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 3.8 or higher.