{"name":"napari-filaments","display_name":"napari filaments","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-filaments.make_qwidget","title":"Open Filament Analyzer","python_name":"napari_filaments._widget:FilamentAnalyzer","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-filaments.make_qwidget","display_name":"Open Filament Analyzer","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"napari-filaments","version":"0.3.0","dynamic":null,"platform":null,"supported_platform":null,"summary":"A napari plugin for filament analysis","description":"# napari-filaments\n\n[![License BSD-3](https://img.shields.io/pypi/l/napari-filaments.svg?color=green)](https://github.com/hanjinliu/napari-filaments/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-filaments.svg?color=green)](https://pypi.org/project/napari-filaments)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-filaments.svg?color=green)](https://python.org)\n[![tests](https://github.com/hanjinliu/napari-filaments/workflows/tests/badge.svg)](https://github.com/hanjinliu/napari-filaments/actions)\n[![codecov](https://codecov.io/gh/hanjinliu/napari-filaments/branch/main/graph/badge.svg)](https://codecov.io/gh/hanjinliu/napari-filaments)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-filaments)](https://napari-hub.org/plugins/napari-filaments)\n\nA napari plugin for filament analysis.\n\nThis plugin helps you to manually track filaments using path shapes of `Shapes` layer.\n\n![](https://github.com/hanjinliu/napari-filaments/raw/main/resources/fit.gif)\n\nCurrently implemented functions\n\n- Fit paths to filaments in an image as a 2-D spline curve.\n- Clip/extend paths.\n- Measurement of filament length at sub-pixel precision.\n- Basic quantification (mean, std, etc.) along paths.\n- Import paths from ImageJ ROI file.\n\nBasic Usage\n-----------\n\nClick `Layers > open image` to open a tif file. You'll find the image you chose and a shapes layer are added to the layer list.\n\n![](https://github.com/hanjinliu/napari-filaments/raw/main/resources/fig-1.png)\n\n- The \"target filaments\" box shows the working shapes layer.\n- The \"target image\" box shows the image layer on which fitting and quantification will be conducted.\n- The \"filament\" box shows currently selected shape (initially this box is empty).\n\nAdd path shapes and push key `F1` to fit the shape to the filament in the target image layer.\n\n- In the \"Spline\" tab, you can cut/extend or re-fit splines.\n- In the \"Measure\" tab, click \"measure property\" to measure mean instensity etc along each spline.\n\nHow it works\n------------\n\nSpline fitting is done as following.\n\n![](https://github.com/hanjinliu/napari-filaments/raw/main/resources/fig-2.png)\n\n\n----------------------------------\n\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.\n\n\n## Installation\n\nYou can install `napari-filaments` via [pip]:\n\n    pip install napari-filaments\n\n\n\nTo install latest development version :\n\n    pip install git+https://github.com/hanjinliu/napari-filaments.git\n\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-filaments\" 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/hanjinliu/napari-filaments/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/hanjinliu/napari-filaments","download_url":null,"author":"Hanjin Liu","author_email":"liuhanjin-sc@g.ecc.u-tokyo.ac.jp","maintainer":null,"maintainer_email":null,"license":"BSD-3-Clause","classifier":["Development Status :: 2 - Pre-Alpha","Framework :: napari","Intended Audience :: Developers","License :: OSI Approved :: BSD License","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3 :: Only","Topic :: Software Development :: Testing"],"requires_dist":["magic-class (>=0.7.3)","magicgui","matplotlib","numpy","qtpy","scipy","napari ; extra == 'testing'","pyqt5 ; extra == 'testing'","pytest ; extra == 'testing'","pytest-cov ; extra == 'testing'","pytest-qt ; extra == 'testing'","roifile ; extra == 'testing'","tox ; extra == 'testing'"],"requires_python":">=3.9","requires_external":null,"project_url":["Bug Tracker, https://github.com/hanjinliu/napari-filaments/issues","Documentation, https://github.com/hanjinliu/napari-filaments#README.md","Source Code, https://github.com/hanjinliu/napari-filaments","User Support, https://github.com/hanjinliu/napari-filaments/issues"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}