--- a/README.md +++ b/README.md @@ -1,56 +1,56 @@ -# SAML & A Multi-site Dataset for Prostate MRI Segmentation -by [Quande Liu](https://github.com/liuquande), [Qi Dou](http://www.cse.cuhk.edu.hk/~qdou/), [Pheng-Ann Heng](http://www.cse.cuhk.edu.hk/~pheng/). - -### Introduction - -* The Tensorflow implementation for our MICCAI 2020 paper '[Shape-aware Meta-learning for Generalizing Prostate MRI Segmentation to Unseen Domains](https://arxiv.org/pdf/2007.02035.pdf)'. - -<p align="center"> - <img src="figure/saml.png" width="650"/> -</p> - -* A well-organized multi-site dataset (from six data sources) for prostate MRI segmentation, that can support research in various problem settings with need of multi-site data, such as Domain Generalization, Multi-site Learning and Life-long Learning, etc. For more details and downloading link of the dataset, please [Find Here](https://liuquande.github.io/SAML/). - - -<p align="center"> - <img src="figure/protocol.png" width="650"/> -</p> - - -### Setup & Usage for the Code - -1. Check dependencies: - ```shell - python==2.7.17 - numpy==1.16.6 - scipy==1.2.1 - tensorflow-gpu==1.12.0 - tensorboard==1.12.2 - SimpleITK==1.2.0 - ``` -2. To train the model, you need to specify the training configurations (can simply use the default setting) in main.py, then run: - ```shell - python main.py --phase=train - ``` - -2. To evaluate the model, run: - ```shell - python main.py --phase=test --restore_model='/path/to/test_model.cpkt' - ``` - You will see the output results in the folder `./output/`. - -### Citation -If this repository is useful for your research, please cite: - -``` -@article{liu2020shape, - title={Shape-aware Meta-learning for Generalizing Prostate MRI Segmentation to Unseen Domains}, - author={Liu, Quande and Dou, Qi and Heng, Pheng-Ann}, - journal={International Conference on Medical Image Computing and Computer Assisted Intervention}, - year={2020} -} -``` - -### Questions - -For further question about the code or dataset, please contact 'qdliu@cse.cuhk.edu.hk' +# SAML & A Multi-site Dataset for Prostate MRI Segmentation +by [Quande Liu](https://github.com/liuquande), [Qi Dou](http://www.cse.cuhk.edu.hk/~qdou/), [Pheng-Ann Heng](http://www.cse.cuhk.edu.hk/~pheng/). + +### Introduction + +* The Tensorflow implementation for our MICCAI 2020 paper '[Shape-aware Meta-learning for Generalizing Prostate MRI Segmentation to Unseen Domains](https://arxiv.org/pdf/2007.02035.pdf)'. + +<p align="center"> + <img src="https://github.com/liuquande/SAML/blob/master/figure/saml.png?raw=true" width="650"/> +</p> + +* A well-organized multi-site dataset (from six data sources) for prostate MRI segmentation, that can support research in various problem settings with need of multi-site data, such as Domain Generalization, Multi-site Learning and Life-long Learning, etc. For more details and downloading link of the dataset, please [Find Here](https://liuquande.github.io/SAML/). + + +<p align="center"> + <img src="https://github.com/liuquande/SAML/blob/master/figure/protocol.png?raw=true" width="650"/> +</p> + + +### Setup & Usage for the Code + +1. Check dependencies: + ```shell + python==2.7.17 + numpy==1.16.6 + scipy==1.2.1 + tensorflow-gpu==1.12.0 + tensorboard==1.12.2 + SimpleITK==1.2.0 + ``` +2. To train the model, you need to specify the training configurations (can simply use the default setting) in main.py, then run: + ```shell + python main.py --phase=train + ``` + +2. To evaluate the model, run: + ```shell + python main.py --phase=test --restore_model='/path/to/test_model.cpkt' + ``` + You will see the output results in the folder `./output/`. + +### Citation +If this repository is useful for your research, please cite: + +``` +@article{liu2020shape, + title={Shape-aware Meta-learning for Generalizing Prostate MRI Segmentation to Unseen Domains}, + author={Liu, Quande and Dou, Qi and Heng, Pheng-Ann}, + journal={International Conference on Medical Image Computing and Computer Assisted Intervention}, + year={2020} +} +``` + +### Questions + +For further question about the code or dataset, please contact 'qdliu@cse.cuhk.edu.hk'