| Name | bfio JSON |
| Version |
2.3.5
JSON |
| download |
| home_page | |
| Summary | Simple reading and writing classes for tiled tiffs using Bioformats. |
| upload_time | 2024-02-05 18:19:23 |
| maintainer | |
| docs_url | None |
| author | |
| 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 in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: 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, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
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| requirements |
No requirements were recorded.
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| Travis-CI |
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| coveralls test coverage |
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# **B**io**F**ormats **I**nput/**O**utput utility (bfio 2.3.5)
[](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
[Bioformats](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. Only files in tiled OME Tiff or OME Zarr format can be
read/written.
In order to use the `Java` 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:2.3.5
Ubuntu based container with bfio and all dependencies (including Java).
### polusai/bfio:2.3.5-imagej
Same as above, except comes with ImageJ and PyImageJ.
### polusai/bfio:2.3.5-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.
**NOTE**
Bioformats is licensed under GPL, and as a consequence so is the `bioformats_jar`
package. These packages and libraries are installed when using the `bfio[bioformats]` option.
## Acknowledgments
- Parts of this code were written/modified from existing code found in
`tifffile`.
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