Pytorch implementation for paper RetiGen: A Framework for Generalized Retinal Diagnosis Using Multi-View Fundus Images
This study introduces a novel framework for enhancing domain generalization in medical imaging, specifically focusing on utilizing unlabelled multi-view colour fundus photographs. Unlike traditional approaches that rely on single-view imaging data and face challenges in generalizing across diverse clinical settings, our method leverages the rich information in the unlabelled mul 7E2A ti-view imaging data to improve model robustness and accuracy. By incorporating a class balancing method, a test-time adaptation technique and a multi-view optimization strategy, we address the critical issue of domain shift that often hampers the performance of machine learning models in real-world applications. Experiments comparing various state-of-the-art domain generalization and test-time optimization methodologies show that our approach consistently outperforms when combined with existing baseline and state-of-the-art methods. We also show our online method improves all existing techniques. Our framework demonstrates improvements in domain generalization capabilities and offers a practical solution for real-world deployment by facilitating online adaptation to new, unseen datasets.
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Clone this repository and navigate to retigen folder
git clone https://github.com/zgy600/RetiGen.git cd RetiGen/retigen -
Install Package
conda create -n retigen python=3.10 -y conda activate retigen pip install --upgrade pip conda install pytorch==2.0.1 torchvision==0.15.1 torchaudio==2.0.2 pytorch-cuda=11.7 -c pytorch -c nvidia -
Install other dependencies
pip install -r requirements.txt
Your dataset should be organized as:
.
├── images
│ ├── DATASET1
│ │ ├── mild_npdr
│ │ ├── moderate_npdr
│ │ ├── nodr
│ │ ├── pdr
│ │ └── severe_npdr
│ ├── DATASET2
│ │ ├── mild_npdr
│ │ ├── moderate_npdr
│ │ ├── nodr
│ │ ├── pdr
│ │ └── severe_npdr
│ ├── DATASET3
│ │ ...
│ ... ...
│
├── masks
│ ├── DATASET1
│ │ ├── mild_npdr
│ │ ├── moderate_npdr
│ │ ├── nodr
│ │ ├── pdr
│ │ └── severe_npdr
│ ├── DATASET2
│ │ ├── mild_npdr
│ │ ├── moderate_npdr
│ │ ├── nodr
│ │ ├── pdr
│ │ └── severe_npdr
│ ├── DATASET3
│ │ ...
│ ... ...
│
└── splits
├── DATASET1_crossval.txt
├── DATASET1_train.txt
├── DATASET2_crossval.txt
├── DATASET2_train.txt
├── DATASET3_crossval.txt
├── DATASET3_train.txt
...
cd run/
table_1_origin_DG_MFIDDR_DRTiD.sh
cd run/
table_1_target_DG_MFIDDR.sh
If this repo is useful for your research, please consider citing our paper:
@misc{chen2024retigen,
title={RetiGen: A Framework for Generalized Retinal Diagnosis Using Multi-View Fundus Images},
author={Ze Chen and Gongyu Zhang and Jiayu Huo and Joan Nunez do Rio and Charalampos Komninos and Yang Liu and Rachel Sparks and Sebastien Ourselin and Christos Bergeles and Timothy Jackson},
year={2024},
eprint={2403.15647},
archivePrefix={arXiv},
primaryClass={cs.CV}
}