napari-imagej

A napari plugin for access to ImageJ2

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 for future directions.

Getting Started

Learn more about the project here, or jump straight to installation!

Usage

• Image Processing with ImageJ Ops
• Puncta Segmentation with SciJava Scripts

Troubleshooting

The FAQ outlines solutions to many common issues.

For more obscure issues, feel free to reach out on 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.

For technical details involved with contributing, please see here

License

Distributed under the terms of the BSD-2 license, "napari-imagej" is free and open source software.

Citing

Selzer, G.J., Rueden, C.T., Hiner, M.C. *et al.* napari-imagej: ImageJ ecosystem access from napari. *Nat Methods* **20**, 1443–1444 (2023). https://doi.org/10.1038/s41592-023-01990-0