jasonbunk / napari-oct-segmentation

OCT Image segmentation application based on Napari

Napari Optical Coherence Tomography (OCT) Image Segmentation Applications

This codebase has interactive applications created for two projects at the Cabrera Lab at The University of Washington and Seattle Children's Hospital Departments of Ophthalmology.

The first project focused on analysis of the fovea and parafovea. There are two versions of the application which perform the same task, "app_classic.py" and "app_with_dnn.py" which differ only in the layer detection algorithm. The latter uses an LSTM deep learning model.

The second project added optic nerve analysis in addition to also making measurements of the fovea and parafovea. The second project has two separate applications, "app_disk_analysis.py" and "app_retina_layer_thicknesses_around_fovea.py" for those tasks respectively. This project also used an LSTM deep learning model for retina layer detection / segmentation.

Installation

A more detailed README with installation instructions is provided in the first project.

Installation of the second project should be analogous and scripts are similarly provided in "install_helpers".

Example