# napari-filaments
[](https://github.com/hanjinliu/napari-filaments/raw/main/LICENSE)
[](https://pypi.org/project/napari-filaments)
[](https://python.org)
[](https://github.com/hanjinliu/napari-filaments/actions)
[](https://codecov.io/gh/hanjinliu/napari-filaments)
[](https://napari-hub.org/plugins/napari-filaments)
A napari plugin for filament analysis.
This plugin helps you to manually track filaments using path shapes of `Shapes` layer.
Currently implemented functions
- Fit paths to filaments in an image as a 2-D spline curve.
- Clip/extend paths.
- Measurement of filament length at sub-pixel precision.
- Basic quantification (mean, std, etc.) along paths.
- Import paths from ImageJ ROI file.
Basic Usage
-----------
Click `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.
- The "target filaments" box shows the working shapes layer.
- The "target image" box shows the image layer on which fitting and quantification will be conducted.
- The "filament" box shows currently selected shape (initially this box is empty).
Add path shapes and push key `F1` to fit the shape to the filament in the target image layer.
- In the "Spline" tab, you can cut/extend or re-fit splines.
- In the "Measure" tab, click "measure property" to measure mean instensity etc along each spline.
How it works
------------
Spline fitting is done as following.
----------------------------------
This [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.
## Installation
You can install `napari-filaments` via [pip]:
pip install napari-filaments
To install latest development version :
pip install git+https://github.com/hanjinliu/napari-filaments.git
## Contributing
Contributions are very welcome. Tests can be run with [tox], please ensure
the coverage at least stays the same before you submit a pull request.
## License
Distributed under the terms of the [BSD-3] license,
"napari-filaments" is free and open source software
## Issues
If you encounter any problems, please [file an issue] along with a detailed description.
[napari]: https://github.com/napari/napari
[Cookiecutter]: https://github.com/audreyr/cookiecutter
[@napari]: https://github.com/napari
[MIT]: http://opensource.org/licenses/MIT
[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
[file an issue]: https://github.com/hanjinliu/napari-filaments/issues
[napari]: https://github.com/napari/napari
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/
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"description": "# napari-filaments\r\n\r\n[](https://github.com/hanjinliu/napari-filaments/raw/main/LICENSE)\r\n[](https://pypi.org/project/napari-filaments)\r\n[](https://python.org)\r\n[](https://github.com/hanjinliu/napari-filaments/actions)\r\n[](https://codecov.io/gh/hanjinliu/napari-filaments)\r\n[](https://napari-hub.org/plugins/napari-filaments)\r\n\r\nA napari plugin for filament analysis.\r\n\r\nThis plugin helps you to manually track filaments using path shapes of `Shapes` layer.\r\n\r\n\r\n\r\nCurrently implemented functions\r\n\r\n- Fit paths to filaments in an image as a 2-D spline curve.\r\n- Clip/extend paths.\r\n- Measurement of filament length at sub-pixel precision.\r\n- Basic quantification (mean, std, etc.) along paths.\r\n- Import paths from ImageJ ROI file.\r\n\r\nBasic Usage\r\n-----------\r\n\r\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.\r\n\r\n\r\n\r\n- The \"target filaments\" box shows the working shapes layer.\r\n- The \"target image\" box shows the image layer on which fitting and quantification will be conducted.\r\n- The \"filament\" box shows currently selected shape (initially this box is empty).\r\n\r\nAdd path shapes and push key `F1` to fit the shape to the filament in the target image layer.\r\n\r\n- In the \"Spline\" tab, you can cut/extend or re-fit splines.\r\n- In the \"Measure\" tab, click \"measure property\" to measure mean instensity etc along each spline.\r\n\r\nHow it works\r\n------------\r\n\r\nSpline fitting is done as following.\r\n\r\n\r\n\r\n\r\n----------------------------------\r\n\r\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.\r\n\r\n\r\n## Installation\r\n\r\nYou can install `napari-filaments` via [pip]:\r\n\r\n pip install napari-filaments\r\n\r\n\r\n\r\nTo install latest development version :\r\n\r\n pip install git+https://github.com/hanjinliu/napari-filaments.git\r\n\r\n\r\n## Contributing\r\n\r\nContributions are very welcome. Tests can be run with [tox], please ensure\r\nthe coverage at least stays the same before you submit a pull request.\r\n\r\n## License\r\n\r\nDistributed under the terms of the [BSD-3] license,\r\n\"napari-filaments\" is free and open source software\r\n\r\n## Issues\r\n\r\nIf you encounter any problems, please [file an issue] along with a detailed description.\r\n\r\n[napari]: https://github.com/napari/napari\r\n[Cookiecutter]: https://github.com/audreyr/cookiecutter\r\n[@napari]: https://github.com/napari\r\n[MIT]: http://opensource.org/licenses/MIT\r\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\r\n[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt\r\n[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt\r\n[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0\r\n[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt\r\n[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\r\n\r\n[file an issue]: https://github.com/hanjinliu/napari-filaments/issues\r\n\r\n[napari]: https://github.com/napari/napari\r\n[tox]: https://tox.readthedocs.io/en/latest/\r\n[pip]: https://pypi.org/project/pip/\r\n[PyPI]: https://pypi.org/\r\n",
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