A plugin to exchange data with FIJI and to use FIJI image analysis from napari

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A plugin to exchange data with FIJI and to use FIJI image analysis from napari. Current features are:

  • get the active image from FIJI
  • send a screenshot to FIJI
  • get a set of points from the FIJI results table
  • filter the points in napari
  • send the filtered points back to FIJI

Known problems:

  • Crashes on linux when the file-dialog is opened. Workaround: Set the option Use JFileChooser to open/save from the Edit>Options>Input/Output menu.
  • 03.05.2022 - Currently you need to have the range of the quality values for point between 0 and 255, in the new version they can have any range, but we are waiting for the bug in napari 0.4.15 to be fixed to release this.

This napari plugin was generated with Cookiecutter using with @napari's cookiecutter-napari-plugin template.


You can install napari-J via pip:

pip install napari-J


Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.


Distributed under the terms of the MIT license, "napari-J" is free and open source software


If you encounter any problems, please file an issue along with a detailed description.


  • 0.3

Last updated:

  • 03 March 2023

First released:

  • 07 January 2022


Supported data:

  • Information not submitted

Plugin type:

GitHub activity:

  • Stars: 3
  • Forks: 2
  • Issues + PRs: 1

Python versions supported:

Operating system:


  • JPype1 (>=1.2.1)
  • matplotlib
  • imageio-ffmpeg

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