https://github.com/scverse/napari-spatialdata
Interactive visualization of spatial omics data
https://github.com/scverse/napari-spatialdata
napari napari-plugin spatial-analysis spatial-omics visualization
Last synced: 3 months ago
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Interactive visualization of spatial omics data
- Host: GitHub
- URL: https://github.com/scverse/napari-spatialdata
- Owner: scverse
- License: bsd-3-clause
- Created: 2022-04-02T10:27:54.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2025-07-04T09:22:01.000Z (3 months ago)
- Last Synced: 2025-07-04T10:29:45.993Z (3 months ago)
- Topics: napari, napari-plugin, spatial-analysis, spatial-omics, visualization
- Language: Python
- Homepage: https://spatialdata.scverse.org/projects/napari/en/latest/
- Size: 45.8 MB
- Stars: 61
- Watchers: 13
- Forks: 18
- Open Issues: 65
-
Metadata Files:
- Readme: README.md
- Contributing: docs/contributing.md
- License: LICENSE
Awesome Lists containing this project
README
# napari-spatialdata: interactive exploration and annotation of spatial omics data
[](https://github.com/scverse/napari-spatialdata/raw/main/LICENSE)
[](https://pypi.org/project/napari-spatialdata)
[](https://python.org)
[](https://github.com/scverse/napari-spatialdata/actions)
[](https://codecov.io/gh/scverse/napari-spatialdata)
[](https://results.pre-commit.ci/latest/github/scverse/napari-spatialdata/main)
[](https://napari-hub.org/plugins/napari-spatialdata)
[](https://zenodo.org/badge/latestdoi/477021400)
[![Documentation][badge-pypi]][link-pypi]
[](https://anaconda.org/conda-forge/napari-spatialdata)
[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.
