A command line tool for converting optical coherence tomography angiography (OCTA) data.
via pip:
pip install oct-to-tiff
via conda:
conda install -c conda-forge oct-to-tiff
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.
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.
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:
- 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)
- Angio Disc
- Angio Retina
- HD Angio Disc
- HD Angio Retina
To view these options at any time, run oct-to-tiff --help
.
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
Description: overwrite output file if it exists.
Usage:
oct-to-tiff /path/to/image.OCT --overwrite
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
Description: sets the logging level (default: WARNING
)
Usage:
oct-to-tiff /path/to/image.OCT --log-level INFO
Description: show program's version number and exit.
Usage:
oct-to-tiff --version
Description: convert extracted OCTA data.
Requires --size SIZE
.
Usage:
oct-to-tiff /path/to/data --angio --size 4.5
Description: convert extracted en face data.
Requires --size SIZE
.
Usage:
oct-to-tiff /path/to/data --en-face --size 4.5
Description: convert extracted segmentation data.
Usage:
oct-to-tiff /path/to/data --seg-curve
Description: extract segmentation lines.
Usage:
oct-to-tiff /path/to/curve.xml --boundaries
This project uses Ruff for linting and formatting.
Requires Python 3.10 or higher.