Awesome

Introduction

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

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

Please keep an eye on this repository. I plan to complete it by the end of September 2024.

Contents

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

Networks

• CNN-based UNet

UNet, Attention UNet, DenseUNet, ConvUNeXt,

• ViT-based UNet

TransUNet, SwinUNet

• Mamba-based UNet

Mamba-UNet, VM-UNet

• KAN-based UNet

U-KAN, etc

Datasets

• Dataset of GLAS -> [Official], [Google Drive], [Baidu Netdisk] with passcode: 'fp42'
• Dataset of BUSI -> [Official], [Google Drive], [Baidu Netdisk] with passcode: '5m5m'
• Dataset of 2018DSB -> [Official], [Google Drive], [Baidu Netdisk] with passcode: 'yavx'
• Dataset of CVC-ClinicDB -> [Official], [Google Drive], [Baidu Netdisk] with passcode: '3tpy'
• Dataset of Kvasir-SEG -> [Official], [Google Drive], [Baidu Netdisk] with passcode: '6fgs'
• Dataset of ISIC2016 -> [Official], [Google Drive], [Baidu Netdisk] with passcode: 'm2fw'
• Dataset of PH2 -> [Official], [Google Drive], [Baidu Netdisk] with passcode: 'aiax'

Metrics

Dice, IoU, Accuracy, Precision, Sensitivity, Specificity

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

1. Download the Code.

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

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

3. 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

4. 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

Reference

TBC

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