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SAM-Med3D [Paper] [Supplementary] [Data]

The official repo of "SAM-Med3D: Towards General-purpose Segmentation Models for Volumetric Medical Images".

🔥🌻📰 News 📰🌻🔥

• [Examples] SAM-Med3D is now supported in MedIM, you can easily get our model with one-line Python code. Our new example is in medim_infer.py.
• [Data] We have now released all labels of our training dataset SA-Med3D-140K. Due to the large volume of image data (over 1T), we are currently seeking an appropriate release method. For now, you can directly contact small_dark@sina.com to obtain it. Download Link: Baidu Netdisk and Google Drive.
• [Paper] SAM-Med3D is accepted as ECCV BIC 2024 Oral
• [Model] A newer version of finetuned SAM-Med3D named SAM-Med3D-turbo is released now. We fine-tuned it on 44 datasets (list) to improve the performance. Hope this update can help you 🙂.
• [Model] Finetuned SAM-Med3D for organ/brain segmentation is released now! Hope you enjoy the enhanced performance for specific tasks 😉. Details are in results and ckpt.
• [Repos] If you are interested in computer vision, we recommend checking out OpenGVLab for more exciting projects like SAM-Med2D!

🌟 Highlights

• 📚 Curated the most extensive volumetric medical dataset to date for training, boasting 143K 3D masks and 245 categories.
• 🚤 Achieved efficient promptable segmentation, requiring 10 to 100 times fewer prompt points for satisfactory 3D outcomes.
• 🏆 Conducted a thorough assessment of SAM-Med3D across 16 frequently used volumetric medical image segmentation datasets.

🔨 Usage

Quick Start for SAM-Med3D inference

Note: Currently, labels are required to generate prompt points for inference.

First, set up your environment with the following commands:

conda create --name sammed3d python=3.10 
conda activate sammed3d
pip install light-the-torch && ltt install torch
pip install torchio opencv-python-headless matplotlib prefetch_generator monai edt medim

Then, use medim_infer.py to test the inference:

python medim_infer.py

If you want to run inference on your own data, refer to medim_infer.py for more details. You can simply modify the paths in the script to use your own data. Here's the main logic:

  ''' 1. read and pre-process your input data '''
  img_path = "./test_data/kidney_right/AMOS/imagesVal/amos_0013.nii.gz"
  gt_path =  "./test_data/kidney_right/AMOS/labelsVal/amos_0013.nii.gz"
  category_index = 3  # the index of your target category in the gt annotation
  output_dir = "./test_data/kidney_right/AMOS/pred/"
  roi_image, roi_label, meta_info = data_preprocess(img_path, gt_path, category_index=category_index)
  
  ''' 2. prepare the pre-trained model with local path or huggingface url '''
  ckpt_path = "https://huggingface.co/blueyo0/SAM-Med3D/blob/main/sam_med3d_turbo.pth"
  # or you can use the local path like: ckpt_path = "./ckpt/sam_med3d_turbo.pth"
  model = medim.create_model("SAM-Med3D",
                              pretrained=True,
                              checkpoint_path=ckpt_path)
  
  ''' 3. infer with the pre-trained SAM-Med3D model '''
  roi_pred = sam_model_infer(model, roi_image, roi_gt=roi_label)

  ''' 4. post-process and save the result '''
  output_path = osp.join(output_dir, osp.basename(img_path).replace(".nii.gz", "_pred.nii.gz"))
  data_postprocess(roi_pred, meta_info, output_path, img_path)

  print("result saved to", output_path)

Training / Fine-tuning

(we recommend fine-tuning with SAM-Med3D pre-trained weights from link)

To train the SAM-Med3D model on your own data, follow these steps:

0. (Recommend) Prepare the Pre-trained Weights

Note: You can easily get PyTorch SAM-Med3D model with pre-trained weights from huggingface use MedIM.

ckpt_path = "https://huggingface.co/blueyo0/SAM-Med3D/blob/main/sam_med3d_turbo.pth"
model = medim.create_model("SAM-Med3D", pretrained=True, checkpoint_path=ckpt_path)

Download the checkpoint from ckpt section and move the pth file into SAM_Med3D/ckpt/ (We recommand to use SAM-Med3D-turbo.pth).

1. Prepare Your Training Data (from nnU-Net-style dataset):

Ensure that your training data is organized according to the structure shown in the data/medical_preprocessed directories. The target file structures should be like the following:

data/medical_preprocessed
      ├── adrenal
      │ ├── ct_WORD
      │ │ ├── imagesTr
      │ │ │ ├── word_0025.nii.gz
      │ │ │ ├── ...
      │ │ ├── labelsTr
      │ │ │ ├── word_0025.nii.gz
      │ │ │ ├── ...
      ├── ...

If the original data are in the nnU-Net style, follow these steps:

For a nnU-Net style dataset, the original file structure should be:

Task010_WORD
     ├── imagesTr
     │ ├── word_0025_0000.nii.gz
     │ ├── ...
     ├── labelsTr
     │ ├── word_0025.nii.gz
     │ ├── ...

Then you should resample and convert the masks into binary. (You can use script for nnU-Net folder)

data/train
      ├── adrenal
      │ ├── ct_WORD
      │ │ ├── imagesTr
      │ │ │ ├── word_0025.nii.gz
      │ │ │ ├── ...
      │ │ ├── labelsTr
      │ │ │ ├── word_0025.nii.gz (binary label)
      │ │ │ ├── ...
      ├── liver
      │ ├── ct_WORD
      │ │ ├── imagesTr
      │ │ │ ├── word_0025.nii.gz
      │ │ │ ├── ...
      │ │ ├── labelsTr
      │ │ │ ├── word_0025.nii.gz (binary label)
      │ │ │ ├── ...
      ├── ...

Then, modify the utils/data_paths.py according to your own data.

img_datas = [
"data/train/adrenal/ct_WORD",
"data/train/liver/ct_WORD",
...
]

2. Run the Training Script:

Run bash train.sh to execute the following command in your terminal:

python train.py --multi_gpu --task_name ${tag}

This will start the training process of the SAM-Med3D model on your prepared data. If you use only one GPU, remove the --multi_gpu flag.

The key options are listed below:

• task_name: task name
• checkpoint: pre-trained checkpoint
• work_dir: results folder for log and ckpt
• multi_gpu: use multiple GPU with DDP
• gpu_ids: set gpu ids used for training
• num_epochs: number of epoches
• batch_size: batch size for training
• lr: learning rate for training

Hint: Use the --checkpoint to set the pre-trained weight path, the model will be trained from scratch if no ckpt in the path is found!

Evaluation & Inference

Prepare your own dataset and refer to the samples in data/validation to replace them according to your specific scenario. Then you can simply run bash val.sh to quickly validate SAM-Med3D on your data. Or you can use bash infer.sh to generate full-volume results for your application. Make sure the masks are processed into the one-hot format (have only two values: the main image (foreground) and the background). We highly recommend using the spacing of 1.5mm for the best experience.

python validation.py --seed 2023\
 -vp ./results/vis_sam_med3d \
 -cp ./ckpt/sam_med3d_turbo.pth \
 -tdp ./data/medical_preprocessed -nc 1 \
 --save_name ./results/sam_med3d.py

• vp: visualization path, dir to save the final visualization files
• cp: checkpoint path
• tdp: test data path, where your data is placed
• nc: number of clicks of prompt points
• save_name: filename to save evaluation results
• (optional) skip_existing_pred: skip and not predict if output file is found existing

Sliding-window Inference (experimental): To extend the application scenario of SAM-Med3D and support more choices for full-volume inference. We provide the sliding-window mode here within inference.py.

python inference.py --seed 2024\
 -cp ./ckpt/sam_med3d_turbo.pth \
 -tdp ./data/medical_preprocessed -nc 1 \
 --output_dir ./results  --task_name test_amos_move \
 --sliding_window --save_image_and_gt

• cp: checkpoint path
• tdp: test data path, where your data is placed
• output_dir&task_name: all your output will be saved to <output_dir>/<task_name>
• (optional) sliding_window: enable the sliding-window mode. model will infer 27 patches with improved accuracy and slower responce.
• (optional) save_image_and_gt: enable saving the full-volume image and ground-truth into output_dir, plz ensure your disk has enough free space when you turn on this

For validation of SAM and SAM-Med2D on 3D volumetric data, you can refer to scripts/val_sam.sh and scripts/val_med2d.sh for details.

Hint: We also provide a simple script sum_result.py to help summarize the results from files like ./results/sam_med3d.py.

🔗 Checkpoint

Our most recommended version is SAM-Med3D-turbo

Other checkpoints are available with their official link: SAM and SAM-Med2D.

🗼 Method

🏆 Results

💡 Overall Performance

Note: Quantitative comparison of different methods on our evaluation dataset. Here, N denotes the count of slices containing the target object (10 ≤ N ≤ 200). Inference time is calculated with N=100, excluding the time for image processing and simulated prompt generation.

💡 Dice on Different Anatomical Architecture and Lesions

Note: Comparison from the perspective of anatomical structure and lesion. A&T represents Abdominal and Thorax targets. N denotes the count of slices containing the target object (10 ≤ N ≤ 200).

💡 Visualization

📬 Citation

@misc{wang2023sammed3d,
      title={SAM-Med3D}, 
      author={Haoyu Wang and Sizheng Guo and Jin Ye and Zhongying Deng and Junlong Cheng and Tianbin Li and Jianpin Chen and Yanzhou Su and Ziyan Huang and Yiqing Shen and Bin Fu and Shaoting Zhang and Junjun He and Yu Qiao},
      year={2023},
      eprint={2310.15161},
      archivePrefix={arXiv},
      primaryClass={cs.CV}
}

🎫 License

This project is released under the Apache 2.0 license.

💬 Discussion Group

BTW, welcome to follow our Zhihu official account, we will share more information on medical imaging there.

🙏 Acknowledgement

• We thank all medical workers and dataset owners for making public datasets available to the community.
• Thanks to the open-source of the following projects:
  • Segment Anything  
  • SAM-Med2D

👋 Hiring & Global Collaboration

• Hiring: We are hiring researchers, engineers, and interns in General Vision Group, Shanghai AI Lab. If you are interested in Medical Foundation Models and General Medical AI, including designing benchmark datasets, general models, evaluation systems, and efficient tools, please contact us.
• Global Collaboration: We're on a mission to redefine medical research, aiming for a more universally adaptable model. Our passionate team is delving into foundational healthcare models, promoting the development of the medical community. Collaborate with us to increase competitiveness, reduce risk, and expand markets.
• Contact: Junjun He(hejunjun@pjlab.org.cn), Jin Ye(yejin@pjlab.org.cn), and Tianbin Li (litianbin@pjlab.org.cn).