Design and Validation of a Deep Learning Model for Renal Stone Detection and Segmentation on Kidney–Ureter–Bladder Images
Abstract
:1. Introduction
2. Materials and Methods
2.1. Molecular Structure of Renal Stones
- Calcium (Ca)-containing stones:
- Non-calcium-containing stones:
2.2. Datasets
2.3. Image Preprocessing
2.3.1. Contrast-Limited Adaptive Histogram Equalization
2.3.2. Image Mask
2.3.3. Image Cropping
2.4. Data Augmentation
2.5. Deep Learning Model
2.5.1. Residual Network
2.5.2. Inception-ResNetV2
2.5.3. U-Net
2.6. System Architecture
3. Results
3.1. Evaluation Metrics
3.2. Effect of Data Augmentation on the Training of the Classification Model
3.3. Subsystem 1—Classification Model for Medical Images
3.4. Subsystem 2—Segmentation Model for Medical Images
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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CPU | Graphics Card | Memory |
---|---|---|
Intel Core i7-8700 @ 3.19 GHz | Nvidia GeForce RTX3070 8 G | 32 G |
Epochs | 50 |
---|---|
Batch size | 16 |
Learning rate | 0.001 |
Loss function | Binary cross-entropy |
Optimization algorithm | Ranger |
Predicted Label | |||
---|---|---|---|
Have Stone | NO Stone | ||
True label | Have stone | 182 | 3 |
No stone | 1 | 184 |
Accuracy | Sensitivity | Specificity | Precision | F1-Score | |
---|---|---|---|---|---|
Testing dataset | 0.989 | 0.995 | 0.984 | 0.984 | 0.989 |
Predicted Label | |||
---|---|---|---|
Have Stone | No Stone | ||
True label | Have stone | 184 | 0 |
No stone | 1 | 185 |
Accuracy | Sensitivity | Specificity | Precision | F1-Score | |
---|---|---|---|---|---|
Testing dataset | 0.997 | 1.000 | 0.995 | 0.995 | 0.997 |
ResNet50 [31] | Inception-ResNetV2 | |
---|---|---|
Accuracy | 0.989 | 0.997 |
Sensitivity | 0.995 | 1.000 |
Specificity | 0.984 | 0.995 |
Precision | 0.984 | 0.995 |
F1-score | 0.989 | 0.997 |
Epochs | 100 |
---|---|
Batch size | 8 |
Learning rate | 0.0001 |
Loss function | Focal loss + Jaccard loss |
Optimization algorithm | Ranger |
Bce_dice_loss | Bce_jaccard_loss | Binary_focal_dice_loss | Binary_focal_jaccard_loss | |
---|---|---|---|---|
TP | 270,382 | 267,678 | 259,717 | 268,203 |
FP | 72,813 | 75,517 | 83,478 | 74,992 |
TN | 1,480,475 | 1,480,115 | 1,481,879 | 1,482,633 |
FN | 26,330 | 26,690 | 24,926 | 27,751 |
Bce_dice_loss | Bce_jaccard_loss | Binary_focal_dice_loss | Binary_focal_jaccard_loss | |
---|---|---|---|---|
TP | 268,540 | 270,597 | 256,915 | 266,816 |
FP | 74,655 | 72,598 | 86,280 | 76,379 |
TN | 1,479,054 | 1,472,688 | 1,487,191 | 1,480,639 |
FN | 27,751 | 34,117 | 19,614 | 26,166 |
Bce_dice_loss | Bce_jaccard_loss | Binary_focal_dice_loss | Binary_focal_jaccard_loss | |||||
---|---|---|---|---|---|---|---|---|
Positive | Negative | Positive | Negative | Positive | Negative | Positive | Negative | |
Accuracy | 0.946 | 0.946 | 0.945 | 0.945 | 0.941 | 0.941 | 0.946 | 0.946 |
Sensitivity | 0.953 | 0.911 | 0.951 | 0.909 | 0.947 | 0.912 | 0.952 | 0.917 |
Precision | 0.983 | 0.788 | 0.982 | 0.780 | 0.983 | 0.757 | 0.984 | 0.781 |
F1-score | 0.968 | 0.845 | 0.967 | 0.840 | 0.965 | 0.827 | 0.968 | 0.844 |
IoU | 0.937 | 0.732 | 0.935 | 0.724 | 0.932 | 0.706 | 0.937 | 0.730 |
MIoU | 0.834 | 0.834 | 0.830 | 0.830 | 0.819 | 0.819 | 0.834 | 0.834 |
FWIoU | 0.904 | 0.904 | 0.902 | 0.902 | 0.897 | 0.897 | 0.905 | 0.905 |
Bce_dice_loss | Bce_jaccard_loss | Binary_focal_dice_loss | Binary_focal_jaccard_loss | |||||
---|---|---|---|---|---|---|---|---|
Positive | Negative | Positive | Negative | Positive | Negative | Negative | Positive | |
Accuracy | 0.945 | 0.945 | 0.942 | 0.942 | 0.943 | 0.943 | 0.945 | 0.945 |
Sensitivity | 0.952 | 0.906 | 0.953 | 0.888 | 0.945 | 0.929 | 0.951 | 0.911 |
Precision | 0.982 | 0.782 | 0.977 | 0.788 | 0.987 | 0.749 | 0.983 | 0.777 |
F1-score | 0.967 | 0.840 | 0.965 | 0.836 | 0.966 | 0.829 | 0.967 | 0.839 |
IoU | 0.935 | 0.724 | 0.932 | 0.717 | 0.934 | 0.708 | 0.935 | 0.722 |
MIoU | 0.830 | 0.830 | 0.825 | 0.825 | 0.821 | 0.821 | 0.829 | 0.829 |
FWIoU | 0.901 | 0.901 | 0.897 | 0.897 | 0.900 | 0.900 | 0.902 | 0.902 |
ResNet34′s Bce_dice_loss | ResNet34′s Binary_focal_jaccard_loss | ResNet50′s Bce_dice_loss | ResNet50′s Binary_focal_jaccard_loss | |
---|---|---|---|---|
Accuracy | 0.946 | 0.946 | 0.945 | 0.945 |
Sensitivity | 0.953 | 0.952 | 0.952 | 0.951 |
Precision | 0.983 | 0.984 | 0.982 | 0.983 |
F1-score | 0.968 | 0.968 | 0.967 | 0.967 |
IoU | 0.937 | 0.937 | 0.935 | 0.935 |
MIoU | 0.834 | 0.834 | 0.830 | 0.829 |
FWIoU | 0.904 | 0.905 | 0.901 | 0.902 |
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Huang, Z.-H.; Liu, Y.-Y.; Wu, W.-J.; Huang, K.-W. Design and Validation of a Deep Learning Model for Renal Stone Detection and Segmentation on Kidney–Ureter–Bladder Images. Bioengineering 2023, 10, 970. https://doi.org/10.3390/bioengineering10080970
Huang Z-H, Liu Y-Y, Wu W-J, Huang K-W. Design and Validation of a Deep Learning Model for Renal Stone Detection and Segmentation on Kidney–Ureter–Bladder Images. Bioengineering. 2023; 10(8):970. https://doi.org/10.3390/bioengineering10080970
Chicago/Turabian StyleHuang, Zih-Hao, Yi-Yang Liu, Wei-Juei Wu, and Ko-Wei Huang. 2023. "Design and Validation of a Deep Learning Model for Renal Stone Detection and Segmentation on Kidney–Ureter–Bladder Images" Bioengineering 10, no. 8: 970. https://doi.org/10.3390/bioengineering10080970