{"name":"bfio","display_name":"bfio","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"bfio.get_reader","title":"get_reader","python_name":"bfio.bfio:get_reader","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"bfio.get_writer","title":"get_writer","python_name":"bfio.bfio:get_writer","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"bfio.get_reader","filename_patterns":["*"],"accepts_directories":true}],"writers":[{"command":"bfio.get_writer","layer_types":["image"],"filename_extensions":[],"display_name":"image"}],"widgets":null,"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"bfio","version":"2.3.0","dynamic":null,"platform":["UNKNOWN"],"supported_platform":null,"summary":"Simple reading and writing classes for tiled tiffs using Bioformats.","description":"# **B**io**F**ormats **I**nput/**O**utput utility (bfio 2.3.0)\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/filepattern/)\n![PyPI - Downloads](https://img.shields.io/pypi/dm/bfio)\n![Bower](https://img.shields.io/bower/l/MI)\n\nThis tool is a simplified but powerful interface to\n[Bioformats](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 useable. Only files in tiled OME Tiff or OME Zarr format can be\nread/written.\n\nIn order to use the `Java` backend, it is necessary to first install the JDK.\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.\n\n### Installing bfio\n\nThe `bfio` package and the core dependencies (numpy, tifffile, imagecodecs) can\nbe installed using pip:\n\n`pip install bfio`\n\nAdditionally, `bfio` with other dependencies can be installed:\n\n1. `pip install bfio[bioformats]` - Adds support for BioFormats/Java. See [License](#license) for additional information.\n2. `pip install bfio[zarr]` - Adds support for OME Zarr\n3. `pip install bfio[all]` - Installs all dependencies.\n\n## Docker\n\n### labshare/polus-bfio-util:2.3.0\n\nUbuntu based container with bfio and all dependencies (including Java).\n\n### labshare/polus-bfio-util:2.3.0-imagej\n\nSame as above, except comes with ImageJ and PyImageJ.\n\n### labshare/polus-bfio-util:2.3.0-tensorflow\n\nTensorflow container with bfio isntalled.\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@labshare.org)\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**NOTE**\n\nBioformats is licensed under GPL, and as a consequence so is the `bioformats_jar` \npackage. These packages and libraries are installed when using the `bfio[bioformats]` option.\n\n## Acknowledgments\n\n- Parts of this code were written/modified from existing code found in\n    `tifffile`.\n\n\n","description_content_type":"text/markdown","keywords":null,"home_page":"UNKNOWN","download_url":null,"author":"Nick Schaub","author_email":"nick.schaub@nih.gov","maintainer":null,"maintainer_email":null,"license":"UNKNOWN","classifier":["Development Status :: 5 - Production/Stable","Programming Language :: Python :: 3","License :: OSI Approved :: MIT License","Operating System :: OS Independent","Framework :: napari"],"requires_dist":["tifffile (>=2021.8.30)","imagecodecs (>=2021.2.26)","numpy (>=1.20.1)","ome-types (>=0.2.10)","lxml","zarr (>=2.6.1) ; extra == 'all'","bioformats-jar (==6.7.0.post2) ; extra == 'all'","bioformats-jar (==6.7.0.post2) ; extra == 'bioformats'","zarr (>=2.6.1) ; extra == 'dev'","requests (>=2.26.0) ; extra == 'dev'","bioformats-jar (==6.7.0.post2) ; extra == 'dev'","zarr (>=2.6.1) ; extra == 'zarr'"],"requires_python":">=3.6","requires_external":null,"project_url":["Documentation, https://bfio.readthedocs.io/en/latest/","Source, https://github.com/labshare/bfio"],"provides_extra":["all","bioformats","dev","zarr"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":true}