This code is for our paper "VTGAN: Semi-supervised Retinal Image Synthesis and Disease Prediction using Vision Transformers"

Related tags

Deep Learninggenerative-adversarial-networksemi-supervised-learningdiabetic-retinopathy-detectiondisease-predictionfundus-image-analysisfluorescein-angiographyvision-transformervision-transformers
Overview

ICCV Workshop 2021 VTGAN

PWC

This code is for our paper "VTGAN: Semi-supervised Retinal Image Synthesis and Disease Prediction using Vision Transformers" which is part of the supplementary materials for ICCV 2021 Workshop on Computer Vision for Automated Medical Diagnosis. The paper has since been accpeted and presented at ICCV 2021 Workshop.

Arxiv Pre-print

https://arxiv.org/abs/2104.06757

CVF ICCVW 2021

https://openaccess.thecvf.com/content/ICCV2021W/CVAMD/html/Kamran_VTGAN_Semi-Supervised_Retinal_Image_Synthesis_and_Disease_Prediction_Using_Vision_ICCVW_2021_paper.html

IEE Xplore ICCVW 2021

https://ieeexplore.ieee.org/document/9607858

Citation

@INPROCEEDINGS{9607858,
  author={Kamran, Sharif Amit and Hossain, Khondker Fariha and Tavakkoli, Alireza and Zuckerbrod, Stewart Lee and Baker, Salah A.},
  booktitle={2021 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW)}, 
  title={VTGAN: Semi-supervised Retinal Image Synthesis and Disease Prediction using Vision Transformers}, 
  year={2021},
  volume={},
  number={},
  pages={3228-3238},
  doi={10.1109/ICCVW54120.2021.00362}
}

Pre-requisite

  • Ubuntu 18.04 / Windows 7 or later
  • NVIDIA Graphics card

Installation Instruction for Ubuntu

sudo add-apt-repository ppa:deadsnakes/ppa
sudo apt install python3.7
  • Install Tensorflow-Gpu version-2.5.0 and Keras version-2.5.0
sudo pip3 install tensorflow-gpu
sudo pip3 install keras
  • Install packages from requirements.txt
sudo pip3 install -r requirements.txt

Dataset download link for Hajeb et al.

https://sites.google.com/site/hosseinrabbanikhorasgani/datasets-1/fundus-fluorescein-angiogram-photographs--colour-fundus-images-of-diabetic-patients
  • Please cite the paper if you use their data
@article{hajeb2012diabetic,
  title={Diabetic retinopathy grading by digital curvelet transform},
  author={Hajeb Mohammad Alipour, Shirin and Rabbani, Hossein and Akhlaghi, Mohammad Reza},
  journal={Computational and mathematical methods in medicine},
  volume={2012},
  year={2012},
  publisher={Hindawi}
}
  • Folder structure for data-preprocessing given below. Please make sure it matches with your local repository.
├── Dataset
|   ├──ABNORMAL
|   ├──NORMAL

Dataset Pre-processing

  • Type this in terminal to run the random_crop.py file
python3 random_crop.py --output_dir=data --input_dim=512 --datadir=Dataset
  • There are different flags to choose from. Not all of them are mandatory.
    '--input_dim', type=int, default=512
    '--n_crops', type=int, default=50
    '--datadir', type=str, required=True, help='path/to/data_directory',default='Dataset'
    '--output_dir', type=str, default='data'

NPZ file conversion

  • Convert all the images to npz format
python3 convert_npz.py --outfile_name=vtgan --input_dim=512 --datadir=data --n_crops=50
  • There are different flags to choose from. Not all of them are mandatory.
    '--input_dim', type=int, default=512
    '--n_crops', type=int, default=50
    '--datadir', type=str, required=True, help='path/to/data_directory',default='data'
    '--outfile_name', type=str, default='vtgan'
    '--n_images', type=int, default=17

Training

  • Type this in terminal to run the train.py file
python3 train.py --npz_file=vtgan --batch=2 --epochs=100 --savedir=VTGAN
  • There are different flags to choose from. Not all of them are mandatory
    '--epochs', type=int, default=100
    '--batch_size', type=int, default=2
    '--npz_file', type=str, default='vtgan', help='path/to/npz/file'
    '--input_dim', type=int, default=512
    '--n_patch', type=int, default=64
    '--savedir', type=str, required=False, help='path/to/save_directory',default='VTGAN'
    '--resume_training', type=str, required=False,  default='no', choices=['yes','no']

License

The code is released under the BSD 3-Clause License, you can read the license file included in the repository for details.

Owner
Sharif Amit Kamran
Interested in Deep learning for Medical Imaging and Computer Vision. Designing robust generative architectures for Ophthalmology and Calcium Imaging.
Sharif Amit Kamran
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