{"name":"napari-locpix","display_name":"napari-locpix","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-locpix.make_sample_data","title":"Load sample data from napari-locpix","python_name":"napari_locpix._sample_data:make_sample_data","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-locpix.widget","title":"Annotate","python_name":"napari_locpix._widget:DatastrucWidget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-locpix.widget","display_name":"Annotate","autogenerate":false}],"sample_data":[{"command":"napari-locpix.make_sample_data","key":"unique_id.1","display_name":"napari-locpix"}],"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"napari-locpix","version":"0.0.6","dynamic":null,"platform":null,"supported_platform":null,"summary":"Load in SMLM data and annotate within napari","description":"# napari-locpix\n\n[![License MIT](https://img.shields.io/pypi/l/napari-locpix.svg?color=green)](https://github.com/oubino/napari-locpix/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-locpix.svg?color=green)](https://pypi.org/project/napari-locpix)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-locpix.svg?color=green)](https://python.org)\n[![tests](https://github.com/oubino/napari-locpix/workflows/tests/badge.svg)](https://github.com/oubino/napari-locpix/actions)\n[![codecov](https://codecov.io/gh/oubino/napari-locpix/branch/main/graph/badge.svg)](https://codecov.io/gh/oubino/napari-locpix)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-locpix)](https://napari-hub.org/plugins/napari-locpix)\n\nLoad in SMLM data and annotate within napari\n\n----------------------------------\n\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.\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/stable/plugins/index.html\n-->\n\n## Installation\n\nYou can install `napari-locpix` via [pip]:\n\n    pip install napari-locpix\n\n\nTo install latest development version :\n\n    pip install git+https://github.com/oubino/napari-locpix.git\n\n\n## Usage\n\nThis plugin allows a user to\n\n1. Read in SMLM data\n2. Visualise SMLM data in a histogram\n3. Add segmentations to the data\n4. Extract the underlying localisations from the segmentations\n\n### IO\n\nThe input data can be in the form of a .csv or .parquet.\n\nWe expect there to be 4 columns at least, which should he identified inthe file column selection:\n\n* X coordinate\n* Y coordinate\n* Frame\n* Channel\n\nIf the data has been annotated with this software we can also load this in.\nNote however we currently only support loading in annotated data saved as a .parquet folder.\nTherefore, we recommend always keeping a .parquet copy until loading in an annotated .csv\nis supported.\n\nThe data can be outputted to a .parquet or a .csv\n\nDrop localisations with zero label, gives you the option to only save the localisations which have been annotated i.e. labels 1 and above.\n\nChannels labels allows you to give a real name label to each of the channels e.g. Chan 0 label: 'Alexa 647'\n\n### Visualisation\n\nUsing the render button you can render the loaded in data according to the histogram settings\n\nX/Y bins defines the number of bins for the histogram\n\nVis interpolation defines how to interpolate the image before viewing\n\n### Annotations\n\nAnnotations can be added using Napari's viewer.\n\nSimply click the add Labels.\n\nNote that this software will expect the labels to be called \"Labels\"\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 [MIT] license,\n\"napari-locpix\" 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\n[file an issue]: https://github.com/oubino/napari-locpix/issues\n\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","description_content_type":"text/markdown","keywords":null,"home_page":"https://github.com/oubino/napari-locpix","download_url":null,"author":"Oliver Umney","author_email":"scou@leeds.ac.uk","maintainer":null,"maintainer_email":null,"license":"MIT","classifier":["Development Status :: 2 - Pre-Alpha","Framework :: napari","Intended Audience :: Developers","License :: OSI Approved :: MIT License","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3 :: Only","Programming Language :: Python :: 3.8","Programming Language :: Python :: 3.9","Programming Language :: Python :: 3.10","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["numpy","qtpy","polars","pyarrow","tox ; extra == 'testing'","pytest ; extra == 'testing'","pytest-cov ; extra == 'testing'","pytest-qt ; extra == 'testing'","napari ; extra == 'testing'","pyqt5 ; extra == 'testing'"],"requires_python":">=3.8","requires_external":null,"project_url":["Bug Tracker, https://github.com/oubino/napari-locpix/issues","Documentation, https://github.com/oubino/napari-locpix#README.md","Source Code, https://github.com/oubino/napari-locpix","User Support, https://github.com/oubino/napari-locpix/issues"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}