napari-imagej offers two different mechanisms for accessing napari-imagej functionality - both are described below:
The napari-imagej widget
The napari-imagej widget provides headless access to all ImageJ2 functionality, and all third-party plugins written in the ImageJ2 framework. These plugins can be found and run with the napari-imagej searchbar, as shown in the figure below:
By clicking on an item in the search results, a set of actions is displayed at the bottom of the widget. To execute the selected functionality, users can click the
Run button to launch a modal dialog, or they can click the
Widget buton to launch a new napari widget (as shown below). Either button will allow the user to provide inputs to the ImageJ2 routine, and once the user confirms the selections the outputs of the routine will appear within the napari application.
Using the ImageJ2 UI
Many ImageJ ecosystem routines cannot be used headlessly - for this reason, napari-imagej also exposes the ImageJ UI to allow their execution within napari.
To launch the ImageJ UI, press the button in the napari-imagej menu. Once the ImageJ UI is visible, ImageJ can be used as normal (to learn more, see the ImageJ2 documentation).
To run ImageJ functionality through the ImageJ UI, users must export their data to the ImageJ UI. This can be accomplished on basic images using the button, which transfers the active napari
Layer to the ImageJ UI. Additionally, users can press the button to provide additional details towards the transfer, including:
Layerto be linked as ROIs
Dimension labels for each axis of the image
Note that these buttons are only enabled when there is a
Layer that can be transferred.