https://github.com/polusai/bfio

Interface to the Bioformats Java library
https://github.com/polusai/bfio

image-io image-processing napari-plugin

Last synced: 3 months ago
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Interface to the Bioformats Java library

• Host: GitHub
• URL: https://github.com/polusai/bfio
• Owner: PolusAI
• License: mit
• Created: 2021-04-12T19:42:43.000Z (about 5 years ago)
• Default Branch: master
• Last Pushed: 2025-01-16T20:49:31.000Z (over 1 year ago)
• Last Synced: 2025-06-14T23:05:49.601Z (about 1 year ago)
• Topics: image-io, image-processing, napari-plugin
• Language: Python
• Homepage:
• Size: 60.5 MB
• Stars: 13
• Watchers: 13
• Forks: 8
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# **B**io**F**ormats **I**nput/**O**utput utility (bfio 2.5.0)

[![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`, `zarr`, `zarr3`, and `tensorstore`

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:2.5.0

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

### polusai/bfio:2.5.0-imagej

Same as above, except comes with ImageJ and PyImageJ.

### polusai/bfio:2.5.0-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`.