Frequently asked questions
What is the JIPipe.tmp.dir directory?
JIPipe stores temporary files into this directory. You can delete it safely if no JIPipe project in the containing directory is currently open.
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 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 tab on the right-hand side. Go to the page and click the Configure... button at the item. Select one of the provided options.
- Overriding on an application level
Navigate to 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.
I have many files to process. How can I make a loop?
You have two options:
If you have a small and self-contained set of nodes that should be looped, create a looped group.
If you want to loop a section of your pipeline, setup graph partitions.
Question not listed?
Please visit the image.sc forum. Here you can ask the community, including JIPipe users and developers for solutions.