Metadata-Version: 2.1
Name: bfio
Version: 2.1.3
Summary: Simple reading and writing classes for tiled tiffs using Bioformats.
Home-page: UNKNOWN
Author: Nick Schaub
Author-email: nick.schaub@nih.gov
License: UNKNOWN
Project-URL: Documentation, https://bfio.readthedocs.io/en/latest/
Project-URL: Source, https://github.com/Nicholas-Schaub/polus-plugins/tree/master/utils/polus-bfio-util
Description: # **B**io**F**ormats **I**nput/**O**utput utility (bfio v2.1.3)
        
        [![Documentation Status](https://readthedocs.org/projects/bfio/badge/?version=latest)](https://bfio.readthedocs.io/en/latest/?badge=latest)
        [![PyPI](https://img.shields.io/pypi/v/bfio)](https://pypi.org/project/filepattern/)
        ![PyPI - Downloads](https://img.shields.io/pypi/dm/bfio)
        ![Bower](https://img.shields.io/bower/l/MI)
        
        This tool is a simplified but powerful interface to the
        [Bioformats java library](https://www.openmicroscopy.org/bio-formats/).
        It makes use of parts of Cell Profilers
        [python-bioformats](https://github.com/CellProfiler/python-bioformats)
        package to access the Bioformats library. One of the issues with using the
        `python-bioformats` package is reading and writing large image planes (>2GB).
        The challenge lies in the way Bioformats reads and writes large image planes,
        using an `int` value to index the file. To get around this, files can be read or
        written in chunks and the classes provided in `bfio` handle this automatically.
        The `BioWriter` class in this package only writes files in the `.ome.tif`
        format, and automatically sets the tile sizes to 1024.
        
        Docker containers with all necessary components are available (see
        **Docker Containers** section).
        
        ## Summary
        
          - [Installation](#installation)
          - [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 useable. 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.
        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.
        
        ### Installing bfio
        
        The `bfio` package and the core dependencies (numpy, tifffile, imagecodecs) can
        be installed using pip:
        
        `pip install bfio`
        
        Additionally, `bfio` with other dependencies can be installed:
        
        1. `pip install bfio[jpype]` - Adds support for BioFormats/Java
        2. `pip install bfio[zarr]` - Adds support for OME Zarr
        3. `pip install bfio[all]` - Installs all dependencies.
        
        ## 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@labshare.org)
        
        ## 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
            `python-bioformats` and `tifffile`.
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Provides-Extra: jpype
Provides-Extra: zarr
Provides-Extra: all
