JIPipe can be installed in multiple ways:

  1. Install JIPipe via the ImageJ update manager (currently not available)
  2. Use our pre-packaged JIPipe distributions
  3. Use the online installer (currently not available)
  4. Install JIPipe manually

After a successful installation, JIPipe will warn you about third-party software (Python, R, …).

Installation with the update manager

This option is currently not available, as we are preparing the upload to 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)

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 JIPipe app
  6. You can find JIPipe here: Plugins > JIPipe > JIPipe GUI (or use the search)

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!

Online installer

This option is currently not available, as we are preparing the upload to the ImageJ update system.

Internet access is required during the installation.

  1. Download the online installer
  2. Windows: Run the setup and follow the instructions
  3. Linux: Set the executable flag of the setup and run it. Follow the instructions.
  4. MacOS: Extract the ZIP file. Run the app. The setup will automatically download all software.
  5. You can start JIPipe directly from your Desktop/Menu

Manual installation

This requires an existing ImageJ installation. Please download the appropriate package from 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

JIPipe might complain about missing plugins and show a list of missing dependencies. This is expected and caused by missing plugins.

  1. Click the Resolve button and wait until the missing dependencies were detected
  2. Click Apply changes
  3. Click Close ImageJ and restart ImageJ afterwards
  4. Run JIPipe again. No error should be present, anymore.

Missing dependencies Missing dependencies Missing dependencies

Third-party software

JIPipe relies on additional third-party software to provide some functionality. This includes the integration of Python, R, and Cellpose. At the first start, these are not known to JIPipe, which in return will notify about these issues.

To open the notifications tab, click the blinking notification button at the top right.

You will be offered various options to resolve each notification:

In the case of Python, R, and Cellpose, JIPipe directly offers installers that automatically handle the correct setup of these environments. In this case, you don’t need to configure anything else. If you want to enter settings manually or use alternative options (e.g., selecting an existing Python environment), click the configuration item.