A PyTorch based package for automated OCT tissue masking.
Project description
oct_tissuemasking
This package contains a basic 3D UNet and patching scripts to create training data.
1 Installation
1.1 Create a new mamba environment
Create a new mamba environment called oct_tissuemasking with python 3.9.
mamba create -n oct_tissuemasking python=3.9
mamba activate oct_tissuemasking
1.2 Install dependencies
We will need to install cyclopts (command line interface utility) and synthspline (for vasculature synthesis).
pip install git+https://github.com/BrianPugh/cyclopts.git#b862234
pip install git+https://github.com/balbasty/synthspline.git#f78ba23
1.3 Set cuda parameters
We need to identify and set our cuda version to make sure we install the right prebuilt wheel for cupy.
export CUDA_VERSION=<cuda-version>
1.4 Install oct_tissuemasking
This will take a while so we will set the timeout for a 20,000 seconds!
pip install oct_tissuemasking --default-timeout=20000
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