Metadata-Version: 2.1
Name: napari-spatialdata
Version: 0.2.8
Summary: Interactive visualization of spatial omics data with napari
Home-page: https://github.com/scverse/napari-spatialdata.git
Author: giovanni palla
Author-email: giov.pll@gmail.com
License: BSD-3-Clause
Project-URL: Bug Tracker, https://github.com/scverse/napari-spatialdata/issues
Project-URL: Documentation, https://github.com/scverse/napari-spatialdata#README.md
Project-URL: Source Code, https://github.com/scverse/napari-spatialdata
Project-URL: User Support, https://github.com/scverse/napari-spatialdata/issues
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: Framework :: napari
Classifier: Topic :: Software Development :: Testing
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Operating System :: OS Independent
Classifier: License :: OSI Approved :: BSD License
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: magicgui
Requires-Dist: qtpy
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Requires-Dist: anndata
Requires-Dist: scikit-image
Requires-Dist: napari
Requires-Dist: loguru
Requires-Dist: typing-extensions >=4.8.0
Requires-Dist: napari-matplotlib
Requires-Dist: scikit-learn
Requires-Dist: spatialdata >=0.0.15
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![SpatialData banner](https://github.com/scverse/spatialdata/blob/main/docs/_static/img/spatialdata_horizontal.png?raw=true)

# napari-spatialdata: interactive exploration and annotation of spatial omics data

[![License](https://img.shields.io/pypi/l/napari-spatialdata.svg?color=green)](https://github.com/scverse/napari-spatialdata/raw/main/LICENSE)
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This repository contains a napari plugin for interactively exploring and annotating SpatialData objects. `napari-spatialdata` is part of the `SpatialData` ecosystem. To learn more about SpatialData, please see the [documentation](https://spatialdata.scverse.org/).

## Installation

You can install `napari-spatialdata` via [pip]:

    pip install napari-spatialdata[extra]

The `extra` command will install the qt bindings `PyQt5`.

Note: if you have an M1/M2 Mac then you may get an error when installing `PyQt5` via `pip`. A solution is to first install `napari` via conda (which will correctly install `PyQt5`), using

```
mamba install -c conda-forge napari pyqt
```

and then install `napari-spatialdata` via `pip`, but without the `extra` option:

```
pip install napari-spatialdata
```

You can find more details on this in the [installation instructions](https://spatialdata.scverse.org/en/latest/installation.html).

## Development Version

You can install `napari-spatialdata` from Github with:

    pip install git+https://github.com/scverse/napari-spatialdata

Or, you can also install in editable mode after cloning the repo by:

    git clone https://github.com/scverse/napari-spatialdata
    cd napari-spatialdata
    pip install -e .

Note: when performing an editable install of `napari-spatialdata`, `spatialdata` will be reinstalled from `pip`. So, if you previously also made an editable install of `spatialdata`, you need to re-run `pip install -e .` on the `spatialdata` repository. Please find more details on this in the [installation instructions](https://spatialdata.scverse.org/en/latest/installation.html).

## Getting started

To learn how to use the `napari-spatialdata` plugin, please see the [documentation](https://spatialdata.scverse.org/projects/napari/en/latest/notebooks/spatialdata.html). To learn how to integrate napari-spatialdata into your analysis workflows, please see the [SpatialData tutorials](https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks.html). In particular:

- [Annotating regions of interest with napari](https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/napari_rois.html)
- [Use landmark annotations to align multiple -omics layers](https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/alignment_using_landmarks.html)

## Contributing

Contributions are very welcome. Tests can be run with [tox], please ensure
the coverage at least stays the same before you submit a pull request.

## License

Distributed under the terms of the [BSD-3] license,
"napari-spatialdata" is free and open source software

## Issues

If you encounter any problems, please file an [issue] along with a detailed description.

[napari]: https://github.com/napari/napari
[cookiecutter]: https://github.com/audreyr/cookiecutter
[@napari]: https://github.com/napari
[mit]: http://opensource.org/licenses/MIT
[bsd-3]: http://opensource.org/licenses/BSD-3-Clause
[gnu gpl v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
[gnu lgpl v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
[apache software license 2.0]: http://www.apache.org/licenses/LICENSE-2.0
[mozilla public license 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[pypi]: https://pypi.org/
[issue]: https://github.com/scverse/napari-spatialdata/issues
