{"name":"napari-spatialdata","display_name":"napari spatialdata","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","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.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}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"napari-spatialdata","version":"0.2.8","dynamic":null,"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\nThis 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/).\n\n## Installation\n\nYou can install `napari-spatialdata` via [pip]:\n\n    pip install napari-spatialdata[extra]\n\nThe `extra` command will install the qt bindings `PyQt5`.\n\nNote: 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\n\n```\nmamba install -c conda-forge napari pyqt\n```\n\nand then install `napari-spatialdata` via `pip`, but without the `extra` option:\n\n```\npip install napari-spatialdata\n```\n\nYou can find more details on this in the [installation instructions](https://spatialdata.scverse.org/en/latest/installation.html).\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` 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).\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/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:\n\n- [Annotating regions of interest with napari](https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/napari_rois.html)\n- [Use landmark annotations to align multiple -omics layers](https://spatialdata.scverse.org/en/latest/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[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","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 :: 3.9","Programming Language :: Python :: 3.10","Operating System :: OS Independent","License :: OSI Approved :: BSD License"],"requires_dist":["numpy","magicgui","qtpy","numba","anndata","scikit-image","napari","loguru","typing-extensions >=4.8.0","napari-matplotlib","scikit-learn","spatialdata >=0.0.15","PyQt5 ; extra == 'all'","sphinx >=4.5 ; extra == 'doc'","sphinx-book-theme >=1.0.0 ; extra == 'doc'","myst-parser ; extra == 'doc'","sphinxcontrib-bibtex >=1.0.0 ; 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 ; extra == 'doc'","pydantic <2 ; extra == 'readthedocs'","tox ; extra == 'test'","pytest ; extra == 'test'","pytest-cov ; extra == 'test'","pytest-qt ; extra == 'test'","pre-commit >=2.9.0 ; extra == 'test'","towncrier >=21.3.0 ; extra == 'test'"],"requires_python":">=3.9","requires_external":null,"project_url":["Bug Tracker, https://github.com/scverse/napari-spatialdata/issues","Documentation, https://github.com/scverse/napari-spatialdata#README.md","Source Code, https://github.com/scverse/napari-spatialdata","User Support, https://github.com/scverse/napari-spatialdata/issues"],"provides_extra":["all","doc","readthedocs","test"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}