Manual installation

Manual JIPipe installation

1. Download a version of Fiji for your operating system. Extract the package with the tools provided by your operating system.

2. Start Fiji and go start the update manager by navigating to Help | Update.... Follow the instructions until the update manager is ready. You should be able to see a button Manage Update Sites.

3. Please select the following update sites from the list:

   • 3D ImageJ Suite

   • clij

   • clij2

   • IJ-OpenCV-Plugins

   • IJPB-Plugins

   • ImageScience

   • Multi-Template-Matching

   • OMERO 5.5-5.6

   • N5

4. Click Apply and Close and then Apply Changes.

5. Restart ImageJ as instructed.

6. If applicable, download the JAR package (custom installation) package from the JIPipe website.

7. Extract the package and copy its contents into the Fiji.app/plugins/JIPipe directory (create the directory if needed).

8. Restart Fiji

9. To start JIPipe navigate to Plugins | JIPipe | JIPipe GUI