Installation

Installation with the update manager

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

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:

• Various JIPipe extensions require the presence of specific ImageJ plugins. You will be prompted to install the ImageJ dependencies if JIPipe detects missing ones.
• Some extensions integrate third-party tools (e.g., Cellpose) that are not available as ImageJ plugin. JIPipe will notify you to install these tools and/or configure their usage within JIPipe.
• The default installation of JIPipe leaves some functionality deactivated to reduce the number of dependencies. You will be notified about these extensions.