{"name":"napari-locpix","display_name":"napari-locpix","visibility":"public","icon":"","categories":[],"schema_version":"0.2.1","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.open_widget","title":"Annotate","python_name":"napari_locpix._widget:open_datastruc_widget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-locpix.open_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":"2.4","name":"napari-locpix","version":"0.0.7","dynamic":["license-file"],"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\nInstall napari via [pip]:\n\n    pip install \"napari[all]\"\n\nYou can install `napari-locpix` via [pip]:\n\n    pip install napari-locpix\n\nTo install latest development version :\n\n    pip install git+https://github.com/oubino/napari-locpix.git\n\n\n## Usage\n\nFirst launch napari\n\n    napari\n\nThen can find the plugin in napari, in the plugins menu, titled 'Annotate (napari-locpix)'\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. Use the X/Y bins ratio to retain the original aspect ratio of the FOV (or close) in the visualisation, if desired. The aspect ratio in this rendering does not affect the underlying localisation position data.\n\nVis interpolation defines how to interpolate the image before viewing\n\n### Annotations\n\nAnnotations can be added using Napari's viewer.\n\nClick on the Napari button to create a new labels layer.\n\nRename the new labels layer to \"Labels\", otherwise the annotations will not be saved.\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 :: 3.10","Programming Language :: Python :: 3.11","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["numpy<3.0,>=1.23","qtpy<3,>=2.3","polars<2.0,>=1.0","pyarrow<25,>=12","tox; extra == \"testing\"","pytest<9; extra == \"testing\"","pytest-cov; extra == \"testing\"","pytest-qt<5; extra == \"testing\"","napari[pyqt]; extra == \"testing\""],"requires_python":">=3.10","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}