Metadata-Version: 2.1
Name: bfio
Version: 2.0.3
Summary: Simple reading and writing classes for tiled tiffs using Bioformats.
Home-page: UNKNOWN
Author: Nick Schaub
Author-email: nick.schaub@labshare.com
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)
        
        This tool is a simplified but powerful interface to the
        [Bioformats java library](https://www.openmicroscopy.org/bio-formats/).
        It makes use 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 do 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).
        
        ## Documentation
        
        Documentation is available on
        [Read the Docs](https://bfio.readthedocs.io/en/latest/).
        
        ## Universal Container Components
        
        All containers contain the follow components:
        
        1. Python 3.8
        2. [numpy](https://pypi.org/project/numpy/1.19.1/) (1.19.1)
        3. [imagecodecs](https://pypi.org/project/imagecodecs/2020.5.30/) (2020.5.30, built with `--lite` option)
        4. [tifffile](https://pypi.org/project/tifffile/2020.7.4/) (2020.7.4)
        5. bfio (version 2.0.3)
        
        Containers ending with `-java` also contain:
        
        6. openjdk-8
        7. [python-javabridge](https://pypi.org/project/python-javabridge/4.0.0/) (version 4.0.0)
        8. [python-bioformats](https://pypi.org/project/python-bioformats/4.0.0/) (version 4.0.0)
        9. [loci-tools.jar](https://downloads.openmicroscopy.org/bio-formats/6.1.0/artifacts/) (Version 6.1.0)
        
        ## Docker Containers
        
        All containers can use the Python backend, but only the containers with Java may
        use the Java backend. 
        
        ### labshare/polus-bfio-util:2.0.3
        
        *Additional Python container tags:* `2.0.3-alpine`, `2.0.3-python`,
        `2.0.3-alpine-python`
        
        *Containers with Java:* `2.0.3-java`, `2.0.3-alpine-java`
        
        This container is built on Alpine Linux. This is the smallest bfio container,
        but also the most difficult to install additional requirements on. The Python
        containers (98MB) are much smaller than the Java containers (383MB).
        
        ### labshare/polus-bfio-util:2.0.3-slim-buster
        
        *Additional Python container tags:* `2.0.3-slim-buster-python`
        
        *Containers with Java:* `2.0.3-slim-buster-java`
        
        This container is built on a stripped down version of Debian Buster. This
        container is larger than the `alpine` version, but easier to install new Python
        packages on since `manylinux` wheels can be installed on it. However, if a
        package requires compilation, a compiler will need to be installed.
        
        ### labshare/polus-bfio-util:2.0.3-tensorflow
        
        *Additional Python container tags:* `2.0.3-tensorflow-python`
        
        *Containers with Java:* No Java containers
        
        This container is built on Debian Buster and includes Tensorflow 2.1.0 and all
        necessary GPU drivers to run Tensorflow on an NVIDIA graphics card.
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
