Metadata-Version: 2.1
Name: bioio-ome-tiff
Version: 1.0.0
Summary: A BioIO reader plugin for reading tiff files in the OME format.
Author-email: bioio-devs <brian.whitney@alleninstitute.org>
License: MIT License
Project-URL: Homepage, https://github.com/bioio-devs/bioio-ome-tiff
Project-URL: Bug Tracker, https://github.com/bioio-devs/bioio-ome-tiff/issues
Project-URL: User Support, https://github.com/bioio-devs/bioio-ome-tiff/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: dask[array] >=2021.4.1
Requires-Dist: fsspec >=2022.8.0
Requires-Dist: imagecodecs >=2020.5.30
Requires-Dist: numpy >=1.21
Requires-Dist: ome-types[lxml] >=0.4.0
Requires-Dist: pydantic >=1.10.0
Requires-Dist: PyYAML >=6.0
Requires-Dist: tifffile >=2022.4.22
Requires-Dist: xarray >=0.16.1
Requires-Dist: xmlschema
Requires-Dist: zarr >=2.6
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-ome-tiff

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A BioIO reader plugin for reading OME TIFF files using `tifffile`

---


## 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-ome-tiff`<br>
**Development Head:** `pip install git+https://github.com/bioio-devs/bioio-ome-tiff.git`

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

Install bioio-ome-tiff alongside bioio:

`pip install bioio bioio-ome-tiff`


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_ome_tiff

img = BioImage("my_file.ome.tiff", reader=bioio_ome_tiff.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.
