| # Data Preparing | |
| 1. Access to the synapse multi-organ dataset: | |
| 1. Sign up in the [official Synapse website](https://www.synapse.org/#!Synapse:syn3193805/wiki/) 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. | |
| 2. You can also send an Email directly to jienengchen01 AT gmail.com to request the preprocessed data for reproduction. | |
| 2. The directory structure of the whole project is as follows: | |
| ```bash | |
| . | |
| ├── TransUNet | |
| │ ├──datasets | |
| │ │ └── dataset_*.py | |
| │ ├──train.py | |
| │ ├──test.py | |
| │ └──... | |
| ├── model | |
| │ └── vit_checkpoint | |
| │ └── imagenet21k | |
| │ ├── R50+ViT-B_16.npz | |
| │ └── *.npz | |
| └── data | |
| └──Synapse | |
| ├── test_vol_h5 | |
| │ ├── case0001.npy.h5 | |
| │ └── *.npy.h5 | |
| └── train_npz | |
| ├── case0005_slice000.npz | |
| └── *.npz | |
| ``` | |