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Python-based tools for reading OCT and fundus data.
In ophthalmology, data acquired from the scanner is often exported in the manufacturer's proprietary file format. OCT-Converter provides python-based tools for extracting images (optical coherence tomography and fundus), as well as associated metadata, from these files.
Requires python 3.7 or higher.
pip install oct-converter
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(show_contours=True) # plots a montage of the volume, with layer segmentations is available
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
oct_volume.save_projection('projection.png') # save 2D projection
fundus_image = fds.read_fundus_image() # returns a Fundus image with additional metadata if available
fundus_image.save('fds_testing_fundus.jpg')
metadata = fds.read_all_metadata(verbose=True) # extracts all other metadata
with open("fds_metadata.json", "w") as outfile:
outfile.write(json.dumps(metadata, indent=4))
# create and save a DICOM
dcm = create_dicom_from_oct(filepath)
Are welcome! Here is a development roadmap, including some easy first issues. Please open a new issue to discuss any potential contributions.
9 November 2023
22 September 2023
28 March 2023
31 January 2023
7 August 2022
16 June 2022
24 Aug 2021
11 June 2021
14 May 2021
30 October 2020
22 August 2020
14 July 2020
We can't guarantee images extracted with OCT-Converter will match those extracted or viewed with the manufacturer's software. Any use in clinical settings is at the user's own risk.
FAQs
Extract OCT and fundus data from proprietary file formats.
We found that oct-converter demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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