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SimAda: A Simple Unified Framework for Adapting Segment Anything Model in Underperformed Scenes

The official code for SimAda.

Requirement

conda env create -f environment.yml

Download SAM checkpoint, and put it at ./checkpoint/sam/

Getting Started

Melanoma Segmentation from Skin Images (2D)

1. Download ISIC dataset part 1 from https://challenge.isic-archive.com/data/. Then put the csv files in "./data/ISIC" under your data path. Your dataset folder under "your_data_path" should be like:

ISIC/

 ISBI2016_ISIC_Part1_Test_Data/...
 
 ISBI2016_ISIC_Part1_Training_Data/...
 
 ISBI2016_ISIC_Part1_Test_GroundTruth.csv
 
 ISBI2016_ISIC_Part1_Training_GroundTruth.csv

2. Begin Adapting! run: python train.py -net sam -mod sam_adpt -exp_name *msa_test_isic* -sam_ckpt ./checkpoint/sam/sam_vit_b_01ec64.pth -image_size 1024 -b 32 -dataset isic --data_path *../data* change "data_path" and "exp_name" for your own useage.

You can edit the encoder part of sam in PATH SimAda/models/sam/modeling/ to change model to different variants.

4. Evaluation: The code can automatically evaluate the model on the test set during traing, set "--val_freq" to control how many epoches you want to evaluate once. You can also run val.py for the independent evaluation.

5. Result Visualization: You can set "--vis" parameter to control how many epoches you want to see the results in the training or evaluation process.

In default, everything will be saved at ./logs/

Run on your own dataset

It is simple to run BA-SAM on the other datasets. Just write another dataset class following which in ./dataset.py. You only need to make sure you return a dict with

 {
             'image': A tensor saving images with size [C,H,W] for 2D image, size [C, H, W, D] for 3D data.
             D is the depth of 3D volume, C is the channel of a scan/frame, which is commonly 1 for CT, MRI, US data. 
             If processing, say like a colorful surgical video, D could the number of time frames, and C will be 3 for a RGB frame.

             'label': The target masks. Same size with the images except the resolutions (H and W).

             'p_label': The prompt label to decide positive/negative prompt. To simplify, you can always set 1 if don't need the negative prompt function.

             'pt': The prompt. Should be the same as that in SAM, e.g., a click prompt should be [x of click, y of click], one click for each scan/frame if using 3d data.

             'image_meta_dict': Optional. if you want save/visulize the result, you should put the name of the image in it with the key ['filename_or_obj'].

             ...(others as you want)
 }

Welcome to open issues if you meet any problem. It would be appreciated if you could contribute your dataset extensions. Unlike natural images, medical images vary a lot depending on different tasks. Expanding the generalization of a method requires everyone's efforts.

TODO LIST

• Release base code.
• Fix bugs
• More details

Cite

If you use SimAda in your research, please use the following BibTeX entry.

@article{wu2023medical,
  title={Medical SAM Adapter: Adapting Segment Anything Model for Medical Image Segmentation},
  author={Wu, Junde and Fu, Rao and Fang, Huihui and Liu, Yuanpei and Wang, Zhaowei and Xu, Yanwu and Jin, Yueming and Arbel, Tal},
  journal={arXiv preprint arXiv:2304.12620},
  year={2023}
}