Frequently asked questions

Can I convert a JIPipe workflow into an ImageJ macro?

No, JIPipe has its own implementation of a workflow engine (the component that runs the pipeline) that does not involve ImageJ macros in any form. This way, we ensure that JIPipe is not limited by the design of the ImageJ macro language that was not made for visual pipelines. Additionally, we gain a lot of additional flexibility regarding data types (for example, ImageJ does not understand what a Cellpose model is).

How do I use my own installation of Python/Conda/R?

You can override environments on a node, project, and application level.

Overriding on a node level: To for example make a node use a custom Python version, select the node, and enable the Override Python environment parameter. Click the Configure... button and select one of the provided options.
Overriding on a project level: To change the Python environment for a whole project, click the Info & Settings button at the top right of the window and go to the Settings tab on the right-hand side. Go to the Plugins | Python integration page and click the Configure... button at the Project default environment item. Select one of the provided options.
Overriding on an application level: This will only affect new projects, unless the project's Project default environment item is turned off.
Navigate to Project | Application settings | Plugins | Python integration and edit the default environment.

JIPipe is available as plugin. Why do you provide installers/packages instead?

We experienced multiple times already that when ImageJ updates plugins/components, some functionality might break. This is avoided by providing a JIPipe installation as-is.