Installation

If you do not know where to start, we recommend to follow the guide “Installation with the update manager

Installation with the update manager

Internet access is required during the installation.

  1. Start ImageJ/Fiji
  2. Go to Help > Update…
  3. Click Manage update sites
  4. Select JIPipe and close the manage window
  5. Click Apply changes
  6. Restart ImageJ
  7. You can find JIPipe here: Plugins > JIPipe > JIPipe GUI (or use the search)
  8. Please read about the additional steps after the installation

Pre-packaged JIPipe distributions

  1. Download a pre-packaged JIPipe distribution
  2. Extract the ZIP file
  3. Windows: Run ImageJ-win64.exe
  4. Linux: Run ImageJ-linux64
  5. MacOS: Run the Fiji app
  6. You can find JIPipe here: Plugins > JIPipe > JIPipe GUI (or use the search)
  7. Please read about the additional steps after the installation

We currently have only limited capabilities of testing the MacOS version and appreciate any help of creating a smooth experience. Feel free to contact us!

Manual installation

This requires an existing Fiji installation. Please download the appropriate package from https://fiji.sc to get ImageJ. We strongly recommend to update ImageJ (via Help > Update...) before installing JIPipe.

  1. Download the JAR files
  2. Windows/Linux: Navigate to the ImageJ directory. MacOS: Right-click the app and click Show Package Contents.
  3. Go into the plugins directory
  4. Extract the downloaded JAR files
  5. Copy the JAR files into the ImageJ plugins directory. Do not copy the dependencies directory.
  6. Copy the contents of dependencies into the ImageJ jars directory (you can click “Skip” if there are existing files)
  7. Start ImageJ
  8. Run Plugins > JIPipe > JIPipe GUI (or use the search) to open the JIPipe GUI
  9. Please read about the additional steps after the installation

Post installation

Depending on your ImageJ installation and the selection of available/activated JIPipe extensions, the following additional steps will be required to install all functionality: