UpwardTrajectory / OCT-Converter

Extract the raw optical coherence tomography (OCT) and fundus data from proprietary file formats.

OCT file converter

This repository contains code for extracting the raw optical coherence tomography (OCT) and fundus data from manufacturer's proprietary file formats.

Motivation

Research in ophthalmology is often hindered by manufacturer's usage of proprietary data formats for storing their data. For example, until recently, the ~200,000 OCT scans in the UK Biobank project was only available in Topcon's .fds file format, which prevented bulk processing and analysis. The only freely available software that allows these scans to be accessed is uocte, which is written in C++ and is no longer maintained. This repository aims to make available python-based tools for reading these proprietary formats.

Supported file formats

• .fds (Topcon)
• .fda (Topcon)
• .e2e (Heidelberg)
• .img (Zeiss)
• .dcm

Installation

Requires python3.

To install run:

git clone https://github.com/marksgraham/OCT-Converter.git
pip install -e OCT-Converter

Usage

Example usage scripts are included in examples/.

Contributions

Are welcome!