{"id":29303538,"url":"https://github.com/scverse/napari-spatialdata","last_synced_at":"2025-07-07T01:08:58.260Z","repository":{"id":37212604,"uuid":"477021400","full_name":"scverse/napari-spatialdata","owner":"scverse","description":"Interactive visualization of spatial omics 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banner](https://github.com/scverse/spatialdata/blob/main/docs/_static/img/spatialdata_horizontal.png?raw=true)\n\n# napari-spatialdata: interactive exploration and annotation of spatial omics data\n\n[![License](https://img.shields.io/pypi/l/napari-spatialdata.svg?color=green)](https://github.com/scverse/napari-spatialdata/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-spatialdata.svg?color=green)](https://pypi.org/project/napari-spatialdata)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-spatialdata.svg?color=green)](https://python.org)\n[![tests](https://github.com/scverse/napari-spatialdata/workflows/tests/badge.svg)](https://github.com/scverse/napari-spatialdata/actions)\n[![codecov](https://codecov.io/gh/scverse/napari-spatialdata/branch/main/graph/badge.svg?token=ASqlOKnOj7)](https://codecov.io/gh/scverse/napari-spatialdata)\n[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/scverse/napari-spatialdata/main.svg)](https://results.pre-commit.ci/latest/github/scverse/napari-spatialdata/main)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-spatialdata)](https://napari-hub.org/plugins/napari-spatialdata)\n[![DOI](https://zenodo.org/badge/477021400.svg)](https://zenodo.org/badge/latestdoi/477021400)\n[![Documentation][badge-pypi]][link-pypi]\n[![Anaconda-Server Badge](https://anaconda.org/conda-forge/napari-spatialdata/badges/version.svg)](https://anaconda.org/conda-forge/napari-spatialdata)\n\n[badge-pypi]: https://badge.fury.io/py/napari-spatialdata.svg\n[link-pypi]: https://pypi.org/project/napari-spatialdata/\n\nThis repository contains a napari plugin for interactively exploring and annotating\nSpatialData 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/).\n\n## Installation\n\nYou can install `napari-spatialdata` via [pip]:\n\n    pip install napari-spatialdata[all]\n\nThe `all` command will install the qt bindings `PyQt5`.\n\nNapari now also includes multiple triangulation backends. These improve the speed by which a napari 'Shapes' layer gets\nloaded (this does not improve the speed of editing large numbers of shapes yet!). See also the napari\n[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\npip:\n\n    pip install napari-spatialdata[all, bermuda]\n\nYou can find more details on this in the [installation instructions](https://spatialdata.scverse.org/en/stable/installation.html).\n\n## Using napari-spatialdata as default zarr reader\n\nIf you would like to use the plugin as the default zarr reader, in napari please go to `File` -\u003e `Preferences`\n-\u003e `Plugins` and follow the instructions under `File extension readers`.\n\n## Development Version\n\nYou can install `napari-spatialdata` from Github with:\n\n    pip install git+https://github.com/scverse/napari-spatialdata\n\nOr, you can also install in editable mode after cloning the repo by:\n\n    git clone https://github.com/scverse/napari-spatialdata\n    cd napari-spatialdata\n    pip install -e .\n\nNote: when performing an editable install of `napari-spatialdata`, `spatialdata`\nwill be reinstalled from `pip`. So, if you previously also made an editable install\nof `spatialdata`, you need to re-run `pip install -e .` on the `spatialdata`\nrepository. Please find more details on this in the [installation instructions](https://spatialdata.scverse.org/en/stable/installation.html).\n\n## Getting started\n\nTo learn how to use the `napari-spatialdata` plugin, please see the [documentation](https://spatialdata.scverse.org/projects/napari/en/stable/notebooks/spatialdata.html).\nTo learn how to integrate napari-spatialdata into your analysis workflows, please\nsee the [SpatialData tutorials](https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks.html). In particular:\n\n- [Annotating regions of interest with napari](https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks/examples/napari_rois.html)\n- [Use landmark annotations to align multiple -omics layers](https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks/examples/alignment_using_landmarks.html)\n\n## Contributing\n\nContributions are very welcome. Tests can be run with [tox], please ensure\nthe coverage at least stays the same before you submit a pull request.\n\n## License\n\nDistributed under the terms of the [BSD-3] license,\n\"napari-spatialdata\" is free and open source software\n\n## Issues\n\nIf you encounter any problems, please file an [issue] along with a detailed description.\n\n## Citation\n\nMarconato, 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\n\n[napari]: https://github.com/napari/napari\n[cookiecutter]: https://github.com/audreyr/cookiecutter\n[@napari]: https://github.com/napari\n[mit]: http://opensource.org/licenses/MIT\n[bsd-3]: http://opensource.org/licenses/BSD-3-Clause\n[gnu gpl v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt\n[gnu lgpl v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt\n[apache software license 2.0]: http://www.apache.org/licenses/LICENSE-2.0\n[mozilla public license 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt\n[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\n[tox]: https://tox.readthedocs.io/en/latest/\n[pip]: https://pypi.org/project/pip/\n[pypi]: https://pypi.org/\n[issue]: https://github.com/scverse/napari-spatialdata/issues\n[//]: # \"numfocus-fiscal-sponsor-attribution\"\n\nnapari-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/).\nIf 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.\n\n\u003cdiv align=\"center\"\u003e\n\u003ca href=\"https://numfocus.org/project/scverse\"\u003e\n  \u003cimg\n    src=\"https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png\"\n    width=\"200\"\n  \u003e\n\u003c/a\u003e\n\u003c/div\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscverse%2Fnapari-spatialdata","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fscverse%2Fnapari-spatialdata","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscverse%2Fnapari-spatialdata/lists"}