Official implementation of Cross-Scan Attention Transformer (CSAT)

Prepare Dataset

Download pickle.zip from link

To prepare your own OCT dataset for SCR detection

cd csat/
python make_pickle_data.py

Each pickle file is a dictionary of tensors with the following entries

tensor = {'img':image, 'box':bounding_boxes, 'label':SCR_label, 'name':filename}

Generate positive and negative pairs for pre-training

python util/util.py

The directory structure should be similar to

- csat
  - data
    - positive_<fold>.txt
    - negative_<fold>.txt
    - scr.yaml
  - pickle
  - eval
  - loss
  - ...

Download pre-trained model from link

Train the pre-training model

# to run with default arguments
python pretrain.py

# to modify arguments
python pretrain.py --root <str> --world_size <int> --resume <bool> --resume_weight <str> --train_folder <str> --val_folder <str> --epochs <int> --folds <int> --cf <int> --batch_size <int>

Train the detection model

# to run with default arguments
python train.py

# to modify arguments
python train.py --root <str> --dataroot <str> --world_size <int> --resume <bool> --resume_weight <str> --pretrain <bool> --pretrain_weights <str> --epochs <int> --nc <int> --r <int> --space <int> --train_batch <int> --val_batch <int>

Run validation directly on the detection model

# to run with default arguments
python validate.py

# to modify arguments
python validate.py --root <str> --dataroot <str> --world_size <int> --weights <str> --nc <int> --r <int> --space <int> --batch <int>

Citation

@InProceedings{csat_scr,
author="Bhattarai, Ashuta
and Jin, Jing
and Kambhamettu, Chandra",
title="Analyzing Adjacent B-Scans to Localize Sickle Cell Retinopathy In OCTs",
booktitle="Medical Image Computing and Computer Assisted Intervention -- MICCAI 2024",
year="2024",
publisher="Springer Nature Switzerland",
pages="574--584"}