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napari-spatialdata

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Interactive visualization of spatial omics data

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

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[badge-pypi]: https://badge.fury.io/py/napari-spatialdata.svg
[link-pypi]: https://pypi.org/project/napari-spatialdata/

This repository contains a napari plugin for interactively exploring and annotating
SpatialData objects. Here you can find the [napari-spatialdata documentation](https://spatialdata.scverse.org/projects/napari/en/stable/notebooks/spatialdata.html). `napari-spatialdata` is part of the `SpatialData` ecosystem. To learn more about SpatialData, please see the [spatialdata documentation](https://spatialdata.scverse.org/).

## Installation

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

pip install napari-spatialdata[all]

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

Napari now also includes multiple triangulation backends. These improve the speed by which a napari 'Shapes' layer gets
loaded (this does not improve the speed of editing large numbers of shapes yet!). See also the napari
[documentation](https://napari.org/stable/guides/triangulation.html) and already slightly older [blog post](https://napari.org/island-dispatch/blog/triangles_speedup_beta.html). For installation via
pip:

pip install napari-spatialdata[all, bermuda]

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

## Using napari-spatialdata as default zarr reader

If you would like to use the plugin as the default zarr reader, in napari please go to `File` -> `Preferences`
-> `Plugins` and follow the instructions under `File extension readers`.

## 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/stable/installation.html).

## Getting started

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

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

## Citation

Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and universal data framework for spatial omics. Nat Methods (2024). https://doi.org/10.1038/s41592-024-02212-x

[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
[//]: # "numfocus-fiscal-sponsor-attribution"

napari-spatialdata is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).
If you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.

napari-spatialdata

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