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This repository is dedicated to the segmentation of optical coherence tomography (OCT) images and the analysis of the plaques that appear on them.
Step 1: Download and install Miniconda
wget https://repo.anaconda.com/miniconda/Miniconda3-py38_22.11.1-1-Linux-x86_64.sh
chmod +x Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh
Step 2: Install FFmpeg and verify that the installation is correct
sudo apt update
sudo apt upgrade
sudo apt install ffmpeg -u
ffmpeg -version
brew update
brew upgrade
brew install ffmpeg
ffmpeg
Step 3: Clone the repository, create a conda environment, and install the requirements for the repository
git clone https://github.com/ViacheslavDanilov/oct_segmentation.git
cd oct_segmentation
chmod +x create_env.sh
source create_env.sh
Step 4: Initialize git hooks using the pre-commit framework
pre-commit install
Step 5 (optional): Download a raw dataset using DVC
dvc pull dvc/data/raw.dvc
NOTE: Since data storage is organized through Google Drive, you should first request access to the DVC repository.
Source image | Pre-processed image |
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