Awesome
Unsupervised Bidirectional Cross-Modality Adaptation via Deeply Synergistic Image and Feature Alignment for Medical Image Segmentation
Tensorflow implementation of our unsupervised cross-modality domain adaptation framework. <br/> This is the version of our TMI paper. <br/> Please refer to the branch SIFA-v1 for the version of our AAAI paper. <br/>
Paper
Unsupervised Bidirectional Cross-Modality Adaptation via Deeply Synergistic Image and Feature Alignment for Medical Image Segmentation <br/> IEEE Transactions on Medical Imaging <br/> <br/>
<p align="center"> <img src="figure/framework.png"> </p>Installation
- Install TensorFlow 1.10 and CUDA 9.0
- Clone this repo
git clone https://github.com/cchen-cc/SIFA
cd SIFA
Data Preparation
- Raw data needs to be written into
tfrecord
format to be decoded by./data_loader.py
. The pre-processed data has been released from our work PnP-AdaNet. The training data can be downloaded here. The testing CT data can be downloaded here. The testing MR data can be downloaded here. - Put
tfrecord
data of two domains into corresponding folders under./data
accordingly. - Run
./create_datalist.py
to generate the datalists containing the path of each data.
Train
- Modify the data statistics in data_loader.py according to the specifc dataset in use. Note that this is a very important step to correctly convert the data range to [-1, 1] for the network inputs and ensure the performance.
- Modify paramter values in
./config_param.json
- Run
./main.py
to start the training process
Evaluate
- Our trained models can be downloaded from Dropbox. Note that the data statistics in evaluate.py need to be changed accordingly as specificed in the script.
- Specify the model path and test file path in
./evaluate.py
- Run
./evaluate.py
to start the evaluation.
Citation
If you find the code useful for your research, please cite our paper.
@article{chen2020unsupervised,
title = {Unsupervised Bidirectional Cross-Modality Adaptation via
Deeply Synergistic Image and Feature Alignment for Medical Image Segmentation},
author = {Chen, Cheng and Dou, Qi and Chen, Hao and Qin, Jing and Heng, Pheng Ann},
journal = {arXiv preprint arXiv:2002.02255},
year = {2020}
}
@inproceedings{chen2019synergistic,
author = {Chen, Cheng and Dou, Qi and Chen, Hao and Qin, Jing and Heng, Pheng-Ann},
title = {Synergistic Image and Feature Adaptation:
Towards Cross-Modality Domain Adaptation for Medical Image Segmentation},
booktitle = {Proceedings of The Thirty-Third Conference on Artificial Intelligence (AAAI)},
pages = {865--872},
year = {2019},
}
Acknowledgement
Part of the code is revised from the Tensorflow implementation of CycleGAN.
Note
- The repository is being updated
- Contact: Cheng Chen (chencheng236@gmail.com)