oct-to-tiff

A command line tool for converting optical coherence tomography angiography (OCTA) data.

Installation

via uv (recommended):

uv pip install oct-to-tiff

via pip:

pip install oct-to-tiff

via conda:

conda install 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

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.

Usage:

oct-to-tiff /path/to/data --angio --size 4.5

--en-face

Description: convert extracted en face data.

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: convert segmentation lines to ImageJ ROIs.

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.