{"id":19671246,"url":"https://github.com/cgohlke/oiffile","last_synced_at":"2026-02-09T06:20:10.696Z","repository":{"id":60482746,"uuid":"242422920","full_name":"cgohlke/oiffile","owner":"cgohlke","description":"Read Olympus image files (OIF and OIB).","archived":false,"fork":false,"pushed_at":"2025-05-10T19:38:55.000Z","size":269,"stargazers_count":13,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-07-11T18:50:25.079Z","etag":null,"topics":["fluorescence-microscopy-imaging","format-reader","image","life-sciences-image","olympus","python"],"latest_commit_sha":null,"homepage":"https://pypi.org/project/oiffile","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/cgohlke.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-02-22T22:50:23.000Z","updated_at":"2025-05-10T19:38:58.000Z","dependencies_parsed_at":"2024-11-11T17:18:17.917Z","dependency_job_id":null,"html_url":"https://github.com/cgohlke/oiffile","commit_stats":{"total_commits":50,"total_committers":2,"mean_commits":25.0,"dds":0.26,"last_synced_commit":"06baa258d90ad65fb4286c0ba46517a954e38dbf"},"previous_names":[],"tags_count":11,"template":false,"template_full_name":null,"purl":"pkg:github/cgohlke/oiffile","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cgohlke%2Foiffile","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cgohlke%2Foiffile/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cgohlke%2Foiffile/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cgohlke%2Foiffile/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cgohlke","download_url":"https://codeload.github.com/cgohlke/oiffile/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cgohlke%2Foiffile/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":265563112,"owners_count":23788646,"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":["fluorescence-microscopy-imaging","format-reader","image","life-sciences-image","olympus","python"],"created_at":"2024-11-11T17:08:15.867Z","updated_at":"2026-02-09T06:20:10.685Z","avatar_url":"https://github.com/cgohlke.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"..\n  This file is generated by setup.py\n\nRead Olympus image files (OIF and OIB)\n======================================\n\nOiffile is a Python library to read image and metadata from Olympus Image\nFormat files. OIF is the native file format of the Olympus FluoView(tm)\nsoftware for confocal microscopy.\n\nThere are two variants of the format:\n\n- OIF (Olympus Image File) is a multi-file format that includes a main setting\n  file (.oif) and an associated directory with data and setting files (.tif,\n  .bmp, .txt, .pty, .roi, and .lut).\n\n- OIB (Olympus Image Binary) is a compound document file, storing OIF and\n  associated files within a single file.\n\n:Author: `Christoph Gohlke \u003chttps://www.cgohlke.com\u003e`_\n:License: BSD-3-Clause\n:Version: 2026.2.8\n:DOI: `10.5281/zenodo.17905223 \u003chttps://doi.org/10.5281/zenodo.17905223\u003e`_\n\nQuickstart\n----------\n\nInstall the oiffile package and all dependencies from the\n`Python Package Index \u003chttps://pypi.org/project/oiffile/\u003e`_::\n\n    python -m pip install -U \"oiffile[all]\"\n\nView image and metadata stored in an OIF or OIB file::\n\n    python -m oiffile file.oif\n\nSee `Examples`_ for using the programming interface.\n\nSource code and support are available on\n`GitHub \u003chttps://github.com/cgohlke/oiffile\u003e`_.\n\nRequirements\n------------\n\nThis revision was tested with the following requirements and dependencies\n(other versions may work):\n\n- `CPython \u003chttps://www.python.org\u003e`_ 3.11.9, 3.12.10, 3.13.12, 3.14.3 64-bit\n- `NumPy \u003chttps://pypi.org/project/numpy\u003e`_ 2.4.2\n- `Tifffile \u003chttps://pypi.org/project/tifffile/\u003e`_ 2026.1.28\n\nRevisions\n---------\n\n2026.2.8\n\n- Fix code review issues.\n\n2026.1.8\n\n- Improve code quality.\n\n2025.12.12\n\n- Derive OifFileError from ValueError.\n- Drop support for Python 3.10.\n\n2025.5.10\n\n- Remove doctest command line option.\n- Support Python 3.14.\n\n2025.1.1\n\n- Improve type hints.\n- Drop support for Python 3.9, support Python 3.13.\n\n2024.5.24\n\n- …\n\nRefer to the CHANGES file for older revisions.\n\nNotes\n-----\n\nNo specification document is available.\n\nTested only with files produced on Olympus FV1000 hardware.\n\nExamples\n--------\n\nRead the image from an OIB file as numpy array:\n\n.. code-block:: python\n\n    \u003e\u003e\u003e image = imread('test.oib')\n    \u003e\u003e\u003e image.shape\n    (3, 256, 256)\n    \u003e\u003e\u003e image[:, 95, 216]\n    array([820,  50, 436], dtype=uint16)\n\nRead the image from a single TIFF file in an OIB file:\n\n.. code-block:: python\n\n    \u003e\u003e\u003e from tifffile import natural_sorted\n    \u003e\u003e\u003e with OifFile('test.oib') as oib:\n    ...     filename = natural_sorted(oib.glob('*.tif'))[0]\n    ...     image = oib.asarray(filename)\n    ...\n    \u003e\u003e\u003e filename\n    'Storage00001/s_C001.tif'\n    \u003e\u003e\u003e print(image[95, 216])\n    820\n\nAccess metadata and the OIB main file:\n\n.. code-block:: python\n\n    \u003e\u003e\u003e with OifFile('test.oib') as oib:\n    ...     oib.axes\n    ...     oib.shape\n    ...     oib.dtype\n    ...     dataname = oib.mainfile['File Info']['DataName']\n    ...\n    'CYX'\n    (3, 256, 256)\n    dtype('uint16')\n    \u003e\u003e\u003e dataname\n    'Cell 1 mitoEGFP.oib'\n\nExtract the OIB file content to an OIF file and associated data directory:\n\n.. code-block:: python\n\n    \u003e\u003e\u003e import tempfile\n    \u003e\u003e\u003e tempdir = tempfile.mkdtemp()\n    \u003e\u003e\u003e oib2oif('test.oib', location=tempdir)\n    Saving ... done.\n\nRead the image from the extracted OIF file:\n\n.. code-block:: python\n\n    \u003e\u003e\u003e image = imread(f'{tempdir}/{dataname[:-4]}.oif')\n    \u003e\u003e\u003e image[:, 95, 216]\n    array([820,  50, 436], dtype=uint16)\n\nRead OLE compound file and access the 'OibInfo.txt' settings file:\n\n.. code-block:: python\n\n    \u003e\u003e\u003e with CompoundFile('test.oib') as com:\n    ...     info = com.open_file('OibInfo.txt')\n    ...     len(com.files())\n    ...\n    14\n    \u003e\u003e\u003e info = SettingsFile(info, 'OibInfo.txt')\n    \u003e\u003e\u003e info['OibSaveInfo']['Version']\n    '2.0.0.0'","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcgohlke%2Foiffile","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcgohlke%2Foiffile","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcgohlke%2Foiffile/lists"}