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Hierarchical Amortized GAN (HA-GAN)

Official PyTorch implementation for paper Hierarchical Amortized GAN for 3D High Resolution Medical Image Synthesis, accepted to IEEE Journal of Biomedical and Health Informatics

[Paper & Supplementary Material]

Generative Adversarial Networks (GAN) have many potential medical imaging applications. Due to the limited memory of Graphical Processing Units (GPUs), most current 3D GAN models are trained on low-resolution medical images. In this work, we propose a novel end-to-end GAN architecture that can generate high-resolution 3D images. We achieve this goal by using different configurations between training and inference. During training, we adopt a hierarchical structure that simultaneously generates a low-resolution version of the image and a randomly selected sub-volume of the high-resolution image. The hierarchical design has two advantages: First, the memory demand for training on high-resolution images is amortized among sub-volumes. Furthermore, anchoring the high-resolution sub-volumes to a single low-resolution image ensures anatomical consistency between sub-volumes. During inference, our model can directly generate full high-resolution images. We also incorporate an encoder (hidden in the figure to improve clarity) into the model to extract features from the images.

Requirements

  • PyTorch
  • scikit-image
  • nibabel
  • nilearn
  • tensorboardX
  • SimpleITK
conda env create --name hagan -f environment.yml
conda activate hagan

Data Preprocessing

The volume data need to be cropped or resized to 1283 or 2563, and intensity value need to be scaled to [-1,1]. In addition, we would like to advise you to trim blank axial slices. More details can be found at

python preprocess.py

Training

Unconditional HA-GAN

python train.py --workers 8 --img-size 256 --num-class 0 --exp-name 'HA_GAN_run1' --data-dir DATA_DIR

Conditional HA-GAN

python train.py --workers 8 --img-size 256 --num-class N --exp-name 'HA_GAN_cond_run1' --data-dir DATA_DIR

Track your training with Tensorboard:

It will take around 22 hours to train unconditional HA-GAN for 80000 iterations with two NVIDIA Tesla V100 GPU. It is suggested to have at least 3000 images for training to avoid mode collapse, or you may need to consider data augmentation.

Testing

visualization.ipynb
evaluation/visualize_feature_MDS.ipynb
python evaluation/fid_score.py

Sample images

Pretrained weights

Dataset Anatomy Iteration Checkpoint
COPDGene Lung 80000 Download
GSP Brain 80000 Download

Citation

@ARTICLE{hagan2022,
  author={Sun, Li and Chen, Junxiang and Xu, Yanwu and Gong, Mingming and Yu, Ke and Batmanghelich, Kayhan},
  journal={IEEE Journal of Biomedical and Health Informatics}, 
  title={Hierarchical Amortized GAN for 3D High Resolution Medical Image Synthesis}, 
  year={2022},
  volume={26},
  number={8},
  pages={3966-3975},
  doi={10.1109/JBHI.2022.3172976}}