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ProtoSAM - One shot segmentation with foundational models

Link to our paper here.
This work is the successor of DINOv2-based-Self-Supervised-Learning (Link to Paper).

Abstract

This work introduces a new framework, ProtoSAM, for one-shot image segmentation. It combines DINOv2, a vision transformer that extracts features from images, with an Adaptive Local Prototype Pooling (ALP) layer, which generates prototypes from a support image and its mask. These prototypes are used to create an initial coarse segmentation mask by comparing the query image's features with the prototypes. Following the extraction of an initial mask, we use numerical methods to generate prompts, such as points and bounding boxes, which are then input into the Segment Anything Model (SAM), a prompt-based segmentation model trained on natural images. This allows segmenting new classes automatically and effectively without the need for additional training.

How To Run

1. Data preprocessing

1.1 CT and MRI Dataset

Please see the notebook data/data_processing.ipynb for instructions. For convenience i've compiled the data processing instructions from https://github.com/cheng-01037/Self-supervised-Fewshot-Medical-Image-Segmentation to a single notebook.
The CT dataset is available here: https://www.synapse.org/Synapse:syn3553734
The MRI dataset is availabel here: https://chaos.grand-challenge.org

run ./data/CHAOST2/dcm_img_to_nii.sh to convert dicom images to nifti files.

1.2 Polyp Dataset

Data is available here: https://www.kaggle.com/datasets/hngphmv/polypdataset?select=train.csv

Put the dataset data/PolypDataset/

2. Running

2.1 (Optional) Training and Validation of the coarse segmentation networks

./backbone.sh [MODE] [MODALITY] [LABEL_SET]

MODE - validation or training
MODALITY - ct or mri
LABEL_SET - 0 (kidneys), 1 (liver spleen)

for example:

./backbone.sh training mri 1

Please refer to backbone.sh for further configurations.

2.1 Running ProtoSAM

Put all SAM checkpoint like sam_vit_b.pth, sam_vit_h.pth, medsam_vit_b.pth into the pretrained_model directory.
Checkpoints are available at SAM and MedSAM.

./run_protosam.sh [MODALITY] [LABEL_SET]

MODALITY - ct, mri or polyp
LABEL_SET (only relevant if doing ct or mri) - 0 (kidneys), 1 (liver spleen) Please refer to the run_protosam.sh script for further configurations.

Acknowledgements

This work is largely based on ALPNet, DINOv2, SAM and is a continuation of DINOv2-based-Self-Supervised-Learning.

Cite

If you found this repo useful, please consider giving us a citation and a star!

@article{ayzenberg2024protosam,
  title={ProtoSAM-One Shot Medical Image Segmentation With Foundational Models},
  author={Ayzenberg, Lev and Giryes, Raja and Greenspan, Hayit},
  journal={arXiv preprint arXiv:2407.07042},
  year={2024}
}

@misc{ayzenberg2024dinov2,
      title={DINOv2 based Self Supervised Learning For Few Shot Medical Image Segmentation}, 
      author={Lev Ayzenberg and Raja Giryes and Hayit Greenspan},
      year={2024},
      eprint={2403.03273},
      archivePrefix={arXiv},
      primaryClass={cs.CV}
}