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What options are there for interfacing with / controlling ImageJ/Fiji from another program?

I need to use some image filters that are available in Fiji. However, I cannot have Fiji be the centre of my workflow. I am using another system (scripting language) for that. I must manipulate some data in that other system, apply a filter to an image, get the result, then continue manipulating that image.

What are my options? What features does Fiji provide that make this possible?

In particular, is it possible to do this if the system I am using does not have a Java interface? It does have a C interface, and it can invoke command line programs.

For context: I want to interface Fiji with Mathematica. Mathematica does have a Java interface but it appears to lack support for some Java 8 features that ImageJ requires. I also don't know much Java and I am looking for a simple solution that I can set up quickly, rather than a long-term robust solution that requires a high initial investment.

Szabolcs
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1 Answers1

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If you can't run the ImageJ filters through Java integration, you may be able to write the necessary operations into an .igm macro and then get ImageJ to run it in headless mode.

Otherwise, it may be simpler to port the Java code for the particular filters that you need into a more convenient environment. ImageJ is primarily set up for GUI use, and Java/CLI/other integration can get messy very quickly.

Joel
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  • In headless mode, is it possible to start up ImageJ *once*, then run *multiple* macros *on demand*? ImageJ takes very long to start up. It is not realistic to start it again and again for each new operation. – Szabolcs Nov 30 '18 at 10:20