{"id":28712444,"url":"https://github.com/polusai/bfio","last_synced_at":"2026-03-14T16:20:47.357Z","repository":{"id":42384808,"uuid":"357318882","full_name":"PolusAI/bfio","owner":"PolusAI","description":"Interface to the Bioformats Java library","archived":false,"fork":false,"pushed_at":"2025-01-16T20:49:31.000Z","size":63420,"stargazers_count":13,"open_issues_count":2,"forks_count":8,"subscribers_count":13,"default_branch":"master","last_synced_at":"2025-06-14T23:05:49.601Z","etag":null,"topics":["image-io","image-processing","napari-plugin"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/PolusAI.png","metadata":{"files":{"readme":"README.md","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":"2021-04-12T19:42:43.000Z","updated_at":"2025-01-31T13:10:21.000Z","dependencies_parsed_at":"2023-09-28T02:52:55.472Z","dependency_job_id":"1d0bc2fd-fd44-4b46-8b08-b5cfebecd924","html_url":"https://github.com/PolusAI/bfio","commit_stats":null,"previous_names":["labshare/bfio"],"tags_count":25,"template":false,"template_full_name":null,"purl":"pkg:github/PolusAI/bfio","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PolusAI%2Fbfio","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PolusAI%2Fbfio/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PolusAI%2Fbfio/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PolusAI%2Fbfio/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/PolusAI","download_url":"https://codeload.github.com/PolusAI/bfio/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PolusAI%2Fbfio/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":259896235,"owners_count":22928331,"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":["image-io","image-processing","napari-plugin"],"created_at":"2025-06-14T23:05:50.583Z","updated_at":"2026-03-14T16:20:47.352Z","avatar_url":"https://github.com/PolusAI.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# **B**io**F**ormats **I**nput/**O**utput utility (bfio 2.5.0)\n\n[![Documentation Status](https://readthedocs.org/projects/bfio/badge/?version=latest)](https://bfio.readthedocs.io/en/latest/?badge=latest)\n[![PyPI](https://img.shields.io/pypi/v/bfio)](https://pypi.org/project/bfio/)\n![PyPI - Downloads](https://img.shields.io/pypi/dm/bfio)\n[![Conda](https://img.shields.io/conda/v/conda-forge/bfio)](https://anaconda.org/conda-forge/bfio)\n[![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/bfio?label=Conda%20downloads)](https://anaconda.org/conda-forge/bfio)\n![Bower](https://img.shields.io/bower/l/MI)\n\nThis tool is a simplified but powerful interface to\n[Bio-Formats](https://www.openmicroscopy.org/bio-formats/)\nusing jpype for direct access to the library. This tool is designed with\nscalable image analysis in mind, with a simple interface to treat any image\nlike a memory mapped array.\n\nDocker containers with all necessary components are available (see\n**Docker Containers** section).\n\n## Summary\n\n- [Installation](#installation)\n- [Docker](#docker)\n- [Documentation](#documentation)\n- [Contributing](#contributing)\n- [Versioning](#versioning)\n- [Authors](#authors)\n- [License](#license)\n- [Acknowledgments](#acknowledgments)\n\n## Installation\n\n### Setting up Java\n\n**Note:** `bfio` can be used without Java, but only the `python`, `zarr`, `zarr3`, and `tensorstore`\nbackends will be usable. This means only files in tiled OME Tiff or OME Zarr format can be\nread/written.\n\nIn order to use the `bioformats` backend, it is necessary to first install the JDK and Maven.\nThe `bfio` package is generally tested with\n[JDK 8](https://docs.oracle.com/javase/8/docs/technotes/guides/install/install_overview.html),\nbut JDK 11 and later also appear to work.\nHere are some info on installing Maven on various OS ([Windows](https://phoenixnap.com/kb/install-maven-windows) | [Linux](https://www.digitalocean.com/community/tutorials/install-maven-linux-ubuntu) | [Mac](https://www.digitalocean.com/community/tutorials/install-maven-mac-os))\n\n### Installing bfio\n\nThe `bfio` package and the core dependencies (numpy, tifffile, imagecodecs, scyjava) can\nbe installed using pip:\n\n`pip install bfio`\n\n## Docker\n\n### polusai/bfio:2.5.0\n\nUbuntu based container with bfio and all dependencies (including Java).\n\n### polusai/bfio:2.5.0-imagej\n\nSame as above, except comes with ImageJ and PyImageJ.\n\n### polusai/bfio:2.5.0-tensorflow\n\nTensorflow container with bfio installed.\n\n## Documentation\n\nDocumentation and examples are available on\n[Read the Docs](https://bfio.readthedocs.io/en/latest/).\n\n## Versioning\n\nWe use [SemVer](http://semver.org/) for versioning. For the versions\navailable, see the [tags on this\nrepository](https://github.com/PurpleBooth/a-good-readme-template/tags).\n\n## Authors\n\nNick Schaub (nick.schaub@nih.gov, nick.schaub@axleinfo.com)\nSameeul B Samee (sameeul.samee@axleinfo.com)\n\n## License\n\nThis project is licensed under the [MIT License](LICENSE)\nCreative Commons License - see the [LICENSE](LICENSE) file for details.\n\n## Acknowledgments\n\n- Parts of this code were written/modified from existing code found in\n    `tifffile`.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpolusai%2Fbfio","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpolusai%2Fbfio","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpolusai%2Fbfio/lists"}