Metadata-Version: 2.1
Name: bfio
Version: 2.0.5
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 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 2.0.5)
        
        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:2.0.5~
        
        The alpine container for `bfio` is currently unavailable.
        
        ~*Additional Python container tags:* `2.0.5-alpine`, `2.0.5-python`,~
        ~`2.0.5-alpine-python`~
        
        ~*Containers with Java:* `2.0.5-java`, `2.0.5-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:2.0.5-slim-buster
        
        *Additional Python container tags:* `2.0.5-slim-buster-python`
        
        *Containers with Java:* `2.0.5-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:2.0.5-tensorflow
        
        *Additional Python container tags:* `2.0.5-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
