Metadata-Version: 2.1
Name: bfio
Version: 2.3.6
Summary: Simple reading and writing classes for tiled tiffs using Bio-Formats.
Author-email: Nick Schaub <nick.schaub@nih.gov>, Sameeul Bashir Samee <sameeul.samee@axleinfo.com>
Maintainer-email: Sameeul Bashir Samee <sameeul.samee@axleinfo.com>
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,
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Project-URL: Documentation, https://bfio.readthedocs.io/en/latest/
Project-URL: Repository, https://github.com/PolusAI/bfio
Classifier: Development Status :: 5 - Production/Stable
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: imagecodecs>=2021.2.26
Requires-Dist: numpy
Requires-Dist: ome-types>=0.4.2
Requires-Dist: zarr>=2.6.1
Requires-Dist: scyjava
Requires-Dist: jpype1
Requires-Dist: tifffile>=2022.8.12
Provides-Extra: dev
Requires-Dist: ome_zarr; extra == "dev"
Requires-Dist: requests>=2.26.0; extra == "dev"

# **B**io**F**ormats **I**nput/**O**utput utility (bfio 2.3.6)

[![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/bfio/)
![PyPI - Downloads](https://img.shields.io/pypi/dm/bfio)
[![Conda](https://img.shields.io/conda/v/conda-forge/bfio)](https://anaconda.org/conda-forge/bfio)
[![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/bfio?label=Conda%20downloads)](https://anaconda.org/conda-forge/bfio)
![Bower](https://img.shields.io/bower/l/MI)

This tool is a simplified but powerful interface to
[Bio-Formats](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. This means only files in tiled OME Tiff or OME Zarr format can be
read/written.

In order to use the `bioformats` 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:2.3.6

Ubuntu based container with bfio and all dependencies (including Java).

### polusai/bfio:2.3.6-imagej

Same as above, except comes with ImageJ and PyImageJ.

### polusai/bfio:2.3.6-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.

## Acknowledgments

- Parts of this code were written/modified from existing code found in
    `tifffile`.
