This repository provides extensive examples of synthetic liver tumors generated by our novel strategies. Check to see if you could tell which is real tumor and which is synthetic tumor. More importantly, our synthetic tumors can be used for training AI models, and have proven to achieve a similar (actually, better) performance in real tumor segmentation than a model trained on real tumors.
Amazing, right?
Label-Free Liver Tumor Segmentation
Qixin Hu1, Yixiong Chen2, Junfei Xiao3, Shuwen Sun4, Jieneng Chen3, Alan L. Yuille3, and Zongwei Zhou3,*
1 Huazhong University of Science and Technology,
2 The Chinese University of Hong Kong -- Shenzhen,
3 Johns Hopkins University,
4 The First Affiliated Hospital of Nanjing Medical University
CVPR, 2023
paper | code
Synthetic Tumors Make AI Segment Tumors Better
Qixin Hu1, Junfei Xiao2, Yixiong Chen3, Shuwen Sun4, Jieneng Chen2, Alan L. Yuille2, and Zongwei Zhou2,*
1 Huazhong University of Science and Technology,
2 Johns Hopkins University,
3 The Chinese University of Hong Kong -- Shenzhen,
4 The First Affiliated Hospital of Nanjing Medical University
Medical Imaging Meets NeurIPS, 2022
paper | code | slides | poster | demo | talk
git clone https://github.com/MrGiovanni/SyntheticTumors.git
cd SyntheticTumors
wget https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/model_swinvit.pt
See installation instructions.
datapath=/mnt/zzhou82/PublicAbdominalData/
# UNET (no.pretrain)
CUDA_VISIBLE_DEVICES=0 python -W ignore main.py --optim_lr=4e-4 --batch_size=2 --lrschedule=warmup_cosine --optim_name=adamw --model_name=unet --val_every=200 --max_epochs=4000 --save_checkpoint --workers=2 --noamp --distributed --dist-url=tcp://127.0.0.1:12235 --cache_num=200 --val_overlap=0.5 --syn --logdir="runs/synt.no_pretrain.unet" --train_dir $datapath --val_dir $datapath --json_dir datafolds/healthy.json
# Swin-UNETR-Base (pretrain)
CUDA_VISIBLE_DEVICES=0 python -W ignore main.py --optim_lr=4e-4 --batch_size=2 --lrschedule=warmup_cosine --optim_name=adamw --model_name=swin_unetrv2 --swin_type=base --val_every=200 --max_epochs=4000 --save_checkpoint --workers=2 --noamp --distributed --dist-url=tcp://127.0.0.1:12231 --cache_num=200 --val_overlap=0.5 --syn --logdir="runs/synt.pretrain.swin_unetrv2_base" --train_dir $datapath --val_dir $datapath --json_dir datafolds/healthy.json --use_pretrained
# Swin-UNETR-Base (no.pretrain)
CUDA_VISIBLE_DEVICES=0 python -W ignore main.py --optim_lr=4e-4 --batch_size=2 --lrschedule=warmup_cosine --optim_name=adamw --model_name=swin_unetrv2 --swin_type=base --val_every=200 --max_epochs=4000 --save_checkpoint --workers=2 --noamp --distributed --dist-url=tcp://127.0.0.1:12231 --cache_num=200 --val_overlap=0.5 --syn --logdir="runs/synt.no_pretrain.swin_unetrv2_base" --train_dir $datapath --val_dir $datapath --json_dir datafolds/healthy.json
# Swin-UNETR-Small (no.pretrain)
CUDA_VISIBLE_DEVICES=0 python -W ignore main.py --optim_lr=4e-4 --batch_size=2 --lrschedule=warmup_cosine --optim_name=adamw --model_name=swin_unetrv2 --swin_type=small --val_every=200 --max_epochs=4000 --save_checkpoint --workers=2 --noamp --distributed --dist-url=tcp://127.0.0.1:12233 --cache_num=200 --val_overlap=0.5 --syn --logdir="runs/synt.no_pretrain.swin_unetrv2_small" --train_dir $datapath --val_dir $datapath --json_dir datafolds/healthy.json
# Swin-UNETR-Tiny (no.pretrain)
CUDA_VISIBLE_DEVICES=0 python -W ignore main.py --optim_lr=4e-4 --batch_size=2 --lrschedule=warmup_cosine --optim_name=adamw --model_name=swin_unetrv2 --swin_type=tiny --val_every=200 --max_epochs=4000 --save_checkpoint --workers=2 --noamp --distributed --dist-url=tcp://127.0.0.1:12234 --cache_num=200 --val_overlap=0.5 --syn --logdir="runs/synt.no_pretrain.swin_unetrv2_tiny" --train_dir $datapath --val_dir $datapath --json_dir datafolds/healthy.json
datapath=/mnt/zzhou82/PublicAbdominalData/
# UNET (no.pretrain)
CUDA_VISIBLE_DEVICES=0 python -W ignore -W ignore main.py --optim_lr=4e-4 --batch_size=2 --lrschedule=warmup_cosine --optim_name=adamw --model_name=unet --val_every=200 --val_overlap=0.5 --max_epochs=4000 --save_checkpoint --workers=2 --noamp --distributed --dist-url=tcp://127.0.0.1:12235 --cache_num=200 --logdir="runs/real.no_pretrain.unet" --train_dir $datapath --val_dir $datapath --json_dir datafolds/lits.json
# Swin-UNETR-Base (pretrain)
CUDA_VISIBLE_DEVICES=0 python -W ignore -W ignore main.py --optim_lr=4e-4 --batch_size=2 --lrschedule=warmup_cosine --optim_name=adamw --model_name=swin_unetrv2 --swin_type=base --val_every=200 --val_overlap=0.5 --max_epochs=4000 --save_checkpoint --workers=2 --noamp --distributed --dist-url=tcp://127.0.0.1:12231 --cache_num=200 --logdir="runs/real.pretrain.swin_unetrv2_base" --train_dir $datapath --val_dir $datapath --json_dir datafolds/lits.json --use_pretrained
# Swin-UNETR-Base (no.pretrain)
CUDA_VISIBLE_DEVICES=0 python -W ignore -W ignore main.py --optim_lr=4e-4 --batch_size=2 --lrschedule=warmup_cosine --optim_name=adamw --model_name=swin_unetrv2 --swin_type=base --val_every=200 --val_overlap=0.5 --max_epochs=4000 --save_checkpoint --workers=2 --noamp --distributed --dist-url=tcp://127.0.0.1:12232 --cache_num=200 --logdir="runs/real.no_pretrain.swin_unetrv2_base" --train_dir $datapath --val_dir $datapath --json_dir datafolds/lits.json
# Swin-UNETR-Small (no.pretrain)
CUDA_VISIBLE_DEVICES=0 python -W ignore -W ignore main.py --optim_lr=4e-4 --batch_size=2 --lrschedule=warmup_cosine --optim_name=adamw --model_name=swin_unetrv2 --swin_type=small --val_every=200 --val_overlap=0.5 --max_epochs=4000 --save_checkpoint --workers=2 --noamp --distributed --dist-url=tcp://127.0.0.1:12233 --cache_num=200 --logdir="runs/real.no_pretrain.swin_unetrv2_small" --train_dir $datapath --val_dir $datapath --json_dir datafolds/lits.json
# Swin-UNETR-Tiny (no.pretrain)
CUDA_VISIBLE_DEVICES=0 python -W ignore -W ignore main.py --optim_lr=4e-4 --batch_size=2 --lrschedule=warmup_cosine --optim_name=adamw --model_name=swin_unetrv2 --swin_type=tiny --val_every=200 --val_overlap=0.5 --max_epochs=4000 --save_checkpoint --workers=2 --noamp --distributed --dist-url=tcp://127.0.0.1:12234 --cache_num=200 --logdir="runs/real.no_pretrain.swin_unetrv2_tiny" --train_dir $datapath --val_dir $datapath --json_dir datafolds/lits.json
datapath=/mnt/zzhou82/PublicAbdominalData/
# UNET (no.pretrain)
CUDA_VISIBLE_DEVICES=0 python -W ignore validation.py --model=unet --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/lits.json --log_dir runs/synt.no_pretrain.unet --save_dir out
# Swin-UNETR-Base (pretrain)
CUDA_VISIBLE_DEVICES=0 python -W ignore validation.py --model=swin_unetrv2 --swin_type=base --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/lits.json --log_dir runs/synt.pretrain.swin_unetrv2_base --save_dir out
# Swin-UNETR-Base (no.pretrain)
CUDA_VISIBLE_DEVICES=0 python -W ignore validation.py --model=swin_unetrv2 --swin_type=base --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/lits.json --log_dir runs/synt.no_pretrain.swin_unetrv2_base --save_dir out
# Swin-UNETR-Small (no.pretrain)
CUDA_VISIBLE_DEVICES=0 python -W ignore validation.py --model=swin_unetrv2 --swin_type=small --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/lits.json --log_dir runs/synt.no_pretrain.swin_unetrv2_small --save_dir out
# Swin-UNETR-Tiny (no.pretrain)
CUDA_VISIBLE_DEVICES=0 python -W ignore validation.py --model=swin_unetrv2 --swin_type=tiny --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/lits.json --log_dir runs/synt.no_pretrain.swin_unetrv2_tiny --save_dir out
datapath=/mnt/zzhou82/PublicAbdominalData/
# UNET (no.pretrain)
CUDA_VISIBLE_DEVICES=0 python -W ignore validation.py --model=unet --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/lits.json --log_dir runs/real.no_pretrain.unet --save_dir out
# Swin-UNETR-Base (pretrain)
CUDA_VISIBLE_DEVICES=0 python -W ignore validation.py --model=swin_unetrv2 --swin_type=base --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/lits.json --log_dir runs/real.pretrain.swin_unetrv2_base --save_dir out
# Swin-UNETR-Base (no.pretrain)
CUDA_VISIBLE_DEVICES=0 python -W ignore validation.py --model=swin_unetrv2 --swin_type=base --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/lits.json --log_dir runs/real.no_pretrain.swin_unetrv2_base --save_dir out
# Swin-UNETR-Small (no.pretrain)
CUDA_VISIBLE_DEVICES=0 python -W ignore validation.py --model=swin_unetrv2 --swin_type=small --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/lits.json --log_dir runs/real.no_pretrain.swin_unetrv2_small --save_dir out
# Swin-UNETR-Tiny (no.pretrain)
CUDA_VISIBLE_DEVICES=0 python -W ignore validation.py --model=swin_unetrv2 --swin_type=tiny --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/lits.json --log_dir runs/real.no_pretrain.swin_unetrv2_tiny --save_dir out
- Upload the paper to arxiv
- Make a video about Visual Turing Test (will appear in YouTube)
- Make an online app for Visual Turing Test
- Apply for a US patent
- Upload the evaluation code for small tumors
- Upload the evaluation code for the false-positive study
- Make a Jupyter Notebook for tumor synthesis
@article{hu2022synthetic,
title={Synthetic Tumors Make AI Segment Tumors Better},
author={Hu, Qixin and Xiao, Junfei and Chen, Yixiong and Sun, Shuwen and Chen, Jie-Neng and Yuille, Alan and Zhou, Zongwei},
journal={arXiv preprint arXiv:2210.14845},
year={2022}
}
This work was supported by the Lustgarten Foundation for Pancreatic Cancer Research and the McGovern Foundation. The segmentation backbone is based on Swin UNETR; we appreciate the effort of the MONAI Team to provide and maintain open-source code to the community. We thank Camille Torrico and Alexa Delaney for improving the writing of this paper. Paper content is covered by patents pending.