Metadata-Version: 2.4
Name: bioio-ome-zarr
Version: 1.2.0
Summary: A BioIO reader plugin for reading Zarr files in the OME format.
Author-email: bioio-devs <brian.whitney@alleninstitute.org>
License: MIT License
Project-URL: Homepage, https://github.com/BrianWhitneyAI/bioio-ome-zarr
Project-URL: Bug Tracker, https://github.com/BrianWhitneyAI/bioio-ome-zarr/issues
Project-URL: User Support, https://github.com/BrianWhitneyAI/bioio-ome-zarr/issues
Classifier: Development Status :: 4 - Beta
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: bioio-base>=1.0.0
Requires-Dist: fsspec>=2022.8.0
Requires-Dist: ome-zarr>=0.9.0
Requires-Dist: xarray>=0.16.1
Requires-Dist: zarr>=2.18.2
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"
Dynamic: license-file

# bioio-ome-zarr

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A BioIO reader plugin for reading OME ZARR images using `ome-zarr`

---


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

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

Install bioio-ome-zarr alongside bioio:

`pip install bioio bioio-ome-zarr`


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_zarr

img = BioImage("my_file.zarr", reader=bioio_ome_zarr.Reader)
img.data
```

### Reading from AWS S3
To read from private S3 buckets, [credentials](https://docs.aws.amazon.com/cli/latest/userguide/cli-configure-files.html) must be configured. Public buckets can be accessed without credentials.
```python
from bioio import BioImage
path = "https://allencell.s3.amazonaws.com/aics/nuc-morph-dataset/hipsc_fov_nuclei_timelapse_dataset/hipsc_fov_nuclei_timelapse_data_used_for_analysis/baseline_colonies_fov_timelapse_dataset/20200323_09_small/raw.ome.zarr"
image = BioImage(path)
print(image.get_image_dask_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.
