ImageJ integration

Can I use plugins from ImageJ in JIPipe?

Yes. Either there is an integration available, or you just use the macro node and input the corresponding macro code that runs the plugin.

Can I use existing ImageJ macros in JIPipe?

Yes, use Images > ImageJ macro. The input slots are opened as image windows and can be addressed from within the macro with selectWindow(). You can also load an example that shows how to use the node.

Can I use JIPipe from within ImageJ macros?

Yes. You can use both pipelines and individual JIPipe algorithms from within ImageJ macros and the GUI.

Why are some JIPipe algorithms not availabe from within ImageJ?

JIPipe has a very general data model that makes it possible to develop pipelines for processing any kind of data. The communication between JIPipe’s data types and ImageJ is handled by adaptors that will handle the “translation” back & forth. For some of such data types, there is no adaptor. The reason behind this is that ImageJ might not have an equivalent data type or feature.