README.md

December 4, 2024 · View on GitHub

UNet Zoo for Medical Image Segmentation

CNN vs ViT vs Mamba vs KAN

Introduction

The Exploration of CNN-, ViT-, Mamba-, and KAN-based UNet for Medical Image Segmentation.

Over 10 Segmentation Networks, 7 public benchmark datasets, 6 evaluation metrics are public available!

Segmentation Network List
Segmentation Dataset List
Segmentation Metrics List
Environment
Usage
Reference

Networks

Architecture	Name	Reference	Availability
CNN	U-net	Ronneberger et al. (2015)	✅
CNN	Attention U-net	Oktay et al. (2018)	✅
CNN	ResUnet	Diakogiannis et al. (2020)	✅
CNN	DenseUnet	Li et al. (2020)	✅
CNN	ConvUNeXT	Han et al. (2022)	✅
CNN	CMUNeXt	Tang et al. (2023)	⏳
CNN	AMSUnet	Yin et al. (2023)	⏳
CNN	MBSNet	Jin et al. (2023)	⏳
CNN	TriConvUNeXT	Ma et al. (2024)	⏳
ViT	TransUNET	Chen et al. (2021)	✅
ViT	Swin-UNET	Hu et al. (2021)	✅
ViT	H2Former	He et al. (2023)	⏳
ViT	UDTransNet	Wang et al. (2024)	⏳
ViT	CSWin-UNet	Liu et al. (2025)	⏳
Mamba	Mamba-UNet	Wang et al. (2024)	✅
Mamba	VM-UNet	Ruan et al. (2024)	⏳
KAN	U-KAN	Li et al. (2024)	⏳
KAN	KAN-UNet	Wang et al. (2024)	✅

Datasets

Dataset	Reference	Google Drive	Baidu Netdisk	Status
GLAS	Official	Link	Link (Passcode: `fp42`)	✅
BUSI	Official	Link	Link (Passcode: `5m5m`)	✅
2018DSB	Official	Link	Link (Passcode: `yavx`)	✅
CVC-ClinicDB	Official	Link	Link (Passcode: `3tpy`)	✅
Kvasir-SEG	Official	Link	Link (Passcode: `6fgs`)	✅
ISIC2016	Official	Link	Link (Passcode: `m2fw`)	✅
PH2	Official	Link	Link (Passcode: `aiax`)	✅
ACDC	Official			⏳
Synapse	Official			⏳

Metrics

Metric	Description	Formula	Status
Dice	Measures overlap between predicted and ground truth masks	$\frac{2TP}{2TP + FP + FN}$	✅
IoU	Intersection over Union, also known as Jaccard Index	$\frac{TP}{TP + FP + FN}$	✅
Accuracy	Proportion of correctly classified elements	$\frac{TP + TN}{TP + FP + FN + TN}$	✅
Precision	Proportion of true positive predictions	$\frac{TP}{TP + FP}$	✅
Sensitivity	True positive rate (Recall)	$\frac{TP}{TP + FN}$	✅
Specificity	True negative rate	$\frac{TN}{TN + FP}$	✅

Environment

Pytorch
Some basic python packages: Torchio, Numpy, Scikit-image, SimpleITK, Scipy, Medpy, nibabel, tqdm ......
For Mamba-related packages, please see [PyPI (mamba-ssm)], [Official GitHub (mamba)], [PyPI (causal-conv1d)] , [GitHub (causal-conv1d)].
For KAN-related packages, please see [PyPI (pykan)], [Official GitHub (ConvKAN)], [PyPI (convkan)], [Official GitHub (ConvKAN)].

Usage

Download the Code.

git clone https://github.com/ziyangwang007/UNet-Seg.git 
cd UNet-Seg

Download the Dataset via Google Drive or Baidu Netdisk to UNet-Seg/data folder.
Download Pretrained Model

Download through Google Drive for SwinUNet, and [Google Drive] for Mamba-UNet, and save in UNet-Seg/pretrained_ckpt.

Train the model.

CUDA_VISIBLE_DEVICES=0 python -u train.py --network UNet --datasets PH2  && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network UNet --datasets isic16  && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network UNet --datasets BUSI  && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network UNet --datasets GLAS  && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network UNet --datasets CVC-ClinicDB && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network UNet --datasets Kvasir-SEG && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network UNet --datasets 2018DSB && \

CUDA_VISIBLE_DEVICES=0 python -u train.py --network DenseUnet --datasets PH2  && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network DenseUnet --datasets isic16  && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network DenseUnet --datasets BUSI  && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network DenseUnet --datasets GLAS  && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network DenseUnet --datasets CVC-ClinicDB && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network DenseUnet --datasets Kvasir-SEG && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network DenseUnet --datasets 2018DSB && \

CUDA_VISIBLE_DEVICES=0 python -u train.py --network AttU_Net --datasets PH2  && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network AttU_Net --datasets isic16  && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network AttU_Net --datasets BUSI  && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network AttU_Net --datasets GLAS  && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network AttU_Net --datasets CVC-ClinicDB && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network AttU_Net --datasets Kvasir-SEG && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network AttU_Net --datasets 2018DSB && \

CUDA_VISIBLE_DEVICES=0 python -u train.py --network ConvUNeXt --datasets PH2  && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network ConvUNeXt --datasets isic16  && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network ConvUNeXt --datasets BUSI  && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network ConvUNeXt --datasets GLAS  && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network ConvUNeXt --datasets CVC-ClinicDB && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network ConvUNeXt --datasets Kvasir-SEG && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network ConvUNeXt --datasets 2018DSB && \

CUDA_VISIBLE_DEVICES=0 python -u train.py --network SwinUnet --datasets PH2  && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network SwinUnet --datasets isic16  && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network SwinUnet --datasets BUSI  && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network SwinUnet --datasets GLAS  && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network SwinUnet --datasets CVC-ClinicDB && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network SwinUnet --datasets Kvasir-SEG && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network SwinUnet --datasets 2018DSB && \

CUDA_VISIBLE_DEVICES=0 python -u train.py --network TransUNet --datasets PH2  && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network TransUNet --datasets isic16  && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network TransUNet --datasets BUSI  && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network TransUNet --datasets GLAS  && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network TransUNet --datasets CVC-ClinicDB && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network TransUNet --datasets Kvasir-SEG && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network TransUNet --datasets 2018DSB && \

CUDA_VISIBLE_DEVICES=0 python -u train.py --network KANUSeg --datasets PH2  && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network KANUSeg --datasets isic16  && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network KANUSeg --datasets BUSI  && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network KANUSeg --datasets GLAS  && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network KANUSeg --datasets CVC-ClinicDB && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network KANUSeg --datasets Kvasir-SEG && \
CUDA_VISIBLE_DEVICES=0 python -u train.py --network KANUSeg --datasets 2018DSB

Test the model.

CUDA_VISIBLE_DEVICES=0 python -u test.py --network UNet --datasets PH2  && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network UNet --datasets isic16  && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network UNet --datasets BUSI  && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network UNet --datasets GLAS  && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network UNet --datasets CVC-ClinicDB && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network UNet --datasets Kvasir-SEG && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network UNet --datasets 2018DSB && \

CUDA_VISIBLE_DEVICES=0 python -u test.py --network DenseUnet --datasets PH2  && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network DenseUnet --datasets isic16  && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network DenseUnet --datasets BUSI  && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network DenseUnet --datasets GLAS  && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network DenseUnet --datasets CVC-ClinicDB && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network DenseUnet --datasets Kvasir-SEG && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network DenseUnet --datasets 2018DSB && \

CUDA_VISIBLE_DEVICES=0 python -u test.py --network AttU_Net --datasets PH2  && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network AttU_Net --datasets isic16  && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network AttU_Net --datasets BUSI  && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network AttU_Net --datasets GLAS  && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network AttU_Net --datasets CVC-ClinicDB && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network AttU_Net --datasets Kvasir-SEG && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network AttU_Net --datasets 2018DSB && \

CUDA_VISIBLE_DEVICES=0 python -u test.py --network ConvUNeXt --datasets PH2  && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network ConvUNeXt --datasets isic16  && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network ConvUNeXt --datasets BUSI  && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network ConvUNeXt --datasets GLAS  && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network ConvUNeXt --datasets CVC-ClinicDB && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network ConvUNeXt --datasets Kvasir-SEG && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network ConvUNeXt --datasets 2018DSB && \

CUDA_VISIBLE_DEVICES=0 python -u test.py --network SwinUnet --datasets PH2  && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network SwinUnet --datasets isic16  && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network SwinUnet --datasets BUSI  && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network SwinUnet --datasets GLAS  && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network SwinUnet --datasets CVC-ClinicDB && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network SwinUnet --datasets Kvasir-SEG && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network SwinUnet --datasets 2018DSB && \

CUDA_VISIBLE_DEVICES=0 python -u test.py --network TransUNet --datasets PH2  && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network TransUNet --datasets isic16  && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network TransUNet --datasets BUSI  && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network TransUNet --datasets GLAS  && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network TransUNet --datasets CVC-ClinicDB && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network TransUNet --datasets Kvasir-SEG && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network TransUNet --datasets 2018DSB && \

CUDA_VISIBLE_DEVICES=0 python -u test.py --network KANUSeg --datasets PH2  && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network KANUSeg --datasets isic16  && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network KANUSeg --datasets BUSI  && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network KANUSeg --datasets GLAS  && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network KANUSeg --datasets CVC-ClinicDB && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network KANUSeg --datasets Kvasir-SEG && \
CUDA_VISIBLE_DEVICES=0 python -u test.py --network KANUSeg --datasets 2018DSB

You can check the evaluation metrics directly after testing, and find prediction images in UNet-Seg/output.

Reference

If you find this repository useful for your research, please consider citing the following papers.

@article{wang2024mamba,
  title={Mamba-unet: Unet-like pure visual mamba for medical image segmentation},
  author={Wang, Ziyang and Zheng, Jian-Qing and Zhang, Yichi and Cui, Ge and Li, Lei},
  journal={arXiv preprint arXiv:2402.05079},
  year={2024}
}

@article{zhang2024survey,
  title={A survey on visual mamba},
  author={Zhang, Hanwei and Zhu, Ying and Wang, Dan and Zhang, Lijun and Chen, Tianxiang and Wang, Ziyang and Ye, Zi},
  journal={Applied Sciences},
  volume={14},
  number={13},
  pages={5683},
  year={2024},
  publisher={MDPI}
}