- Access to the synapse multi-organ dataset:
- Sign up in the official Synapse website and download the dataset. Convert them to numpy format, clip the images within [-125, 275], normalize each 3D image to [0, 1], and extract 2D slices from 3D volume for training cases while keeping the 3D volume in h5 format for testing cases.
- You can also send an Email directly to jienengchen01 AT gmail.com to request the preprocessed data for reproduction.
- The directory structure of the whole project is as follows:
.
├── TransCASCADE
│ ├──datasets
│ │ └── dataset_*.py
│ ├──train.py
│ ├──test.py
│ └──...
├── model
│ └── vit_checkpoint
│ └── imagenet21k
│ ├── R50+ViT-B_16.npz
│ └── *.npz
└── dataset
└──Synapse
├── test_vol_h5
│ ├── case0001.npy.h5
│ └── *.npy.h5
└── train_npz
├── case0005_slice000.npz
└── *.npz