Metadata-Version: 2.1
Name: bioio-bioformats
Version: 1.0.0
Summary: A BioIO reader for reading bioformats formatted images.
Author-email: bioio-devs <brian.whitney@alleninstitute.org>
License: MIT License
Project-URL: Homepage, https://github.com/bioio-devs/bioio-bioformats
Project-URL: Bug Tracker, https://github.com/bioio-devs/bioio-bioformats/issues
Project-URL: Documentation, https://bioio-devs.github.io/bioio-bioformats
Project-URL: User Support, https://github.com/bioio-devs/bioio-bioformats/issues
Classifier: Development Status :: 4 - Beta
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: bioio-base >=0.3.0
Requires-Dist: bioformats-jar
Requires-Dist: dask[array] <=2023.5.0,>=2021.4.1
Requires-Dist: fsspec >=2022.8.0
Requires-Dist: numpy >=1.21
Requires-Dist: ome-types >=0.3.4
Requires-Dist: resource-backed-dask-array >=0.1.0
Provides-Extra: lint
Requires-Dist: pre-commit >=2.20.0 ; extra == 'lint'
Provides-Extra: test
Requires-Dist: coverage >=5.1 ; extra == 'test'
Requires-Dist: pytest >=5.4.3 ; extra == 'test'
Requires-Dist: pytest-cov >=2.9.0 ; extra == 'test'
Requires-Dist: pytest-raises >=0.11 ; extra == 'test'
Requires-Dist: quilt3 ; extra == 'test'
Requires-Dist: types-PyYAML >=6.0.12.9 ; extra == 'test'

# bioio-bioformats

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[![Python 3.9+](https://img.shields.io/badge/python-3.9,3.10,3.11-blue.svg)](https://www.python.org/downloads/release/python-390/)

A BioIO reader plugin for reading [many file formats like as seen here](https://docs.openmicroscopy.org/bio-formats/5.8.2/supported-formats.html) using `bioformats`

---


## Documentation

[See the full documentation on our GitHub pages site](https://bioio-devs.github.io/bioio/OVERVIEW.html) - the generic use and installation instructions there will work for this package.

Information about the base reader this package relies on can be found in the `bioio-base` repository [here](https://github.com/bioio-devs/bioio-base)

## Installation

**Stable Release:** `pip install bioio-bioformats`<br>
**Development Head:** `pip install git+https://github.com/bioio-devs/bioio-bioformats.git`

## Special Installation Instructions

**This package utilizes bioformats which depends on java**

To install java and maven with conda, run:

`conda install -c conda-forge scyjava`

You may need to deactivate/reactivate your environment after installing. If you are *still* getting a `JVMNotFoundException`, try setting `JAVA_HOME` as follows:

#### Mac / Linux
`export JAVA_HOME=$CONDA_PREFIX`

#### Windows
`set JAVA_HOME=%CONDA_PREFIX%\\Library`

## Example Usage (see full documentation for more examples)

Install bioio-bioformats alongside bioio:

`pip install bioio bioio-bioformats`


This example shows a simple use case for just accessing the pixel data of the image
by explicitly passing this `Reader` into the `BioImage`. Passing the `Reader` into
the `BioImage` instance is optional as `bioio` will automatically detect installed
plug-ins and auto-select the most recently installed plug-in that supports the file
passed in.
```python
from bioio import BioImage
import bioio_bioformats

img = BioImage("my_file.tiff", reader=bioio_bioformats.Reader)
img.data
```

## Issues
[_Click here to view all open issues in bioio-devs organization at once_](https://github.com/search?q=user%3Abioio-devs+is%3Aissue+is%3Aopen&type=issues&ref=advsearch) or check this repository's issue tab.


## Development

See [CONTRIBUTING.md](CONTRIBUTING.md) for information related to developing the code.
