{"name":"napari-spacetx-explorer","display_name":"napari-spacetx-explorer","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-spacetx-explorer.napari_experimental_provide_function","title":"read_spots","python_name":"napari_spacetx_explorer._function:napari_experimental_provide_function","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"napari-spacetx-explorer.napari_get_reader","filename_patterns":["*"],"accepts_directories":true}],"writers":null,"widgets":[{"command":"napari-spacetx-explorer.napari_experimental_provide_function","display_name":"read_spots","autogenerate":true}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"napari-spacetx-explorer","version":"0.1.8","dynamic":null,"platform":["UNKNOWN"],"supported_platform":null,"summary":"visualizer for spatial omic data","description":"# napari-spacetx-explorer\n\n[![License](https://img.shields.io/pypi/l/napari-spacetx-explorer.svg?color=green)](https://github.com/sebgoti/napari-spacetx-explorer/raw/master/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-spacetx-explorer.svg?color=green)](https://pypi.org/project/napari-spacetx-explorer)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-spacetx-explorer.svg?color=green)](https://python.org)\n[![tests](https://github.com/sebgoti/napari-spacetx-explorer/workflows/tests/badge.svg)](https://github.com/sebgoti/napari-spacetx-explorer/actions)\n[![codecov](https://codecov.io/gh/sebgoti/napari-spacetx-explorer/branch/master/graph/badge.svg)](https://codecov.io/gh/sebgoti/napari-spacetx-explorer)\n\nA napari plugin for interactive visualization of decoded spots from spatial transcriptomic data stored as CSV\n\n----------------------------------\n\nThis [napari] plugin was generated with [Cookiecutter] using with [@napari]'s [cookiecutter-napari-plugin] template.\n\nThe plugin code was written by Sebastian Gonzalez-Tirado.\n\n<!--\nDon't miss the full getting started guide to set up your new package:\nhttps://github.com/napari/cookiecutter-napari-plugin#getting-started\n\nand review the napari docs for plugin developers:\nhttps://napari.org/docs/plugins/index.html\n-->\n## Reader hookspec\n\n`napari-spacetx-explorer` allows the user to open and visualize CSV files that\nhave point-data stored in a given format. The main target is for users who\nwant to analyze decoded spot maps from spatial omics experiments but it can\nused as well for any other type of coordinate data where each point has assigned\na label (e. g. a gene) as a string and the x and y-coordinates of the point's center.\nThe header for these data must be 'target', 'xc', and 'yc', respectively.\n\n![img.png](https://github.com/sebgoti/napari-spacetx-explorer/raw/main/docs/Read_Hookspec.png)\n\n## Selecting genes\n\nAfter loading the gene/target maps it is possible to select specific groups for better visualization.\nThis creates a new \"Points\" layer in napari with the selected groups displayed in different colors.\n\n![img.png](https://github.com/sebgoti/napari-spacetx-explorer/raw/main/docs/_function_hookspec.png)\n\n## Loading data in OME.ZARR format\n\nThe plugin napari-ome-zarr can be used to display whole-tissue images in addition to the spot maps produced with the \n`napari-spacetx-explorer` plugin.\n\n![img.png](https://github.com/sebgoti/napari-spacetx-explorer/raw/main/docs/_ome_zarr_napari_spacetx_explorer.png)\n\n## Installation\n\nThe easiest installation is via the \"Install/Uninstall Plugins...\" under the Plugins menu in napari.  \nAnother way is through [pip] \n\n    pip install napari-spacetx-explorer\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-spacetx-explorer\" is free and open source software\n\n## Issues\n\nIf you encounter any problems or would like some support, 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[file an issue]: https://github.com/sebgoti/napari-spacetx-explorer/issues\n[napari]: https://github.com/napari/napari\n[tox]: https://tox.readthedocs.io/en/latest/\n[pip]: https://pypi.org/project/pip/\n[PyPI]: https://pypi.org/\n\n\n","description_content_type":"text/markdown","keywords":null,"home_page":"https://github.com/sebgoti/napari-spacetx-explorer","download_url":null,"author":"Sebastian Gonzalez-Tirado","author_email":"sebastian.gonzalez@embl.de","maintainer":null,"maintainer_email":null,"license":"BSD-3","classifier":["Development Status :: 3 - Alpha","Intended Audience :: Science/Research","Framework :: napari","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3.7","Programming Language :: Python :: 3.8","Programming Language :: Python :: 3.9","Operating System :: OS Independent","License :: OSI Approved :: BSD License"],"requires_dist":["napari","napari-plugin-engine (>=0.1.4)","numpy","pandas"],"requires_python":">=3.7","requires_external":null,"project_url":["Bug Tracker, https://github.com/sebgoti/napari-spacetx-explorer/issues","Documentation, https://github.com/sebgoti/napari-spacetx-explorer#README.md","Source Code, https://github.com/sebgoti/napari-spacetx-explorer","User Support, https://github.com/sebgoti/napari-spacetx-explorer/issues"],"provides_extra":null,"provides_dist":null,"obsoletes_dist":null},"npe1_shim":true}