The Application of Deep Learning for the Segmentation and Classification of Coronary Arteries
Abstract
:1. Introduction
1.1. Diagnosis and Treatment of CAD
1.2. Challenges
1.3. Contribution
- The application of UNet, Unet++ and ResUNet-a for the automatic segmentation of coronary angiograms.
- Comparison of model’s performances for both segmentation and classification tasks.
- One of the major contributions of this study is the application of DL-based transferred learning using several pretrained models (EfficientNet-B0, DenseNet201, Mobilenet-v2, ResNet101 and Xception) for the classification of coronary angiograms.
- Comparison between the performance of models trained on the coronary artery small datasets can aid cardiologists in the selection of the best-performing model and also aid them in making appropriate decision-making.
- Another contribution of this study is the use of raw/unaltered data that are obtained from real patients by the cardiology department of Near East University Hospital, instead of using a dataset curated from an online repository system. We have noticed that a significant number of images available from online repository systems have been altered (i.e., cropped, rotated, and enlarged) to aid the segmentation and classification performance of coronary arteries. However, this is not the case in clinical applications.
- Performance evaluation of models based on accuracy, sensitivity, specificity, precision, Dice Score (F1 Score), Jaccard Index and Matthews correlation coefficient (MCC), negative predictive value (NPV), Cohen’s kappa, Area Under Curve (AUC) and Receiver Operating Characteristic (ROC) curve.
1.4. Related Work
2. Methodology
2.1. Dataset Description
2.2. Image Pre-Processing
2.3. Cross Validation
2.4. Segmentation
2.4.1. U-Net
2.4.2. Deep Residual U-Net (ResUNet)
2.4.3. UNet++
2.5. Classification
2.5.1. DenseNet
2.5.2. EfficientNet
2.5.3. MobileNet
2.5.4. ResNet
2.5.5. Inception
2.6. Experimental Design
2.7. Performance Metrics and Confusion Matrix
3. Experimental Results
3.1. Segmentation Results
3.2. Classification Results
4. Discussion
4.1. Limitations and Clinical Implications
4.2. Comparison of Segmentation Models Performance
4.3. Comparison of Classification Models Performance
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Reference | Image Acquisition | No. of Images | Method | Results |
---|---|---|---|---|
[14] | Cardiology Department of the Mexican Social Security Institute | 130 coronary angiograms | Multiscale versions of the Gaussian filter and Gabor filter | ACC: 0.9698, Sens: 0.6364, Spec: 0.9880, PPV: 0.7434, Dice coefficient: 0.6857 |
[16] | Department of The University Hospital Fattouma Bourguiba, Monastir, Tunisia | 50 coronary angiograms | Sato filter, Vessel enhancing diffusion filter, and Frangi filter Multiscale region growing | Mean precision: 82%, First dataset of Dice coefficient: 80 ± 5%, second dataset of Dice coefficient: 70 ± 5% |
[18] | Asan Medical Center (Internal) Chungnam National University Hospital (External) | Internal:3302 coronary angiograms, External:181 coronary angiograms | U-Net, ResNet101, DenseNet121, InceptionResNet-v2 | Average F1 score: 0.917, and 93.7% of the image |
[19] | University of Michigan Hospital | 462 coronary angiograms | Convolutional neural network, AngioNet | Dice score: 0.864, pixel accuracy (PA):0.983, Sens: 0.918, Spec: 0.987 |
[20] | Fuwai Central China Cardiovascular Hospital | 109 patient’s Coronary angiogram | Threshold segmentation, Region-based segmentation, PSPNet with TL | ACC: 0.957 Sens: 0.865 Spec:0.949 |
[21] | Public Database | 134 Coronary angiograms | CLAHE, Multiresolution strategy and multiscale strategy with U-Net | ACC: 0.9765 Sens: 0.7978 Spec: 0.9885 PPV: 0.8137 Dice coefficient: 0.7905 |
[31] | Mexican Social Security Institute (First dataset), Antczak and Liberadzki dataset (second dataset) | First dataset: 180 coronary angiograms (500 patches) Second dataset: 250 coronary angiograms | SVM-based classifier, UDMA | First database ACC: 0.89 and Jaccard Index: 0.80, and the second database, ACC: 0.88 Jaccard Index. 0.79 |
[32] | Antczak and Liberadzki dataset (public) | 10,000 synthetic images and 250 real coronary angiograms images | Pretrained (VGG16, ResNet50, and Inception-v3 with Transfer Learning | ACC: 0.95, Precis: 0.93, Sens: 0.98, Spec: 0.92, and F1 score: 0.95 |
Folds | Accuracy | Sensitivity | Specificity | Precision | Dice Score | Jaccard Index | MCC |
---|---|---|---|---|---|---|---|
Fold1 | 0.9929 | 0.8477 | 0.9970 | 0.8809 | 0.8611 | 0.7628 | 0.8591 |
Fold2 | 0.9905 | 0.8355 | 0.9960 | 0.8628 | 0.8429 | 0.7390 | 0.8413 |
Fold3 | 0.9917 | 0.8946 | 0.9942 | 0.8006 | 0.8416 | 0.7446 | 0.8405 |
Fold4 | 0.9926 | 0.8397 | 0.9968 | 0.8697 | 0.8521 | 0.7542 | 0.8497 |
Fold5 | 0.9911 | 0.8822 | 0.9942 | 0.7976 | 0.8360 | 0.7266 | 0.8335 |
Average | 0.9918 | 0.8599 | 0.9957 | 0.8423 | 0.8467 | 0.7454 | 0.8448 |
Folds | Accuracy | Sensitivity | Specificity | Precision | Dice Score | Jaccard Index | MCC |
---|---|---|---|---|---|---|---|
Fold1 | 0.9926 | 0.8224 | 0.9975 | 0.8925 | 0.8534 | 0.7508 | 0.8518 |
Fold2 | 0.9892 | 0.7728 | 0.9966 | 0.8760 | 0.8129 | 0.6964 | 0.8134 |
Fold3 | 0.9914 | 0.8133 | 0.9960 | 0.8407 | 0.8238 | 0.7178 | 0.8211 |
Fold4 | 0.9923 | 0.8394 | 0.9966 | 0.8615 | 0.8462 | 0.7452 | 0.8445 |
Fold5 | 0.9921 | 0.8029 | 0.9974 | 0.8872 | 0.8379 | 0.7324 | 0.8376 |
Average | 0.9915 | 0.8101 | 0.9968 | 0.8716 | 0.8348 | 0.7285 | 0.8337 |
Folds | Accuracy | Sensitivity | Specificity | Precision | Dice Score | Jaccard Index | MCC |
---|---|---|---|---|---|---|---|
Fold1 | 0.9878 | 0.9128 | 0.9900 | 0.7092 | 0.7945 | 0.6673 | 0.7969 |
Fold2 | 0.9872 | 0.8673 | 0.9915 | 0.7456 | 0.7932 | 0.6637 | 0.7935 |
Fold3 | 0.9879 | 0.8937 | 0.9904 | 0.7291 | 0.7919 | 0.6779 | 0.7959 |
Fold4 | 0.9907 | 0.9046 | 0.9932 | 0.7709 | 0.8292 | 0.7176 | 0.8288 |
Fold5 | 0.9867 | 0.9086 | 0.9890 | 0.6825 | 0.7742 | 0.6435 | 0.7786 |
Average | 0.9881 | 0.8974 | 0.9908 | 0.7274 | 0.7966 | 0.6740 | 0.7988 |
Folds | Accuracy | Sensitivity | Specificity | PPV | NPV | F1 Score | MCC | Cohen’s Kappa |
---|---|---|---|---|---|---|---|---|
Fold1 | 0.9412 | 0.8889 | 1 | 1 | 0.8889 | 0.9412 | 0.8889 | 0.8826 |
Fold2 | 0.8824 | 0.6923 | 1 | 1 | 0.8400 | 0.8182 | 0.7626 | 0.7354 |
Fold3 | 0.8529 | 0.7000 | 0.9167 | 0.7778 | 0.8800 | 0.7368 | 0.6369 | 0.6352 |
Fold4 | 0.9412 | 0.8182 | 1 | 1 | 0.9200 | 0.9000 | 0.8676 | 0.8589 |
Fold5 | 0.8824 | 0.7500 | 1 | 1 | 0.8182 | 0.8571 | 0.7834 | 0.7606 |
Average | 0.9000 | 0.7699 | 0.9833 | 0.9556 | 0.8694 | 0.8507 | 0.7879 | 0.7746 |
Folds | Accuracy | Sensitivity | Specificity | PPV | NPV | F1 Score | MCC | Cohen’s Kappa |
---|---|---|---|---|---|---|---|---|
Fold1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
Fold2 | 0.8529 | 0.6154 | 1 | 1 | 0.8077 | 0.7619 | 0.7050 | 0.6640 |
Fold3 | 0.8824 | 0.8000 | 0.9167 | 0.8000 | 0.9167 | 0.8000 | 0.7167 | 0.7167 |
Fold4 | 0.7941 | 0.8182 | 0.7826 | 0.6429 | 0.9000 | 0.7200 | 0.5711 | 0.5609 |
Fold5 | 0.9118 | 0.8125 | 1 | 1 | 0.8571 | 0.8966 | 0.8345 | 0.8211 |
Average | 0.8882 | 0.8092 | 0.9399 | 0.8889 | 0.8963 | 0.8357 | 0.7655 | 0.7525 |
Folds | Accuracy | Sensitivity | Specificity | PPV | NPV | F1 Score | MCC | Cohen’s Kappa |
---|---|---|---|---|---|---|---|---|
Fold1 | 0.9118 | 0.8333 | 1 | 1 | 0.8421 | 0.9091 | 0.8377 | 0.8247 |
Fold2 | 0.8824 | 0.6923 | 1 | 1 | 0.8400 | 0.8182 | 0.7626 | 0.7354 |
Fold3 | 0.8824 | 0.8000 | 0.9167 | 0.8000 | 0.9167 | 0.8000 | 0.7167 | 0.7167 |
Fold4 | 0.9118 | 0.8182 | 0.9565 | 0.9000 | 0.9167 | 0.8571 | 0.7954 | 0.7935 |
Fold5 | 0.8235 | 0.6875 | 0.9444 | 0.9167 | 0.7727 | 0.7857 | 0.6600 | 0.6408 |
Average | 0.8824 | 0.7663 | 0.9635 | 0.9233 | 0.8576 | 0.8340 | 0.7545 | 0.7422 |
Folds | Accuracy | Sensitivity | Specificity | PPV | NPV | F1 Score | MCC | Cohen’s Kappa |
---|---|---|---|---|---|---|---|---|
Fold1 | 0.9706 | 0.9444 | 1 | 1 | 0.9412 | 0.9714 | 0.9428 | 0.9412 |
Fold2 | 0.8824 | 0.7692 | 0.9524 | 0.9091 | 0.8696 | 0.8333 | 0.7496 | 0.7434 |
Fold3 | 0.8529 | 0.7000 | 0.9167 | 0.7778 | 0.88000 | 0.7368 | 0.6369 | 0.6352 |
Fold4 | 0.9412 | 0.9091 | 0.9565 | 0.9091 | 0.9565 | 0.9091 | 0.8656 | 0.8656 |
Fold5 | 0.8235 | 0.6875 | 0.9444 | 0.9167 | 0.7727 | 0.7857 | 0.6600 | 0.6408 |
Average | 0.8941 | 0.8021 | 0.9540 | 0.9025 | 0.8840 | 0.8473 | 0.7710 | 0.7652 |
Folds | Accuracy | Sensitivity | Specificity | PPV | NPV | F1 Score | MCC | Cohen’s Kappa |
---|---|---|---|---|---|---|---|---|
Fold1 | 0.9412 | 0.8889 | 1 | 1 | 0.8889 | 0.9412 | 0.8889 | 0.8828 |
Fold2 | 0.8824 | 0.6923 | 1 | 1 | 0.8400 | 0.8182 | 0.7626 | 0.7354 |
Fold3 | 0.7941 | 0.8000 | 0.7917 | 0.6154 | 0.9048 | 0.6957 | 0.5548 | 0.5441 |
Fold4 | 0.9706 | 0.9091 | 1 | 1 | 0.9583 | 0.9524 | 0.9334 | 0.9312 |
Fold5 | 0.8824 | 0.8125 | 0.9444 | 0.9286 | 0.8500 | 0.8667 | 0.7677 | 0.7622 |
Average | 0.8941 | 0.8206 | 0.9472 | 0.9088 | 0.8884 | 0.8548 | 0.7815 | 0.7711 |
Models | Accuracy | Sensitivity | Specificity | Precision | Dice Score | Jaccard Index | MCC |
---|---|---|---|---|---|---|---|
U-Net | 0.9918 | 0.8599 | 0.9957 | 0.8423 | 0.8467 | 0.7454 | 0.8448 |
ResUnet-a | 0.9915 | 0.8101 | 0.9968 | 0.8716 | 0.8348 | 0.7285 | 0.8337 |
UNet++ | 0.9881 | 0.8974 | 0.9908 | 0.7274 | 0.7966 | 0.6740 | 0.7988 |
Task | Models | Accuracy | Sensitivity | Specificity | PPV | NPV | F1 Score | MCC | Cohen’s Kappa |
---|---|---|---|---|---|---|---|---|---|
Normal and Stenosis | Densenet201 | 0.9000 | 0.7699 | 0.9833 | 0.9556 | 0.8694 | 0.8507 | 0.7879 | 0.7746 |
EfficientNet-B0 | 0.8882 | 0.8092 | 0.9399 | 0.8889 | 0.8963 | 0.8357 | 0.7655 | 0.7525 | |
MobileNet-v2 | 0.8824 | 0.7663 | 0.9635 | 0.9233 | 0.8576 | 0.8340 | 0.7545 | 0.7422 | |
ResNet101 | 0.8941 | 0.8021 | 0.9540 | 0.9025 | 0.8840 | 0.8473 | 0.7710 | 0.7652 | |
Xception | 0.8941 | 0.8206 | 0.9472 | 0.9088 | 0.8884 | 0.8548 | 0.7815 | 0.7711 |
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Share and Cite
Kaba, Ş.; Haci, H.; Isin, A.; Ilhan, A.; Conkbayir, C. The Application of Deep Learning for the Segmentation and Classification of Coronary Arteries. Diagnostics 2023, 13, 2274. https://doi.org/10.3390/diagnostics13132274
Kaba Ş, Haci H, Isin A, Ilhan A, Conkbayir C. The Application of Deep Learning for the Segmentation and Classification of Coronary Arteries. Diagnostics. 2023; 13(13):2274. https://doi.org/10.3390/diagnostics13132274
Chicago/Turabian StyleKaba, Şerife, Huseyin Haci, Ali Isin, Ahmet Ilhan, and Cenk Conkbayir. 2023. "The Application of Deep Learning for the Segmentation and Classification of Coronary Arteries" Diagnostics 13, no. 13: 2274. https://doi.org/10.3390/diagnostics13132274
APA StyleKaba, Ş., Haci, H., Isin, A., Ilhan, A., & Conkbayir, C. (2023). The Application of Deep Learning for the Segmentation and Classification of Coronary Arteries. Diagnostics, 13(13), 2274. https://doi.org/10.3390/diagnostics13132274