| Name | bfio JSON |
| Version |
2.4.8
JSON |
| download |
| home_page | None |
| Summary | Simple reading and writing classes for tiled tiffs using Bio-Formats. |
| upload_time | 2025-07-15 17:43:56 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
| license | MIT License
Copyright (c) 2023 PolusAI
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
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copies of the Software, and to permit persons to whom the Software is
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The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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|
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No requirements were recorded.
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|
# **B**io**F**ormats **I**nput/**O**utput utility (bfio 2.4.8)
[](https://bfio.readthedocs.io/en/latest/?badge=latest)
[](https://pypi.org/project/bfio/)
[](https://anaconda.org/conda-forge/bfio)
[](https://anaconda.org/conda-forge/bfio)
This tool is a simplified but powerful interface to
[Bio-Formats](https://www.openmicroscopy.org/bio-formats/)
using jpype for direct access to the library. This tool is designed with
scalable image analysis in mind, with a simple interface to treat any image
like a memory mapped array.
Docker containers with all necessary components are available (see
**Docker Containers** section).
## Summary
- [Installation](#installation)
- [Docker](#docker)
- [Documentation](#documentation)
- [Contributing](#contributing)
- [Versioning](#versioning)
- [Authors](#authors)
- [License](#license)
- [Acknowledgments](#acknowledgments)
## Installation
### Setting up Java
**Note:** `bfio` can be used without Java, but only the `python` and `zarr`
backends will be usable. This means only files in tiled OME Tiff or OME Zarr format can be
read/written.
In order to use the `bioformats` backend, it is necessary to first install the JDK and Maven.
The `bfio` package is generally tested with
[JDK 8](https://docs.oracle.com/javase/8/docs/technotes/guides/install/install_overview.html),
but JDK 11 and later also appear to work.
Here 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))
### Installing bfio
The `bfio` package and the core dependencies (numpy, tifffile, imagecodecs, scyjava) can
be installed using pip:
`pip install bfio`
## Docker
### polusai/bfio:2.4.8
Ubuntu based container with bfio and all dependencies (including Java).
### polusai/bfio:2.4.8-imagej
Same as above, except comes with ImageJ and PyImageJ.
### polusai/bfio:2.4.8-tensorflow
Tensorflow container with bfio installed.
## Documentation
Documentation and examples are available on
[Read the Docs](https://bfio.readthedocs.io/en/latest/).
## Versioning
We use [SemVer](http://semver.org/) for versioning. For the versions
available, see the [tags on this
repository](https://github.com/PurpleBooth/a-good-readme-template/tags).
## Authors
Nick Schaub (nick.schaub@nih.gov, nick.schaub@axleinfo.com)
Sameeul B Samee (sameeul.samee@axleinfo.com)
## License
This project is licensed under the [MIT License](LICENSE)
Creative Commons License - see the [LICENSE](LICENSE) file for details.
## Acknowledgments
- Parts of this code were written/modified from existing code found in
`tifffile`.
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"description": "# **B**io**F**ormats **I**nput/**O**utput utility (bfio 2.4.8)\n\n[](https://bfio.readthedocs.io/en/latest/?badge=latest)\n[](https://pypi.org/project/bfio/)\n\n[](https://anaconda.org/conda-forge/bfio)\n[](https://anaconda.org/conda-forge/bfio)\n\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` and `zarr`\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:2.4.8\n\nUbuntu based container with bfio and all dependencies (including Java).\n\n### polusai/bfio:2.4.8-imagej\n\nSame as above, except comes with ImageJ and PyImageJ.\n\n### polusai/bfio:2.4.8-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",
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