oct-to-tiff
A command line tool for converting optical coherence tomography angiography (OCTA) data.
Science Score: 54.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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✓Academic publication links
Links to: zenodo.org -
○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (13.8%) to scientific vocabulary
Keywords
Repository
A command line tool for converting optical coherence tomography angiography (OCTA) data.
Basic Info
- Host: GitHub
- Owner: camlloyd
- License: bsd-3-clause
- Language: Python
- Default Branch: main
- Homepage: https://pypi.org/project/oct-to-tiff
- Size: 124 KB
Statistics
- Stars: 7
- Watchers: 2
- Forks: 1
- Open Issues: 0
- Releases: 6
Topics
Metadata Files
README.md
oct-to-tiff
A command line tool for converting optical coherence tomography angiography (OCTA) data.
Installation
via pip:
pip install oct-to-tiff
via mamba:
mamba install -c conda-forge oct-to-tiff
Getting started
oct-to-tiff /path/to/image.OCT
will read an OCT volume and write to a single OME-TIFF file, including voxel size in the metadata.
By default, the output file will be written with the same name as the input file and to the same directory:
tree /path/to/images
├── image.OCT
└── image.ome.tif
To specify a custom output directory, see Optional arguments below.
Batch processing
bash
for file in *.OCT; do oct-to-tiff "${file}"; done
will convert all OCT volumes in the current directory to OME-TIFF files, including voxel size in the metadata.
Supported scan patterns
This tool has been developed by reverse engineering data from the Optovue RTVue XR Avanti System.
Due to limited test data, only the following scan patterns are currently supported:
Structural OCT
- 3D Cornea
- 3D Disc
- 3D Retina
- 3D Widefield
- 3D Widefield MCT
- Angle
- Cornea Cross Line
- Cornea Line
- Cross Line
- Enhanced HD Line
- GCC
- Grid
- Line
- ONH (Partial)
- Pachymetry Wide
- Radial Lines
- Raster
- Retina Map (Partial)
OCT Angiography
- Angio Disc
- Angio Retina
- HD Angio Disc
- HD Angio Retina
Optional arguments
To view these options at any time, run oct-to-tiff --help.
--output OUTPUT
Description: specify a custom output directory.
If the path to the output directory does not exist, a new directory (and parent directories) will be created.
Usage:
oct-to-tiff /path/to/image.OCT --output /path/to/output/directory
--overwrite
Description: overwrite output file if it exists.
Usage:
oct-to-tiff /path/to/image.OCT --overwrite
--size SIZE
Description: scan size in mm.
Sets the correct voxel size for scan patterns with adjustable length.
Usage:
oct-to-tiff /path/to/image.OCT --size 4.5
--log-level LEVEL
Description: sets the logging level (default: WARNING)
Usage:
oct-to-tiff /path/to/image.OCT --log-level INFO
--version
Description: show program's version number and exit.
Usage:
oct-to-tiff --version
The following options are mutually exclusive:
--angio
Description: convert extracted OCTA data.
Requires --size SIZE.
Usage:
oct-to-tiff /path/to/data --angio --size 4.5
--en-face
Description: convert extracted en face data.
Requires --size SIZE.
Usage:
oct-to-tiff /path/to/data --en-face --size 4.5
--seg-curve
Description: convert extracted segmentation data.
Usage:
oct-to-tiff /path/to/data --seg-curve
--boundaries
Description: extract segmentation lines.
Usage:
oct-to-tiff /path/to/curve.xml --boundaries
Contributing
This project uses Ruff for linting and formatting.
Requirements
Requires Python 3.11 or higher.
Owner
- Name: Cameron Lloyd
- Login: camlloyd
- Kind: user
- Location: Cambridge, UK
- Website: https://cameronlloyd.com
- Twitter: CameronBLloyd
- Repositories: 32
- Profile: https://github.com/camlloyd
Computational Biologist
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: Lloyd
given-names: Cameron
orcid: https://orcid.org/0000-0003-1055-2282
title: "oct-to-tiff: A command line tool for converting optical coherence tomography angiography (OCTA) data."
version: 0.5.0
doi: 10.5281/zenodo.14289106
date-released: 2024-12-06
GitHub Events
Total
- Create event: 15
- Release event: 1
- Issues event: 2
- Watch event: 3
- Delete event: 18
- Issue comment event: 6
- Push event: 16
- Pull request event: 27
Last Year
- Create event: 15
- Release event: 1
- Issues event: 2
- Watch event: 3
- Delete event: 18
- Issue comment event: 6
- Push event: 16
- Pull request event: 27
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Cameron Lloyd | l****d@m****u | 98 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 6
- Total pull requests: 95
- Average time to close issues: 2 months
- Average time to close pull requests: less than a minute
- Total issue authors: 4
- Total pull request authors: 1
- Average comments per issue: 6.67
- Average comments per pull request: 0.0
- Merged pull requests: 93
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 28
- Average time to close issues: 2 months
- Average time to close pull requests: less than a minute
- Issue authors: 2
- Pull request authors: 1
- Average comments per issue: 3.0
- Average comments per pull request: 0.0
- Merged pull requests: 28
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- camlloyd (3)
- HYenTung (1)
- edwarddu (1)
- AlanZhang1995 (1)
Pull Request Authors
- camlloyd (95)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- pypi 14 last-month
- Total docker downloads: 83
-
Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 1
(may contain duplicates) - Total versions: 8
- Total maintainers: 1
pypi.org: oct-to-tiff
A command line tool for converting optical coherence tomography angiography (OCTA) data.
- Homepage: https://github.com/camlloyd/oct-to-tiff
- Documentation: https://oct-to-tiff.readthedocs.io/
- License: BSD 3-Clause License Copyright (c) 2021, Cameron Lloyd All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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Latest release: 0.5.0
published about 1 year ago
Rankings
Maintainers (1)
conda-forge.org: oct-to-tiff
- Homepage: https://github.com/camlloyd/oct-to-tiff
- License: BSD-3-Clause
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Latest release: 0.3.0
published about 3 years ago
Rankings
Dependencies
- actions/checkout v3 composite
- actions/setup-python v4 composite
- pypa/gh-action-pypi-publish release/v1 composite
- actions/checkout v3 composite
- actions/setup-python v4 composite
- pypa/gh-action-pypi-publish release/v1 composite