# napari-imagej
### A [napari] plugin for access to [ImageJ2]
[](https://github.com/imagej/napari-imagej/raw/main/LICENSE)
[](https://pypi.org/project/napari-imagej)
[](https://python.org)
[](https://github.com/imagej/napari-imagej/actions)
[](https://codecov.io/gh/imagej/napari-imagej)
[](https://napari-hub.org/plugins/napari-imagej)
**napari-imagej** aims to provide access to all [ImageJ2] functionality through the [napari] graphical user interface. It builds on the foundation of [PyImageJ], a project allowing ImageJ2 access from Python.
**With napari-imagej, you can access:**
1. The napari-imagej widget, providing *headless access* to:
* [ImageJ2 Commands] - 100+ image processing algorithms
* [ImageJ Ops] - 500+ *functional* image processing algorithms
* [SciJava Scripts] - migrated from Fiji or ImageJ2, or written yourself!
2. The ImageJ user interface, providing access to *the entire ImageJ ecosystem* within napari.
See the [project roadmap](https://github.com/orgs/imagej/projects/2) for future directions.
## Getting Started
Learn more about the project [here](https://napari-imagej.readthedocs.io/en/latest/), or jump straight to [installation](https://napari-imagej.readthedocs.io/en/latest/Install.html)!
## Usage
* [Image Processing with ImageJ Ops](https://napari-imagej.readthedocs.io/en/latest/examples/ops.html)
* [Puncta Segmentation with SciJava Scripts](https://napari-imagej.readthedocs.io/en/latest/examples/scripting.html)
## Troubleshooting
The [FAQ](https://napari-imagej.readthedocs.io/en/latest/Troubleshooting.html) outlines solutions to many common issues.
For more obscure issues, feel free to reach out on [forum.image.sc](https://forum.image.sc).
If you've found a bug, please [file an issue]!
## Contributing
We welcome any and all contributions made onto the napari-imagej repository.
Development discussion occurs on the [Image.sc Zulip chat](https://imagesc.zulipchat.com/#narrow/stream/328100-scyjava).
For technical details involved with contributing, please see [here](https://napari-imagej.readthedocs.io/en/latest/Development.html)
## License
Distributed under the terms of the [BSD-2] license,
"napari-imagej" is free and open source software.
## Citing
_napari-imagej: ImageJ ecosystem access from napari_, Nature Methods, 2023 Aug 18
DOI: [10.1038/s41592-023-01990-0](https://doi.org/10.1038/s41592-023-01990-0)
[Apache Software License 2.0]: https://www.apache.org/licenses/LICENSE-2.0
[black]: https://github.com/psf/black
[BSD-2]: https://opensource.org/licenses/BSD-2-Clause
[Cookiecutter]: https://github.com/audreyr/cookiecutter
[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
[conda]: https://docs.conda.io/
[conda-forge]: https://conda-forge.org/
[file an issue]: https://github.com/imagej/napari-imagej/issues
[flake8]: https://flake8.pycqa.org/
[GNU GPL v3.0]: https://www.gnu.org/licenses/gpl-3.0.txt
[GNU LGPL v3.0]: https://www.gnu.org/licenses/lgpl-3.0.txt
[ImageJ2]: https://imagej.net/software/imagej2
[ImageJ2 Commands]: https://github.com/imagej/imagej-plugins-commands
[ImageJ Ops]: https://imagej.net/libs/imagej-ops
[install mamba]: https://mamba.readthedocs.io/en/latest/installation.html
[isort]: https://pycqa.github.io/isort/
[mamba]: https://mamba.readthedocs.io/
[MIT]: https://opensource.org/licenses/MIT
[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
[napari]: https://github.com/napari/napari
[napari hub]: https://www.napari-hub.org/
[npe2]: https://github.com/napari/npe2
[pip]: https://pypi.org/project/pip/
[pull request]: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests
[PyImageJ]: https://github.com/imagej/pyimagej
[PyPI]: https://pypi.org/
[SciJava Scripts]: https://imagej.net/scripting
[tox]: https://tox.readthedocs.io/
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"description": "# napari-imagej\r\n\r\n### A [napari] plugin for access to [ImageJ2]\r\n\r\n[](https://github.com/imagej/napari-imagej/raw/main/LICENSE)\r\n[](https://pypi.org/project/napari-imagej)\r\n[](https://python.org)\r\n[](https://github.com/imagej/napari-imagej/actions)\r\n[](https://codecov.io/gh/imagej/napari-imagej)\r\n[](https://napari-hub.org/plugins/napari-imagej)\r\n\r\n**napari-imagej** aims to provide access to all [ImageJ2] functionality through the [napari] graphical user interface. It builds on the foundation of [PyImageJ], a project allowing ImageJ2 access from Python.\r\n\r\n**With napari-imagej, you can access:**\r\n\r\n1. The napari-imagej widget, providing *headless access* to:\r\n * [ImageJ2 Commands] - 100+ image processing algorithms\r\n * [ImageJ Ops] - 500+ *functional* image processing algorithms\r\n * [SciJava Scripts] - migrated from Fiji or ImageJ2, or written yourself!\r\n2. The ImageJ user interface, providing access to *the entire ImageJ ecosystem* within napari.\r\n\r\nSee the [project roadmap](https://github.com/orgs/imagej/projects/2) for future directions.\r\n\r\n## Getting Started\r\n\r\nLearn more about the project [here](https://napari-imagej.readthedocs.io/en/latest/), or jump straight to [installation](https://napari-imagej.readthedocs.io/en/latest/Install.html)!\r\n\r\n## Usage\r\n\r\n* [Image Processing with ImageJ Ops](https://napari-imagej.readthedocs.io/en/latest/examples/ops.html)\r\n* [Puncta Segmentation with SciJava Scripts](https://napari-imagej.readthedocs.io/en/latest/examples/scripting.html)\r\n\r\n## Troubleshooting\r\n\r\nThe [FAQ](https://napari-imagej.readthedocs.io/en/latest/Troubleshooting.html) outlines solutions to many common issues.\r\n\r\nFor more obscure issues, feel free to reach out on [forum.image.sc](https://forum.image.sc).\r\n\r\nIf you've found a bug, please [file an issue]!\r\n\r\n## Contributing\r\n\r\nWe welcome any and all contributions made onto the napari-imagej repository.\r\n\r\nDevelopment discussion occurs on the [Image.sc Zulip chat](https://imagesc.zulipchat.com/#narrow/stream/328100-scyjava).\r\n\r\nFor technical details involved with contributing, please see [here](https://napari-imagej.readthedocs.io/en/latest/Development.html)\r\n\r\n## License\r\n\r\nDistributed under the terms of the [BSD-2] license,\r\n\"napari-imagej\" is free and open source software.\r\n\r\n## Citing\r\n\r\n_napari-imagej: ImageJ ecosystem access from napari_, Nature Methods, 2023 Aug 18\r\n\r\nDOI: [10.1038/s41592-023-01990-0](https://doi.org/10.1038/s41592-023-01990-0)\r\n\r\n[Apache Software License 2.0]: https://www.apache.org/licenses/LICENSE-2.0\r\n[black]: https://github.com/psf/black\r\n[BSD-2]: https://opensource.org/licenses/BSD-2-Clause\r\n[Cookiecutter]: https://github.com/audreyr/cookiecutter\r\n[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\r\n[conda]: https://docs.conda.io/\r\n[conda-forge]: https://conda-forge.org/\r\n[file an issue]: https://github.com/imagej/napari-imagej/issues\r\n[flake8]: https://flake8.pycqa.org/\r\n[GNU GPL v3.0]: https://www.gnu.org/licenses/gpl-3.0.txt\r\n[GNU LGPL v3.0]: https://www.gnu.org/licenses/lgpl-3.0.txt\r\n[ImageJ2]: https://imagej.net/software/imagej2\r\n[ImageJ2 Commands]: https://github.com/imagej/imagej-plugins-commands\r\n[ImageJ Ops]: https://imagej.net/libs/imagej-ops\r\n[install mamba]: https://mamba.readthedocs.io/en/latest/installation.html\r\n[isort]: https://pycqa.github.io/isort/\r\n[mamba]: https://mamba.readthedocs.io/\r\n[MIT]: https://opensource.org/licenses/MIT\r\n[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt\r\n[napari]: https://github.com/napari/napari\r\n[napari hub]: https://www.napari-hub.org/\r\n[npe2]: https://github.com/napari/npe2\r\n[pip]: https://pypi.org/project/pip/\r\n[pull request]: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests\r\n[PyImageJ]: https://github.com/imagej/pyimagej\r\n[PyPI]: https://pypi.org/\r\n[SciJava Scripts]: https://imagej.net/scripting\r\n[tox]: https://tox.readthedocs.io/\r\n",
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