I noticed that a lot of my workflows lack a 3D drift correction node like the imagej plugins “Correct 3D drift” or “stackreg” / “multistackreg”. Currently, I always do this step outside of KNIME which slows everything down considerably (mostly because the image writer node is slow). I was wondering if anyone had tried to implement registration/drift correction functions directly in KNIME yet?
I spent some time attempting to do this myself. The easiest thing looked like taking “Correct 3D drift” script, annotating it for KNIME and using Maven to package the jar.
I ran into a number of problems though, likely because I am a horrendously inexperienced with ImageJ2 macros. Most of the examples I’ve found online (thanks @imagejan, @stelfrich) use Java. “Correct 3D drift” is python, so how do I correctly annotate this for KNIME? Do I need to rewrite everything in Java using command classes? Am I better off / is is possible to run this as a pure python script off of a python node?
Thanks for any help or suggestions!
If anyone would like to take a crack at this themselves, here is a link to 2 a channel image of a cell that moves a little over time.