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.
There’s the Align image node that does registration of images along a dimension (in contrast to what its name suggests). Works quite well for the example data that you have provided!
Unfortunately, that won’t work in KNIME. @Christian_Tischer, however, has worked on a native Java Image Registration Suite some time ago. Progress seems to have stalled a little, though. If you are curious, discussions have happened in this thread:
Ah yes, I didn’t realize the “align” node could be used like that! This works great for my use case. I’ll take a look at Image Registration Suite, thanks for the link.
In case someone needs it in the future, I made a quick example workflow showing how the align node can work in some cases (link). This workflow takes a 2 channel time series. It aligns channel 2 relative to channel 1. Then it aligns both channels through time.
Thanks, Andrew, for sharing the example! The link requires me to request access, is that intended? Did you know you can also share workflows via the KNIME hub now?
