| Name | napari-skimage JSON |
| Version |
0.4.0
JSON |
| download |
| home_page | None |
| Summary | A plugin to apply scikit-image operations |
| upload_time | 2024-09-04 13:18:51 |
| maintainer | None |
| docs_url | None |
| author | Guillaume Witz |
| requires_python | >=3.9 |
| license | Copyright (c) 2024, Guillaume Witz, Data Science Lab, University of Bern All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
| keywords |
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| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# napari-skimage
[](https://github.com/guiwitz/napari-skimage/raw/main/LICENSE)
[](https://pypi.org/project/napari-skimage)
[](https://python.org)
[](https://github.com/guiwitz/napari-skimage/actions)
[](https://codecov.io/gh/guiwitz/napari-skimage)
[](https://napari-hub.org/plugins/napari-skimage)
[](https://renkulab.io/projects/guillaume.witz1/napari-skimage/sessions/new?autostart=1)
napari-skimage gives easy access to scikit-image functions in napari. The main goal of the plugin is to allow new users of napari, especially without coding experience, to easily explore basic image processing, in a similar way to what is possible in Fiji.
This [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.
## Philosophy
The plugin is still in early development and does not cover all functions of scikit-image. If you are interested in a specific function, please open an issue or a pull request. scikit-image functions are turned into interactive widgets mostly via magicgui, a tool that allows to create GUIs from functions in a simple way (in particular not requiring Qt knowledge). The code avoids on purpose complex approaches, e.g. to automate the creation of widgets, in order to keep the code simple and easy to understand for beginners.
## Installation
You can install `napari-skimage` via [pip]:
pip install napari-skimage
To install latest development version :
pip install git+https://github.com/guiwitz/napari-skimage.git
## Usage
The plugin function can be accessed under ```Plugins -> napari-skimage```. Each function will appear as a widget on the right of the napari window. Some functions such as ```Gaussian Filter``` give access to a single operation and its options. Some functions such as ```Thresholding``` give access to variants of the same operation via a dropdown menu. Currently the plugin does not support multi-channel processing and will consider those as stacks. At the moment, the plugin offers access to the following operation types.
### Filtering
A set of classical filters: Gaussian, Prewitt, Laplace etc. as well as rank filters such as median, minimum, maximum etc.
### Thresholding
A set of thresholding methods: Otsu, Li, Yen etc.
### Binary morphological operations
A set of binary morphology operations: binary erosion, binary dilation etc.
### Morphological operations
A set of morphological operations: erosion, dilation, opening, closing etc.
### Restoration
A set of restoration operations such as rolling ball, or non-local means denoising.
### Mathematics
In addition the plugin provides a set of simple mathematical operators to:
- operate on single images e.g. square, square root, log etc.
- operate on two images e.g. add, subtract, multiply etc.
## Code structure
Each set of functions is grouped in a separate module. For example all filtering operations are grouped in ```src/napari_skimge/skimage_filter_widget.py```. A set of test in ```src/_tests/test_basic_widgets.py``` simply check that each widget can be created and generated an output of the correct size using the default settings.
## 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-skimage" 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/guiwitz/napari-skimage/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-skimage\n\n[](https://github.com/guiwitz/napari-skimage/raw/main/LICENSE)\n[](https://pypi.org/project/napari-skimage)\n[](https://python.org)\n[](https://github.com/guiwitz/napari-skimage/actions)\n[](https://codecov.io/gh/guiwitz/napari-skimage)\n[](https://napari-hub.org/plugins/napari-skimage)\n[](https://renkulab.io/projects/guillaume.witz1/napari-skimage/sessions/new?autostart=1)\n\nnapari-skimage gives easy access to scikit-image functions in napari. The main goal of the plugin is to allow new users of napari, especially without coding experience, to easily explore basic image processing, in a similar way to what is possible in Fiji.\n\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.\n\n## Philosophy\n\nThe plugin is still in early development and does not cover all functions of scikit-image. If you are interested in a specific function, please open an issue or a pull request. scikit-image functions are turned into interactive widgets mostly via magicgui, a tool that allows to create GUIs from functions in a simple way (in particular not requiring Qt knowledge). The code avoids on purpose complex approaches, e.g. to automate the creation of widgets, in order to keep the code simple and easy to understand for beginners.\n\n## Installation\n\nYou can install `napari-skimage` via [pip]:\n\n pip install napari-skimage\n\n\n\nTo install latest development version :\n\n pip install git+https://github.com/guiwitz/napari-skimage.git\n\n## Usage\n\nThe plugin function can be accessed under ```Plugins -> napari-skimage```. Each function will appear as a widget on the right of the napari window. Some functions such as ```Gaussian Filter``` give access to a single operation and its options. Some functions such as ```Thresholding``` give access to variants of the same operation via a dropdown menu. Currently the plugin does not support multi-channel processing and will consider those as stacks. At the moment, the plugin offers access to the following operation types.\n\n### Filtering\n\nA set of classical filters: Gaussian, Prewitt, Laplace etc. as well as rank filters such as median, minimum, maximum etc.\n\n\n\n### Thresholding\nA set of thresholding methods: Otsu, Li, Yen etc.\n\n\n### Binary morphological operations\nA set of binary morphology operations: binary erosion, binary dilation etc.\n\n\n### Morphological operations\nA set of morphological operations: erosion, dilation, opening, closing etc.\n\n\n### Restoration\nA set of restoration operations such as rolling ball, or non-local means denoising.\n\n\n### Mathematics \nIn addition the plugin provides a set of simple mathematical operators to:\n- operate on single images e.g. square, square root, log etc.\n- operate on two images e.g. add, subtract, multiply etc.\n\n\n## Code structure\n\nEach set of functions is grouped in a separate module. For example all filtering operations are grouped in ```src/napari_skimge/skimage_filter_widget.py```. A set of test in ```src/_tests/test_basic_widgets.py``` simply check that each widget can be created and generated an output of the correct size using the default settings.\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-skimage\" 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/guiwitz/napari-skimage/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",
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