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https://github.com/imagej/napari-imagej

Use ImageJ functionality from napari
https://github.com/imagej/napari-imagej

fiji imagej java napari python

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Use ImageJ functionality from napari

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README 

        
# napari-imagej



### A [napari] plugin for access to [ImageJ2]



[![License](https://img.shields.io/pypi/l/napari-imagej.svg?color=green)](https://github.com/imagej/napari-imagej/raw/main/LICENSE)

[![PyPI](https://img.shields.io/pypi/v/napari-imagej.svg?color=green)](https://pypi.org/project/napari-imagej)

[![Python Version](https://img.shields.io/pypi/pyversions/napari-imagej.svg?color=green)](https://python.org)

[![tests](https://github.com/imagej/napari-imagej/workflows/tests/badge.svg)](https://github.com/imagej/napari-imagej/actions)

[![codecov](https://codecov.io/gh/imagej/napari-imagej/branch/main/graph/badge.svg)](https://codecov.io/gh/imagej/napari-imagej)

[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/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/