Starting JIPipe the first time – JIPipe for ImageJ

Summary

Start JIPipe by navigating to Plugins > JIPipe > JIPipe GUI (or searching for the JIPipe GUI in the ImageJ search). Follow the instructions that are presented to you while JIPipe prepares the first start.

Info

Unless you used one of our prepackaged Fiji versions, JIPipe will request to install additional ImageJ update sites to ensure that all software components can work. The following steps will guide you through this initial setup.

Step 1

Start JIPipe by navigating to Plugins > JIPipe > JIPipe GUI (or searching for the JIPipe GUI in the ImageJ search).

Step 2

JIPipe will go through its first setup process and depending on the Fiji installation might find missing ImageJ functions. This is normal and will be resolved in the next steps.

JIPipe will present you with a list of all missing ImageJ update sites that are displayed in a Missing ImageJ dependencies dialog.

Please click Install all dependencies to proceed.

If the dialog does not appear, you can skip the next step.

Info

If JIPipe crashes and the dialog does not appear, then please install JIPipe manually (see other installation guides). Your Fiji installation is in this case missing essential libraries.

Step 3

If dependencies have been installed, you will be prompted to restart ImageJ.

Click Close ImageJ and start ImageJ again.

A restart of ImageJ is not required if no dependencies were installed.

Step 4

After the initial setup (and restart of ImageJ if required), start JIPipe.

You should see JIPipe’s welcome screen.