Authors: Razvan-Gabriel Dumitru, Darius Peteleaza & Catalin Craciun
If you wish to contact any of us for any reason, please use the above click-able email links.
The paper was published in Nature Scientific Reports in 16 June 2023
.
The detailed paper can be found at https://www.nature.com/articles/s41598-023-36940-5. Please cite our work if you use it.
A full description of all the components is available in our paper linked above.
Our implementation has been tested and run on Python 3.10
using the libraries from requirements.txt
.
To install the libraries you can run the command:
pip install -r requirements.txt
NOTE: You should be able to use slightly different versions for the libraries than the ones we used as long as they are compatible with one another.
We tested the model on machines using: Windows 10, Windows 11, and Linux Ubuntu 20.04 operating systems.
We trained the model using both an NVIDIA RTX 3090 24GB VRAM and NVIDIA A100 40GB, so 24GB of VRAM should be enough to train the model.
The project can be run using Jupyter Notebook on the file ModelNotebook.ipynb
.
The randomly split datasets we tested the models on are publicly available here.
The datasets used in this study are publicly available at:
- Kvasir-SEG: here.
- CVC-ClinicDB: here.
- ETIS-LaribpolypDB: here.
- CVC-ColonDB: here.
The results presented in the paper are also avaiable here:
Method | DSC | Jaccard | Precision | Recall | Accuracy |
---|---|---|---|---|---|
U-Net (with our augmentations) | 0.8655 | 0.7629 | 0.8593 | 0.8718 | 0.9563 |
HRNetV2 | 0.8530 | 0.7438 | 0.8778 | 0.8297 | 0.9539 |
PraNet (pre-trained) | 0.9094 | 0.8339 | 0.9599 | 0.8640 | 0.9738 |
HarDNet-DFUS (pre-trained) | 0.8626 | 0.7584 | 0.9351 | 0.8005 | 0.9583 |
MSRF-Net | 0.8508 | 0.7404 | 0.8993 | 0.8074 | 0.9543 |
FCN-Transformer (pre-trained) | 0.9220 | 0.8554 | 0.9238 | 0.9203 | 0.9749 |
OURS (no pre-training, 17 filters) | 0.9343 | 0.8769 | 0.9350 | 0.9337 | 0.9789 |
OURS (no pre-training, 34 filters) | 0.9502 | 0.9051 | 0.9628 | 0.9379 | 0.9842 |
Standard Deviation (between methods) | 0.0373 | 0.0615 | 0.0349 | 0.0519 | 0.0115 |
Method | DSC | Jaccard | Precision | Recall | Accuracy |
---|---|---|---|---|---|
U-Net (with our augmentations) | 0.7631 | 0.6169 | 0.7989 | 0.7303 | 0.9599 |
HRNetV2 | 0.7776 | 0.6361 | 0.8260 | 0.7346 | 0.9629 |
PraNet (pre-trained) | 0.8742 | 0.7766 | 0.9608 | 0.8020 | 0.9780 |
HarDNet-DFUS (pre-trained) | 0.7279 | 0.5723 | 0.8945 | 0.6137 | 0.9586 |
MSRF-Net | 0.9060 | 0.8282 | 0.9547 | 0.8621 | 0.9842 |
FCN-Transformer (pre-trained) | 0.9327 | 0.8740 | 0.9728 | 0.8958 | 0.9886 |
OURS (no pre-training, 17 filters) | 0.9450 | 0.8952 | 0.9488 | 0.9406 | 0.9903 |
OURS (no pre-training, 34 filters) | 0.9478 | 0.9009 | 0.9468 | 0.9489 | 0.9907 |
Standard Deviation (between methods) | 0.0837 | 0.1260 | 0.0622 | 0.1099 | 0.0131 |
Method | DSC | Jaccard | Precision | Recall | Accuracy |
---|---|---|---|---|---|
U-Net (with our augmentations) | 0.7984 | 0.6969 | 0.8322 | 0.7724 | 0.9734 |
HRNetV2 | 0.4720 | 0.3089 | 0.4645 | 0.4797 | 0.9433 |
PraNet (pre-trained) | 0.8827 | 0.7900 | 0.9825 | 0.8013 | 0.9877 |
HarDNet-DFUS (pre-trained) | 0.8662 | 0.7640 | 0.9708 | 0.7819 | 0.9869 |
MSRF-Net | 0.7791 | 0.6382 | 0.9191 | 0.6762 | 0.9797 |
FCN-Transformer (pre-trained) | 0.9163 | 0.8455 | 0.9633 | 0.8736 | 0.9915 |
OURS (no pre-training, 17 filters) | 0.9324 | 0.8734 | 0.9539 | 0.9118 | 0.9930 |
OURS (no pre-training, 34 filters) | 0.9354 | 0.8788 | 0.9309 | 0.9400 | 0.9931 |
Standard Deviation (between methods) | 0.1433 | 0.1758 | 0.1620 | 0.1383 | 0.0156 |
Method | DSC | Jaccard | Precision | Recall | Accuracy |
---|---|---|---|---|---|
U-Net (with our augmentations) | 0.8032 | 0.7037 | 0.8100 | 0.8274 | 0.9807 |
HRNetV2 | 0.6383 | 0.4687 | 0.5858 | 0.7010 | 0.9565 |
PraNet (pre-trained) | 0.9131 | 0.8401 | 0.9657 | 0.8659 | 0.9901 |
HarDNet-DFUS (pre-trained) | 0.7398 | 0.5870 | 0.9500 | 0.6057 | 0.9761 |
MSRF-Net | 0.8371 | 0.7198 | 0.8603 | 0.8151 | 0.9829 |
FCN-Transformer (pre-trained) | 0.9073 | 0.8304 | 0.9107 | 0.9040 | 0.9899 |
OURS (no pre-training, 17 filters) | 0.9353 | 0.8785 | 0.9314 | 0.9392 | 0.9929 |
OURS (no pre-training, 34 filters) | 0.9230 | 0.8571 | 0.9113 | 0.9351 | 0.9914 |
Standard Deviation (between methods) | 0.0986 | 0.1367 | 0.1156 | 0.1099 | 0.0112 |
Method | DSC | Jaccard | Precision | Recall | Accuracy |
---|---|---|---|---|---|
U-Net (with our augmentations) | 0.7010 | 0.5397 | 0.6640 | 0.7423 | 0.9441 |
HRNetV2 | 0.7457 | 0.5945 | 0.7642 | 0.7280 | 0.9561 |
PraNet (pre-trained) | 0.7744 | 0.6319 | 0.9494 | 0.6539 | 0.9638 |
HarDNet-DFUS (pre-trained) | 0.5784 | 0.4068 | 0.5974 | 0.5605 | 0.9263 |
MSRF-Net | 0.6763 | 0.5109 | 0.6965 | 0.6572 | 0.9444 |
FCN-Transformer (pre-trained) | 0.8314 | 0.7114 | 0.8839 | 0.7848 | 0.9719 |
OURS (no pre-training, 17 filters) | 0.8014 | 0.6686 | 0.8851 | 0.7321 | 0.9679 |
OURS (no pre-training, 34 filters) | 0.8211 | 0.6965 | 0.8860 | 0.7650 | 0.9705 |
Standard Deviation (between methods) | 0.0803 | 0.0975 | 0.1198 | 0.0692 | 0.0150 |
Method | DSC | Jaccard | Precision | Recall | Accuracy |
---|---|---|---|---|---|
U-Net (with our augmentations) | 0.5369 | 0.3670 | 0.4374 | 0.6951 | 0.8068 |
HRNetV2 | 0.5531 | 0.3822 | 0.4242 | 0.7944 | 0.7931 |
PraNet (pre-trained) | 0.6852 | 0.5212 | 0.7647 | 0.6207 | 0.9130 |
HarDNet-DFUS (pre-trained) | 0.7272 | 0.5714 | 0.9180 | 0.6021 | 0.9261 |
MSRF-Net | 0.5152 | 0.3469 | 0.3939 | 0.7443 | 0.7742 |
FCN-Transformer (pre-trained) | 0.8800 | 0.7858 | 0.9659 | 0.8082 | 0.9645 |
OURS (no pre-training, 17 filters) | 0.7525 | 0.6032 | 0.6873 | 0.8314 | 0.9119 |
OURS (no pre-training, 34 filters) | 0.8251 | 0.7023 | 0.7740 | 0.8834 | 0.9396 |
Standard Deviation (between methods) | 0.1285 | 0.1516 | 0.2121 | 0.0944 | 0.0698 |
An example of qualitative results can be seen below:
The weights for the models that achieved the final results can be found on here on Google Drive.
Dumitru, RG., Peteleaza, D. & Craciun, C. Using DUCK-Net for polyp image segmentation. Sci Rep 13, 9803 (2023). https://doi.org/10.1038/s41598-023-36940-5
To cite the paper please use the following citation:
TY - JOUR
AU - Dumitru, Razvan-Gabriel
AU - Peteleaza, Darius
AU - Craciun, Catalin
PY - 2023
DA - 2023/06/16
TI - Using DUCK-Net for polyp image segmentation
JO - Scientific Reports
SP - 9803
VL - 13
IS - 1
AB - This paper presents a novel supervised convolutional neural network architecture, “DUCK-Net”, capable of effectively learning and generalizing from small amounts of medical images to perform accurate segmentation tasks. Our model utilizes an encoder-decoder structure with a residual downsampling mechanism and a custom convolutional block to capture and process image information at multiple resolutions in the encoder segment. We employ data augmentation techniques to enrich the training set, thus increasing our model's performance. While our architecture is versatile and applicable to various segmentation tasks, in this study, we demonstrate its capabilities specifically for polyp segmentation in colonoscopy images. We evaluate the performance of our method on several popular benchmark datasets for polyp segmentation, Kvasir-SEG, CVC-ClinicDB, CVC-ColonDB, and ETIS-LARIBPOLYPDB showing that it achieves state-of-the-art results in terms of mean Dice coefficient, Jaccard index, Precision, Recall, and Accuracy. Our approach demonstrates strong generalization capabilities, achieving excellent performance even with limited training data.
SN - 2045-2322
UR - https://doi.org/10.1038/s41598-023-36940-5
DO - 10.1038/s41598-023-36940-5
ID - Dumitru2023
ER -
@article{article,
author = {Dumitru, Razvan-Gabriel and Peteleaza, Darius},
year = {2023},
month = {06},
pages = {},
title = {Using DUCK-Net for polyp image segmentation},
volume = {13},
journal = {Scientific Reports},
doi = {10.1038/s41598-023-36940-5}
}