napari-imagej: ImageJ Ecosystem Access within napari
The napari application has brought n-dimensional image browsing and analysis to the Python ecosystem. At the same time, the ImageJ software ecosystem, including ImageJ, ImageJ2, Fiji and thousands of community plugins, have been curated over decades, and are utilized by a highly active community of their own.
The napari-imagej plugin strives to unite these communities by providing access to an ImageJ2 instance within a napari widget. From this widget, users can launch the ImageJ user interface to run any ImageJ ecosystem functionality, and can additionally access ImageJ2 framework functionality directly.
napari-imagej handles the burden of data transfer between these two applications, enabling accessible, convenient, synergistic workflows.
- Basic Usage
- Use Cases
- Tracking HeLa cell nuclei with TrackMate
- Viewing TrackMate Data in the napari Viewer
- Using BoneJ2
- Puncta Segmentation with SciJava Scripts (headless)
- Image Processing with ImageJ Ops (headless)
- Developer’s Guide
- napari-imagej Architecture