Recommended installation method

We recommend to use our JIPipe launcher application that will apply all steps automatically by just double-clicking a file. Please refer to the system-specific instructions for more information.

  • The initial setup will require an internet connection. About 1GB of data will be downloaded.

We also provide offline packages that will require no additional downloads:

Alternative installation methods

You can install JIPipe into an existing Fiji installation via the ImageJ Updater or by manually copying the plugin files.

Additional downloads

The following links and downloads are related to JIPipe:

Source code

The software is Open Source and licensed under BSD-2-Clause. You can find the source code on GitHub at https://github.com/applied-systems-biology/jipipe.


If you need the JIPipe logo for presentations, posters, or publications, feel free to download the logo package. It contains the JIPipe logos (text plus logo, square logo) in PNG and SVG formats.