Metadata-Version: 2.1
Name: bioio
Version: 1.0.0
Summary: Image reading, metadata management, and image writing for Microscopy images in Python
Author-email: Eva Maxfield Brown <evamaxfieldbrown@gmail.com>, Dan Toloudis <danielt@alleninstitute.org>
License: BSD License
Project-URL: Homepage, https://github.com/bioio-devs/bioio
Project-URL: Bug Tracker, https://github.com/bioio-devs/bioio/issues
Project-URL: Documentation, https://bioio-devs.github.io/bioio
Project-URL: User Support, https://github.com/bioio-devs/bioio/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 >=0.9.1
Requires-Dist: dask[array] >=2021.4.1
Requires-Dist: fsspec >=2022.8.0
Requires-Dist: imageio[ffmpeg] <2.28.0,>=2.11.0
Requires-Dist: numpy <2.0.0,>=1.21.0
Requires-Dist: ome-types[lxml] >=0.4.0
Requires-Dist: ome-zarr >=0.6.1
Requires-Dist: semver >=3.0.1
Requires-Dist: tifffile >=2021.8.30
Requires-Dist: zarr <3.0.0,>=2.6.0
Provides-Extra: dev
Requires-Dist: ipython >=8.4.0 ; extra == 'dev'
Provides-Extra: docs
Requires-Dist: gitchangelog >=3.0.4 ; extra == 'docs'
Requires-Dist: m2r2 >=0.2.7 ; extra == 'docs'
Requires-Dist: Sphinx >=4.0.0 ; extra == 'docs'
Requires-Dist: furo >=2022.4.7 ; extra == 'docs'
Requires-Dist: numpydoc ; extra == 'docs'
Requires-Dist: sphinx-copybutton ; extra == 'docs'
Requires-Dist: docutils <0.19,>=0.18 ; extra == 'docs'
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'

# BioIO

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[![Documentation](https://github.com/bioio-devs/bioio/actions/workflows/docs.yml/badge.svg)](https://bioio-devs.github.io/bioio)
[![PyPI version](https://badge.fury.io/py/bioio.svg)](https://badge.fury.io/py/bioio)
[![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
[![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/)

Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python

---

## Documentation

[See the full documentation on our GitHub pages site](https://bioio-devs.github.io/bioio/OVERVIEW.html)

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

Install bioio alongside OME TIFF and OME ZARR plug-ins with pip (this example won't use the OME ZARR plug-in):

`pip install bioio bioio-ome-tiff bioio-ome-zarr`

```python
from bioio import BioImage

# Get a BioImage object
img = BioImage("my_file.tiff")  # selects the first scene found
img.data  # returns 5D TCZYX numpy array
img.xarray_data  # returns 5D TCZYX xarray data array backed by numpy
img.dims  # returns a Dimensions object
img.dims.order  # returns string "TCZYX"
img.dims.X  # returns size of X dimension
img.shape  # returns tuple of dimension sizes in TCZYX order
img.get_image_data("CZYX", T=0)  # returns 4D CZYX numpy array

# Get the id of the current operating scene
img.current_scene

# Get a list valid scene ids
img.scenes

# Change scene using name
img.set_scene("Image:1")
# Or by scene index
img.set_scene(1)

# Use the same operations on a different scene
# ...
```

## 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)
