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oct-converter

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

https://github.com/marksgraham/oct-converter

Science Score: 44.0%

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    Low similarity (12.1%) to scientific vocabulary

Keywords

biobank dicom e2e fda fundus heidelberg oct python topcon zeiss
Last synced: 4 months ago · JSON representation ·

Repository

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

Basic Info
Statistics
  • Stars: 218
  • Watchers: 17
  • Forks: 74
  • Open Issues: 10
  • Releases: 18
Topics
biobank dicom e2e fda fundus heidelberg oct python topcon zeiss
Created over 6 years ago · Last pushed 9 months ago
Metadata Files
Readme License Citation

README.md

OCT Converter

Python-based tools for reading OCT and fundus data.

Description

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.

Supported file formats

  • .fds (Topcon)
  • .fda (Topcon)
  • .e2e (Heidelberg)
  • .img (Zeiss)
  • .oct (Bioptigen)
  • .OCT (Optovue)
  • .dcm

Installation

Requires python 3.7 or higher.

bash pip install oct-converter

Usage

A number of example usage scripts are included in examples/.

Here is an example of reading a .fds file:

```python from octconverter.dicom import createdicomfromoct 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/egoctfds.fds' fds = FDS(filepath)

octvolume = fds.readoctvolume() # returns an OCT volume with additional metadata if available octvolume.peek(showcontours=True) # plots a montage of the volume, with layer segmentations is available octvolume.save('fdstesting.avi') # save volume as a movie octvolume.save('fdstesting.png') # save volume as a set of sequential images, fdstesting[1...N].png octvolume.save_projection('projection.png') # save 2D projection

fundusimage = fds.readfundusimage() # returns a Fundus image with additional metadata if available fundusimage.save('fdstestingfundus.jpg')

metadata = fds.readallmetadata(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 = createdicomfrom_oct(filepath) ```

Contributions

Are welcome! Here is a development roadmap, including some easy first issues. Please open a new issue to discuss any potential contributions.

Updates

9 November 2023 - Can now save .e2e, .img, .oct, and .OCT files as DICOMs with correct headers.

22 September 2023 - DICOM support: can now save .fda/.fds files as DICOMs with correct headers. - Much more complete extraction of .fda/.fds metadata.

28 March 2023 - Metadata extraction for .fds expanded to match that of .fda file.

31 January 2023 - Greatly extended support for extracting metadata from .fda files.

7 August 2022 - Contours (layer segmentations) are now extracted from .e2e files. - Acquisition date is now extracted from .e2e files.

16 June 2022 - Initial support for reading Optovue OCTs. - Laterality is now extracted separately for each OCT/fundus image for .e2e files. - More patient info extracted from .e2e files (name, sex, birthdate, patient ID).

24 Aug 2021 - Reading the Bioptigen .OCT format is now supported.

11 June 2021 - Can now specify whether Zeiss .img data needs to be de-interlaced during reading.

14 May 2021 - Can save 2D projections of OCT volumes.

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.

Related projects

  • uocte inspired and enabled this project
  • LibE2E and LibOctData provided some additional descriptions of the .e2e file spec
  • eyepy for python-based import, visualisation, and analysis of OCT data
  • eyelab is a tool for annotating this data

Clinical use

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.

Owner

  • Name: Mark Graham
  • Login: marksgraham
  • Kind: user
  • Location: London

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: OCT-Converter
message: >-
  If you make use of this software, please cite it
  using the metadata from this file.
type: software
authors:
  - given-names: Mark
    family-names: Graham
    email: markgraham539@gmail.com
    affiliation: King's College London
    orcid: 'https://orcid.org/0000-0002-4170-1095'
version: v0.5.0

GitHub Events

Total
  • Issues event: 2
  • Watch event: 28
  • Issue comment event: 1
  • Push event: 3
  • Pull request review event: 3
  • Pull request event: 6
  • Fork event: 6
Last Year
  • Issues event: 2
  • Watch event: 28
  • Issue comment event: 1
  • Push event: 3
  • Pull request review event: 3
  • Pull request event: 6
  • Fork event: 6

Committers

Last synced: 8 months ago

All Time
  • Total Commits: 281
  • Total Committers: 21
  • Avg Commits per committer: 13.381
  • Development Distribution Score (DDS): 0.448
Past Year
  • Commits: 21
  • Committers: 5
  • Avg Commits per committer: 4.2
  • Development Distribution Score (DDS): 0.524
Top Committers
Name Email Commits
Mark Graham m****9@g****m 155
Susannah Trevino s****o@f****o 53
mark m****k@v****m 21
Susannah Trevino 6****v 10
Dillon Brown D****1@g****m 9
pre-commit-ci-lite[bot] 1****] 5
David Romero-Bascones 5****s 4
Furkan Türkay 5****T 4
gdxaaa d****k@g****m 4
Douglas Moore d****7 3
Atif a****r@i****r 2
Oren Avram o****m@g****m 2
Alan Silva 3****r 1
Cameron Lloyd l****d@m****u 1
David Kaspar 4****y 1
Hua j****8 1
Nathan Richman 6****n 1
Selçuk Karakayalı s****i@g****m 1
Tom Vaucourt t****t@o****r 1
dkermany d****y@g****m 1
yangyikai y****7@g****m 1
Committer Domains (Top 20 + Academic)
orange.fr: 1 med.unideb.hu: 1 insa-rouen.fr: 1 visulytix.com: 1 flywheel.io: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 76
  • Total pull requests: 52
  • Average time to close issues: 3 months
  • Average time to close pull requests: 2 days
  • Total issue authors: 59
  • Total pull request authors: 20
  • Average comments per issue: 5.38
  • Average comments per pull request: 0.92
  • Merged pull requests: 50
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 5
  • Average time to close issues: 17 days
  • Average time to close pull requests: 2 days
  • Issue authors: 2
  • Pull request authors: 1
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • marksgraham (5)
  • benjaminralex (4)
  • antoniohupa (3)
  • FurkyT (3)
  • drombas (2)
  • Jackiecs3 (2)
  • yehudahkay (2)
  • ivanslootweg (2)
  • Rex-Tang (2)
  • RunningDongxu (2)
  • polklin (1)
  • niloofarAzari (1)
  • seslootbeek (1)
  • orenavram (1)
  • JosefKauer (1)
Pull Request Authors
  • marksgraham (18)
  • sustrev (12)
  • Dbrown411 (5)
  • drombas (4)
  • FurkyT (2)
  • big97kai (2)
  • T0mSIlver (2)
  • naterichman (1)
  • dmoore247 (1)
  • working-girl (1)
  • UpwardTrajectory (1)
  • alanwilter (1)
  • RunningDongxu (1)
  • Atif-Anwer (1)
  • orenavram (1)
Top Labels
Issue Labels
enhancement (3) help wanted (1) good first issue (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 2,371 last-month
  • Total dependent packages: 2
  • Total dependent repositories: 1
  • Total versions: 24
  • Total maintainers: 1
pypi.org: oct-converter

Extract OCT and fundus data from proprietary file formats.

  • Homepage: https://github.com/marksgraham/OCT-Converter
  • Documentation: https://oct-converter.readthedocs.io/
  • License: MIT License Copyright (c) 2021 Mark Graham Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  • Latest release: 0.6.2
    published about 2 years ago
  • Versions: 24
  • Dependent Packages: 2
  • Dependent Repositories: 1
  • Downloads: 2,371 Last month
Rankings
Dependent packages count: 3.1%
Forks count: 5.4%
Stargazers count: 5.6%
Downloads: 8.4%
Average: 8.8%
Dependent repos count: 21.7%
Maintainers (1)
markg
Last synced: 4 months ago

Dependencies

setup.py pypi
  • construct *
  • h5py *
  • imageio *
  • imageio-ffmpeg *
  • matplotlib *
  • natsort *
  • numpy *
  • opencv-python *
  • pydicom *
  • pylibjpeg *
  • six *