Skip to content

Latest commit

 

History

History
137 lines (100 loc) · 5.98 KB

README.md

File metadata and controls

137 lines (100 loc) · 5.98 KB
Raw

xLSTM-UNet can be an Effective 2D & 3D Medical Image Segmentation Backbone with Vision-LSTM (ViL) better than its Mamba Counterpart

Tianrun Chen, Chaotao Ding, Lanyun Zhu, Tao Xu, Deyi Ji, Ying Zang, Zejian Li

KOKONI, Moxin Technology (Huzhou) Co., LTD , Zhejiang University, Singapore University of Technology and Design, Huzhou University, University of Science and Technology of China.

Code

Installation

Requirements: Ubuntu 20.04, CUDA 11.8

  1. Create a virtual environment: conda create -n uxlstm python=3.10 -y and conda activate uxlstm
  2. Install Pytorch 2.0.1: pip install torch==2.0.1 torchvision==0.15.2 --index-url https://download.pytorch.org/whl/cu118
  3. Download code: git clone https://github.com/tianrun-chen/xLSTM-UNet-PyTorch.git
  4. cd xLSTM-UNet-PyTorch/UxLSTM and run pip install -e .

Model Training

The dataset used in this project is derived from the following research paper:

Jun Ma, Feifei Li, Bo Wang. "U-Mamba: Enhancing Long-range Dependency for Biomedical Image Segmentation." arXiv preprint arXiv:2401.04722, 2024.

Download dataset here and put them into the data folder. U-xLSTM is built on the popular nnU-Net framework.

Preprocessing

Our data processing approach strictly follows the methods outlined in the U-Mamba study. This includes steps such as data normalization, augmentation techniques, and segmentation algorithms detailed in their publication.

nnUNetv2_plan_and_preprocess -d DATASET_ID --verify_dataset_integrity

Format of the training script

nnUNetv2_train DATASET_ID {dataset_type} {exp_name} -tr {trainer_type} -lr {learning_rate} -bs {batch_size}

  • {dataset_type}: Specifies the type of dataset to be used. There are two options:

    • 2d: For datasets that are 2-dimensional.
    • 3d_fullres: For full-resolution 3-dimensional datasets.

  • {exp_name}: Defines the name or identifier for the experiment. It can be:

    • all: Use this option to include all available configurations.
    • An integer: Specify a particular configuration number to use a specific setup.

  • {trainer_type}: Indicates the type of trainer to use for the training process. Options include:

    • nnUNetTrainerUxLSTMBot: A trainer tailored for the UxLSTMBot model.
    • nnUNetTrainerUxLSTMEnc: A trainer designed for the UxLSTMEnc model architecture.

  • {learning_rate}: Specifies the learning rate for the training process. This should be a floating-point number.

  • {batch_size}: Defines the number of samples to process before the model's internal parameters are updated.

Train 2D models

  • Train 2D U-xLSTM_Bot model
nnUNetv2_train DATASET_ID 2d all -tr nnUNetTrainerUxLSTMBot -lr {learning_rate} -bs {batch_size}
  • Train 2D U-xLSTM_Enc model
nnUNetv2_train DATASET_ID 2d all -tr nnUNetTrainerUxLSTMEnc -lr {learning_rate} -bs {batch_size}

Train 3D models

  • Train 3D U-xLSTM_Bot model
nnUNetv2_train DATASET_ID 3d_fullres all -tr nnUNetTrainerUxLSTMBot -lr {learning_rate} -bs {batch_size}
  • Train 3D U-xLSTM_Enc model
nnUNetv2_train DATASET_ID 3d_fullres all -tr nnUNetTrainerUxLSTMEnc -lr {learning_rate} -bs {batch_size}

Inference

  • Predict testing cases with U-xLSTM_Bot model
nnUNetv2_predict -i INPUT_FOLDER -o OUTPUT_FOLDER -d DATASET_ID -c DATASET_TYPE -f all -tr nnUNetTrainerUxLSTMBot --disable_tta
  • Predict testing cases with U-xLSTM_Enc model
nnUNetv2_predict -i INPUT_FOLDER -o OUTPUT_FOLDER -d DATASET_ID -c DATASET_TYPE -f all -tr nnUNetTrainerUxLSTMEnc --disable_tta

DATASET_TYPE can be 2d and 3d_fullres for 2D and 3D models, respectively.

Metric

  • We provide pretrained models that you can download from this link. Please ensure you save them in the pretrained_model folder. Then, run process_weight.py to verify that the weights are correctly placed in the appropriate file path
python process_weight.py

We also provide additional shell scripts for evaluating our provided pretrained model.

bash metric_bot.sh
bash metric_enc.sh

If you wish to evaluate your own trained model, be sure to change the -f parameter to the {exp_name} used during training. This could be 'all' or a specific integer identifier.

Citation

Please cite this work if you find it inspiring or helpful!

@misc{chen2024xlstmuneteffective2d,
      title={xLSTM-UNet can be an Effective 2D \& 3D Medical Image Segmentation Backbone with Vision-LSTM (ViL) better than its Mamba Counterpart}, 
      author={Tianrun Chen and Chaotao Ding and Lanyun Zhu and Tao Xu and Deyi Ji and Ying Zang and Zejian Li},
      year={2024},
      eprint={2407.01530},
      archivePrefix={arXiv},
      primaryClass={eess.IV},
      url={https://arxiv.org/abs/2407.01530}, 
}

You are also welcomed to check our Segment Anything Adapter (SAM-Adapter) 

@misc{chen2023sam,
      title={SAM Fails to Segment Anything? -- SAM-Adapter: Adapting SAM in Underperformed Scenes: Camouflage, Shadow, and More}, 
      author={Tianrun Chen and Lanyun Zhu and Chaotao Ding and Runlong Cao and Shangzhan Zhang and Yan Wang and Zejian Li and Lingyun Sun and Papa Mao and Ying Zang},
      year={2023},
      eprint={2304.09148},
      archivePrefix={arXiv},
      primaryClass={cs.CV}
}

Acknowledgement

The code is based on Jun Ma, Feifei Li, Bo Wang. "U-Mamba: Enhancing Long-range Dependency for Biomedical Image Segmentation." arXiv preprint arXiv:2401.04722, 2024.