This code is for our paper "VTGAN: Semi-supervised Retinal Image Synthesis and Disease Prediction using Vision 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
A Framework for Encrypted Machine Learning in TensorFlow

TF Encrypted is a framework for encrypted machine learning in TensorFlow. It looks and feels like TensorFlow, taking advantage of the ease-of-use of t

TF Encrypted 0 Jul 06, 2022
Software & Hardware to do multi color printing with Sharpies

3D Print Colorizer is a combination of 3D printed parts and a Cura plugin which allows anyone with an Ender 3 like 3D printer to produce multi colored

343 Jan 06, 2023
Logsig-RNN: a novel network for robust and efficient skeleton-based action recognition

GCN_LogsigRNN This repository holds the codebase for the paper: Logsig-RNN: a novel network for robust and efficient skeleton-based action recognition

7 Oct 14, 2022
Pytorch Lightning code guideline for conferences

Deep learning project seed Use this seed to start new deep learning / ML projects. Built in setup.py Built in requirements Examples with MNIST Badges

Pytorch Lightning 1k Jan 06, 2023
TC-GNN with Pytorch integration

TC-GNN (Running Sparse GNN on Dense Tensor Core on Ampere GPU) Cite this project and paper. @inproceedings{TC-GNN, title={TC-GNN: Accelerating Spars

YUKE WANG 19 Dec 01, 2022
A system for quickly generating training data with weak supervision

Programmatically Build and Manage Training Data Announcement The Snorkel team is now focusing their efforts on Snorkel Flow, an end-to-end AI applicat

Snorkel Team 5.4k Jan 02, 2023
Tensorflow Tutorials using Jupyter Notebook

Tensorflow Tutorials using Jupyter Notebook TensorFlow tutorials written in Python (of course) with Jupyter Notebook. Tried to explain as kindly as po

Sungjoon 2.6k Dec 22, 2022
Self-Supervised Learning of Event-based Optical Flow with Spiking Neural Networks

Self-Supervised Learning of Event-based Optical Flow with Spiking Neural Networks Work accepted at NeurIPS'21 [paper, video]. If you use this code in

TU Delft 43 Dec 07, 2022
TGS Salt Identification Challenge

TGS Salt Identification Challenge This is an open solution to the TGS Salt Identification Challenge. Note Unfortunately, we can no longer provide supp

neptune.ai 123 Nov 04, 2022
The first dataset on shadow generation for the foreground object in real-world scenes.

Object-Shadow-Generation-Dataset-DESOBA Object Shadow Generation is to deal with the shadow inconsistency between the foreground object and the backgr

BCMI 105 Dec 30, 2022
Research on Event Accumulator Settings for Event-Based SLAM

Research on Event Accumulator Settings for Event-Based SLAM This is the source code for paper "Research on Event Accumulator Settings for Event-Based

Robin Shaun 26 Dec 21, 2022
Framework to build and train RL algorithms

RayLink RayLink is a RL framework used to build and train RL algorithms. RayLink was used to build a RL framework, and tested in a large-scale multi-a

Bytedance Inc. 32 Oct 07, 2022
RAFT-Stereo: Multilevel Recurrent Field Transforms for Stereo Matching

RAFT-Stereo: Multilevel Recurrent Field Transforms for Stereo Matching This repository contains the source code for our paper: RAFT-Stereo: Multilevel

Princeton Vision & Learning Lab 328 Jan 09, 2023
Pop-Out Motion: 3D-Aware Image Deformation via Learning the Shape Laplacian (CVPR 2022)

Pop-Out Motion Pop-Out Motion: 3D-Aware Image Deformation via Learning the Shape Laplacian (CVPR 2022) Jihyun Lee*, Minhyuk Sung*, Hyunjin Kim, Tae-Ky

Jihyun Lee 88 Nov 22, 2022
On the Limits of Pseudo Ground Truth in Visual Camera Re-Localization

On the Limits of Pseudo Ground Truth in Visual Camera Re-Localization This repository contains the evaluation code and alternative pseudo ground truth

Torsten Sattler 36 Dec 22, 2022
RARA: Zero-shot Sim2Real Visual Navigation with Following Foreground Cues

RARA: Zero-shot Sim2Real Visual Navigation with Following Foreground Cues FGBG (foreground-background) pytorch package for defining and training model

Klaas Kelchtermans 1 Jun 02, 2022
Axel - 3D printed robotic hands and they controll with Raspberry Pi and Arduino combo

Axel It's our graduation project about 3D printed robotic hands and they control

0 Feb 14, 2022
Bot developed in Python that automates races in pegaxy.

español | português About it: This is a fork from pega-racing-bot. This bot, developed in Python, is to automate races in pegaxy. The game developers

4 Apr 08, 2022
Providing the solutions for high-frequency trading (HFT) strategies using data science approaches (Machine Learning) on Full Orderbook Tick Data.

Modeling High-Frequency Limit Order Book Dynamics Using Machine Learning Framework to capture the dynamics of high-frequency limit order books. Overvi

Chang-Shu Chung 1.3k Jan 07, 2023