{"name":"napari-spatialdata","display_name":"napari spatialdata","visibility":"public","icon":"","categories":[],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-spatialdata.QtAdataScatterWidget","title":"Visualize spatial omics data in napari","python_name":"napari_spatialdata._view:QtAdataScatterWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-spatialdata.QtAdataViewWidget","title":"Visualize spatial omics data in napari","python_name":"napari_spatialdata._view:QtAdataViewWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-spatialdata.QtAdataAnnotationWidget","title":"Annotation in napari","python_name":"napari_spatialdata._view:QtAdataAnnotationWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-spatialdata.get_reader","title":"Get napari Reader for spatialdata","python_name":"napari_spatialdata:get_reader","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"napari-spatialdata.get_reader","filename_patterns":["*.zarr"],"accepts_directories":true}],"writers":null,"widgets":[{"command":"napari-spatialdata.QtAdataScatterWidget","display_name":"Scatter","autogenerate":false},{"command":"napari-spatialdata.QtAdataViewWidget","display_name":"View","autogenerate":false},{"command":"napari-spatialdata.QtAdataAnnotationWidget","display_name":"Annotation","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"napari-spatialdata","version":"0.7.0","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"Interactive visualization of spatial omics data with napari","description":"![SpatialData 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` -> `Preferences`\n-> `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<div align=\"center\">\n<a href=\"https://numfocus.org/project/scverse\">\n  <img\n    src=\"https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png\"\n    width=\"200\"\n  >\n</a>\n</div>\n","description_content_type":"text/markdown","keywords":null,"home_page":"https://github.com/scverse/napari-spatialdata.git","download_url":null,"author":"giovanni palla","author_email":"giov.pll@gmail.com","maintainer":null,"maintainer_email":null,"license":"BSD-3-Clause","classifier":["Development Status :: 2 - Pre-Alpha","Intended Audience :: Developers","Framework :: napari","Topic :: Software Development :: Testing","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3.11","Programming Language :: Python :: 3.12","Programming Language :: Python :: 3.13","Operating System :: OS Independent","License :: OSI Approved :: BSD License"],"requires_dist":["anndata>=0.12.0","click","cycler","dask>=2025.2.0","geopandas","loguru","matplotlib","napari>=0.6.2","napari-matplotlib>=3.0.2","numba","numpy","packaging","pandas","pillow","pyqtgraph","qtpy","scanpy","scipy","shapely","scikit-learn","spatialdata>=0.7.0dev1","superqt","typing_extensions>=4.8.0","vispy","xarray","xarray-datatree","bermuda; extra == \"bermuda\"","loguru; extra == \"test\"","pytest; extra == \"test\"","pytest-cov; extra == \"test\"","pytest-mock; extra == \"test\"","pytest-qt; extra == \"test\"","pre-commit>=2.9.0; extra == \"test\"","sphinx>=4.5; extra == \"doc\"","sphinx-book-theme>=1.0.0; extra == \"doc\"","myst-parser>=2.0.0; extra == \"doc\"","sphinxcontrib-bibtex>=2.5.0; extra == \"doc\"","sphinx-autodoc-typehints>=1.11.0; extra == \"doc\"","sphinx-autobuild; extra == \"doc\"","scanpydoc; extra == \"doc\"","ipykernel; extra == \"doc\"","ipython; extra == \"doc\"","sphinx-copybutton; extra == \"doc\"","sphinx-qt-documentation; extra == \"doc\"","myst-nb>=1.0.0; extra == \"doc\"","squidpy; extra == \"doc\"","pydantic>2; extra == \"readthedocs\"","spatialdata>=0.7.0dev0; extra == \"pre\"","napari[pyqt5]; extra == \"all\""],"requires_python":">=3.11","requires_external":null,"project_url":["Bug Tracker, https://github.com/scverse/napari-spatialdata/issues","Documentation, https://spatialdata.scverse.org/projects/napari/en/latest/notebooks/spatialdata.html","Source Code, https://github.com/scverse/napari-spatialdata","User Support, https://github.com/scverse/napari-spatialdata/issues"],"provides_extra":["bermuda","test","doc","readthedocs","pre","all"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}