Extract OCT and fundus data from proprietary file formats.
Project description
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 The only freely available software that allows these scans to be accessed is uocte, which is written in C++ and is no longer maintained.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.
pip install oct-converter
Usage
A number of example usage scripts are included in examples/.
Here is an example of reading a .fds file:
from oct_converter.readers import FDS
# An example .fds file can be downloaded from the Biobank website:
# https://biobank.ndph.ox.ac.uk/showcase/refer.cgi?id=30
filepath = '/home/mark/Downloads/eg_oct_fds.fds'
fds = FDS(filepath)
oct_volume = fds.read_oct_volume() # returns an OCT volume with additional metadata if available
oct_volume.peek() # plots a montage of the volume
oct_volume.save('fds_testing.avi') # save volume as a movie
oct_volume.save('fds_testing.png') # save volume as a set of sequential images, fds_testing_[1...N].png
fundus_image = fds.read_fundus_image() # returns a Fundus image with additional metadata if available
fundus_image.save('fds_testing_fundus.jpg')
Contributions
Are welcome!
Updates
30 October 2020
- Extract fundus and laterality data from .e2e
- Now attempts to extract additional volumetric data from .e2e files that was previously missed
22 August 2020
- Experimental support for reading OCT data from .fda files.
14 July 2020
- Can now read fundus data from .fda files.
Release history Release notifications | RSS feed
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