{"id":16925334,"url":"https://github.com/camlloyd/oct-to-tiff","last_synced_at":"2025-03-22T11:31:03.307Z","repository":{"id":37893233,"uuid":"382486199","full_name":"camlloyd/oct-to-tiff","owner":"camlloyd","description":"A command line tool for converting optical coherence tomography angiography (OCTA) data.","archived":false,"fork":false,"pushed_at":"2024-12-06T13:37:10.000Z","size":112,"stargazers_count":7,"open_issues_count":1,"forks_count":1,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-03-18T10:51:38.031Z","etag":null,"topics":["angiography","cli","oct","octa"],"latest_commit_sha":null,"homepage":"https://pypi.org/project/oct-to-tiff","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/camlloyd.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE.txt","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2021-07-02T23:36:05.000Z","updated_at":"2025-02-16T04:47:02.000Z","dependencies_parsed_at":"2023-01-20T23:03:19.735Z","dependency_job_id":"9baae3b0-2f8b-40d9-a8c8-e212ddb84b2f","html_url":"https://github.com/camlloyd/oct-to-tiff","commit_stats":{"total_commits":98,"total_committers":1,"mean_commits":98.0,"dds":0.0,"last_synced_commit":"e96566d4b2c1438f325bddf0d07ffc6f2ed71843"},"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/camlloyd%2Foct-to-tiff","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/camlloyd%2Foct-to-tiff/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/camlloyd%2Foct-to-tiff/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/camlloyd%2Foct-to-tiff/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/camlloyd","download_url":"https://codeload.github.com/camlloyd/oct-to-tiff/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244951255,"owners_count":20537347,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["angiography","cli","oct","octa"],"created_at":"2024-10-13T20:09:29.299Z","updated_at":"2025-03-22T11:31:03.300Z","avatar_url":"https://github.com/camlloyd.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# oct-to-tiff\n\n[![DOI](https://zenodo.org/badge/382486199.svg)](https://zenodo.org/badge/latestdoi/382486199)\n[![PyPI - Version](https://img.shields.io/pypi/v/oct-to-tiff)](https://pypi.org/project/oct-to-tiff)\n[![PyPI - License](https://img.shields.io/pypi/l/oct-to-tiff)](https://github.com/camlloyd/oct-to-tiff/blob/main/LICENSE.txt)\n[![PyPI Downloads](https://static.pepy.tech/badge/oct-to-tiff)](https://pepy.tech/projects/oct-to-tiff)\n\n\nA command line tool for converting optical coherence tomography angiography (OCTA) data.\n\n## Installation\nvia pip:\n\n    pip install oct-to-tiff\n\nvia mamba:\n\n    mamba install -c conda-forge oct-to-tiff\n\n## Getting started\n    oct-to-tiff /path/to/image.OCT\n    \nwill read an OCT volume and write to a single OME-TIFF file, including voxel size in the metadata.\n\nBy default, the output file will be written with the same name as the input file and to the same directory:\n\n\n    tree /path/to/images\n        ├── image.OCT\n        └── image.ome.tif\n\nTo specify a custom output directory, see [Optional arguments](#optional-arguments) below.\n\n## Batch processing\n``` bash\nfor file in *.OCT; do oct-to-tiff \"${file}\"; done\n```\nwill convert all OCT volumes in the current directory to OME-TIFF files, including voxel size in the metadata.\n\n## Supported scan patterns\n\nThis tool has been developed by reverse engineering data from the Optovue RTVue XR Avanti System.\n\nDue to limited test data, only the following scan patterns are currently supported:\n\n### Structural OCT\n- 3D Cornea\n- 3D Disc\n- 3D Retina\n- 3D Widefield\n- 3D Widefield MCT\n- Angle\n- Cornea Cross Line\n- Cornea Line\n- Cross Line\n- Enhanced HD Line\n- GCC\n- Grid\n- Line\n- ONH (Partial)\n- Pachymetry Wide\n- Radial Lines\n- Raster\n- Retina Map (Partial)\n\n### OCT Angiography\n- Angio Disc\n- Angio Retina\n- HD Angio Disc\n- HD Angio Retina\n\n\n## Optional arguments\n\nTo view these options at any time, run `oct-to-tiff --help`.\n\n#### `--output OUTPUT`\n**Description**: specify a custom output directory. \n\nIf the path to the output directory does not exist, a new directory (and parent directories) will be created.\n\n**Usage**: \n    \n    oct-to-tiff /path/to/image.OCT --output /path/to/output/directory\n    \n#### `--overwrite`\n**Description**: overwrite output file if it exists.\n\n**Usage**: \n    \n    oct-to-tiff /path/to/image.OCT --overwrite\n    \n#### `--size SIZE`\n**Description**: scan size in mm.\n\nSets the correct voxel size for scan patterns with adjustable length.\n\n**Usage**:\n\n    oct-to-tiff /path/to/image.OCT --size 4.5\n\n#### `--log-level LEVEL`\n**Description**: sets the logging level (default: `WARNING`)\n\n**Usage**:\n\n    oct-to-tiff /path/to/image.OCT --log-level INFO\n\n#### `--version`\n**Description**: show program's version number and exit.\n\n**Usage**:\n\n    oct-to-tiff --version\n\n#### The following options are mutually exclusive:\n    \n#### `--angio`\n**Description**: convert extracted OCTA data. \n\nRequires `--size SIZE`.\n\n**Usage**:\n\n    oct-to-tiff /path/to/data --angio --size 4.5\n    \n#### `--en-face`\n**Description**: convert extracted en face data.\n\nRequires `--size SIZE`.\n\n**Usage**:\n\n    oct-to-tiff /path/to/data --en-face --size 4.5\n    \n#### `--seg-curve`\n**Description**: convert extracted segmentation data.\n\n**Usage**:\n\n    oct-to-tiff /path/to/data --seg-curve\n\n#### `--boundaries`\n**Description**: extract segmentation lines.\n\n**Usage**:\n\n    oct-to-tiff /path/to/curve.xml --boundaries\n\n## Contributing\n\nThis project uses [Ruff](https://github.com/astral-sh/ruff) for linting and formatting.\n\n## Requirements\n\nRequires Python 3.10 or higher.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcamlloyd%2Foct-to-tiff","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcamlloyd%2Foct-to-tiff","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcamlloyd%2Foct-to-tiff/lists"}