, Q.; Zhang, H.; Li, S. A fundus retinal vessels segmentation scheme based on the improved deep learning U-Net model. IEEE Access 2019, 7, 122634–122643. [Google Scholar] [CrossRef]
- Li, D.; Dharmawan, D.A.; Ng, B.P.; Rahardja, S. Residual U-Net for Retinal Vessel Segmentation. In Proceedings of the 2019 IEEE International Conference on Image Processing (ICIP), Taipei, Taiwan, 22–25 September 2019. [Google Scholar]
- Staal, J.; Abràmoff, M.D.; Niemeijer, M.; Viergever, M.A.; Van Ginneken, B. Ridge-based vessel segmentation in color images of the retina. IEEE Trans. Med. Imaging 2004, 23, 501–509. [Google Scholar] [CrossRef] [PubMed]
- Hoover, A.; Kouznetsova, V.; Goldbaum, M. Locating blood vessels in retinal images by piecewise threshold probing of a matched filter response. IEEE Trans. Med. Imaging 2000, 19, 203–210. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Ronneberger, O.; Fischer, P.; Brox, T. U-Net: Convolutional Networks for Biomedical Image Segmentation. In International Conference on Medical Image Computing and Computer-Assisted Intervention, Proceedings of the Medical Image Computing and Computer-Assisted Intervention—MICCAI 2015, Munich, Germany, 5–9 October 2015; Springer: Berlin/Heidelberg, Germany, 2015. [Google Scholar]
- Chen, L.C.; Papandreou, G.; Kokkinos, I.; Murphy, K.; Yuille, A.L. Deeplab: Semantic image segmentation with deep convolutional nets, atrous convolution, and fully connected crfs. IEEE Trans. Pattern Anal. Mach. Intell. 2017, 40, 834–848. [Google Scholar] [CrossRef]
- Ibtehaz, N.; Rahman, M.S. MultiResUNet: Rethinking the U-Net architecture for multimodal biomedical image segmentation. Neural Netw. 2020, 121, 74–87. [Google Scholar] [CrossRef] [PubMed]
- Xiao, X.; Lian, S.; Luo, Z.; Li, S. Weighted Res-UNet for high-quality retina vessel segmentation. In Proceedings of the 2018 9th International Conference on Information Technology in Medicine and Education (ITME), Hangzhou, China, 19–21 October 2018; pp. 327–331. [Google Scholar]
- Lu, J.; Xu, Y.; Chen, M.; Luo, Y. A Coarse-to-Fine Fully Convolutional Neural Network for Fundus Vessel Segmentation. Symmetry 2018, 10, 607. [Google Scholar] [CrossRef] [Green Version]
- Gao, X.; Cai, Y.; Qiu, C.; Cui, Y. Retinal blood vessel segmentation based on the Gaussian matched filter and U-net. In Proceedings of the 2017 10th International Congress on Image and Signal Processing, BioMedical Engineering and Informatics (CISP-BMEI), Shanghai, China, 14–16 October 2017; pp. 1–5. [Google Scholar]
- Hu, K.; Zhang, Z.; Niu, X.; Zhang, Y.; Cao, C.; Xiao, F.; Gao, X. Retinal vessel segmentation of color fundus images using multiscale convolutional neural network with an improved cross-entropy loss function. Neurocomputing 2018, 309, 179–191. [Google Scholar] [CrossRef]
- Feng, S.; Zhuo, Z.; Pan, D.; Tian, Q. CcNet: A cross-connected convolutional network for segmenting retinal vessels using multi-scale features. Neurocomputing 2020, 392, 268–276. [Google Scholar] [CrossRef]
- Jin, Q.; Meng, Z.; Pham, T.D.; Chen, Q.; Wei, L.; Su, R. DUNet: A deformable network for retinal vessel segmentation. Knowl. Based Syst. 2019, 178, 149–162. [Google Scholar] [CrossRef] [Green Version]
- Guo, S.; Wang, K.; Kang, H.; Zhang, Y.; Gao, Y.; Li, T. BTS-DSN: Deeply supervised neural network with short connections for retinal vessel segmentation. Int. J. Med. Inform. 2019, 126, 105–113. [Google Scholar] [CrossRef] [Green Version]
- Sekou, T.B.; Hidane, M.; Olivier, J.; Cardot, H. From Patch to Image Segmentation using Fully Convolutional Networks—Application to Retinal Images. arXiv 2019, arXiv:1904.03892. [Google Scholar]
- Orujov, F.; Maskeliunas, R.; Damaševičius, R.; Wei, W. Fuzzy based image edge detection algorithm for blood vessel detection in retinal images. Appl. Soft Comput. 2020, 94, 106452. [Google Scholar] [CrossRef]
- Dasgupta, A.; Singh, S. A fully convolutional neural network based structured prediction approach towards the retinal vessel segmentation. In Proceedings of the 2017 IEEE 14th International Symposium on Biomedical Imaging (ISBI 2017), Melbourne, Australia, 18–21 April 2017; pp. 248–251. [Google Scholar]
- Liskowski, P.; Krawiec, K. Segmenting Retinal Blood Vessels With Deep Neural Networks. IEEE Trans. Med. Imaging 2016, 35, 2369–2380. [Google Scholar] [CrossRef] [PubMed]
- Jebaseeli, T.J.; Durai, C.A.D.; Peter, J.D. Segmentation of retinal blood vessels from ophthalmologic Diabetic Retinopathy images. Comput. Electr. Eng. 2018, 73, 245–258. [Google Scholar] [CrossRef]
- Fu, H.; Xu, Y.; Lin, S.; Wong, D.W.K.; Liu, J. DeepVessel: Retinal Vessel Segmentation via Deep Learning and Conditional Random Field. In Proceedings of the International Conference on Medical Image Computing and Computer-Assisted Intervention, Medical Image Computing and Computer-Assisted Intervention—MICCAI 2016, Athens, Greece, 17–21 October 2016; Springer: Berlin/Heidelberg, Germany, 2016. [Google Scholar]
- Girard, F.; Kavalec, C.; Cheriet, F. Joint segmentation and classification of retinal arteries/veins from fundus images. Artif. Intell. Med. 2019, 94, 96–109. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Li, Q.; Feng, B.; Xie, L.; Liang, P.; Zhang, H.; Wang, T. A cross-modality learning approach for vessel segmentation in retinal images. IEEE Trans. Med. Imaging 2015, 35, 109–118. [Google Scholar] [CrossRef]
Method | Year | AUC | F1 | ACC | SE | Jaccard |
---|---|---|---|---|---|---|
U-Net | - | 0.9740 | 0.8203 | 0.9517 | 0.7978 | - |
Gao et al. [22] | 2017 | 0.9772 | - | 0.9636 | 0.7802 | - |
Hu et al. [23] | 2018 | 0.9759 | - | 0.9533 | 0.7772 | - |
Xiao et al. [20] | 2018 | - | - | 0.9655 | 0.7715 | - |
Feng et al. [24] | 2019 | 0.9678 | - | 0.9528 | 0.7625 | - |
Jin et al. [25] | 2019 | - | 0.8237 | 0.9566 | 0.7963 | - |
Guo et al. [26] | 2019 | 0.9806 | 0.8249 | 0.9561 | 0.7891 | - |
Gu et al. [6] | 2019 | 0.9779 | - | 0.9545 | 0.8309 | - |
Pan et al. [13] | 2019 | 0.9811 | - | 0.9650 | 0.8310 | - |
Sekou et al. [27] | 2019 | 0.9874 | 0.8252 | 0.9690 | 0.8398 | 0.7026 |
Cheng et al. [11] | 2020 | 0.9793 | - | 0.9559 | 0.7672 | - |
Orujov et al. [28] | 2020 | - | 0.5500 | 0.9390 | - | 0.3800 |
Our | 2020 | 0.9837 | 0.8444 | 0.9611 | 0.8618 | 0.7291 |
Method | Year | AUC | F1 | ACC | SE | Jaccard |
---|---|---|---|---|---|---|
U-Net | - | 0.9827 | 0.7917 | 0.9648 | 0.7128 | - |
Dasgupta et al. [29] | 2017 | - | 0.8133 | - | 0.7872 | - |
Hu et al. [23] | 2018 | 0.9751 | - | 0.9632 | 0.7543 | - |
Xiao et al. [20] | 2018 | - | - | 0.9693 | 0.7469 | - |
Lu et al. [21] | 2018 | 0.9801 | - | 0.9628 | 0.8090 | - |
Feng et al. [24] | 2019 | 0.9700 | - | 0.9633 | 0.7709 | - |
Jin et al. [25] | 2019 | 0.9832 | 0.8143 | 0.9641 | 0.7595 | - |
Sekou et al. [27] | 2019 | 0.9849 | 0.7929 | 0.9705 | 0.7695 | 0.6682 |
Tamim et al. [10] | 2020 | - | 0.7717 | 0.9632 | 0.7806 | - |
Orujov et al. [28] | 2020 | - | 0.5335 | 0.8650 | - | 0.3677 |
Our | 2020 | 0.9856 | 0.8143 | 0.9662 | 0.7887 | 0.6864 |
Data Set | AUC | F1 | ACC | SE |
---|---|---|---|---|
DRIVE | 0.0060 | 0.0002 | 0.0956 | |
STARE | 0.0216 | 0.0454 | 0.1787 | 0.0173 |
Methods | Time | GPU |
---|---|---|
[30] | 92 s | Tesla K20c |
[31] | 0.64 s | - |
[32] | 1.3 s | Tesla K40 |
[33] | 0.5 s | - |
[24] | 0.063 | GTX1070 |
[34] | 70 s | - |
Our | 2.2 s | GTX 1080Ti |
DRIVE | FF | Resnet |
---|---|---|
AUC | 0.9825 | 0.9773 |
F1 | 0.8420 | 0.8167 |
ACC | 0.9618 | 0.9548 |
SE | 0.8310 | 0.7905 |
© 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
Share and Cite
Ding, H.; Cui, X.; Chen, L.; Zhao, K. MRU-NET: A U-Shaped Network for Retinal Vessel Segmentation. Appl. Sci. 2020, 10, 6823. https://doi.org/10.3390/app10196823
Ding H, Cui X, Chen L, Zhao K. MRU-NET: A U-Shaped Network for Retinal Vessel Segmentation. Applied Sciences. 2020; 10(19):6823. https://doi.org/10.3390/app10196823
Chicago/Turabian StyleDing, Hongwei, Xiaohui Cui, Leiyang Chen, and Kun Zhao. 2020. "MRU-NET: A U-Shaped Network for Retinal Vessel Segmentation" Applied Sciences 10, no. 19: 6823. https://doi.org/10.3390/app10196823
APA StyleDing, H., Cui, X., Chen, L., & Zhao, K. (2020). MRU-NET: A U-Shaped Network for Retinal Vessel Segmentation. Applied Sciences, 10(19), 6823. https://doi.org/10.3390/app10196823