ImageJ Macro - 'Subtract Background' dialog popping up


I recently noticed in some of our workflows which include the ImageJ Macro node with the ‘Subtract Background’ Snippet that the dialog pops up during execution.

This happens randomly, I have not found a way to reproduce this behavior. However, the whole execution pauses until the dialog is confirmed. Has this been reported and is there a suggestion/solution to switch this off again?
OS: Mac OS X 10.14.6
KNIME: 14.1.0

Many thanks!

I have the same issue with some of my workflows that include a ImageJ Macro node with the following code:
run("Set Measurements...", "bounding fit redirect=None decimal=3"); run("Rotate... ", "angle="+angle+" grid=1 interpolation=Bilinear enlarge");

I noticed the behavior between KNIME version 3. to 4. It is really frustrating, I have a loop of hundreds of images…

Any solutions?



I confirm that the behavior doesn’t happen with old version of KNIME 3.7.2
For the moment this is my solution…




Thank you both for the reports, @Manuel and @Elisabet_T! I will look into what has changed and keep you posted on my investigation.


Could you please check which version of KNIME Image Processing - ImageJ Integration (Beta) you have installed in the instance, where the dialogs don’t open? Thanks!

Hi Stefan,

thanks for looking into this, my version of KNIME Image Processing - ImageJ Integration (Beta): 0.11.6.v20190717124.
EDIT: just saw that this was not your question, sorry, I have no other version currently.


True, but it is still useful information!

As you have mentioned before, @Manuel, I have a hard time reproducing the issue! You are using the vanilla “Subtract Background” snippet without any changes?

Which operation system are you on, @Elisabet_T?

Could you both give the following workflow a try to see if a dialog pops up during one of the 10000 runs? It runs both Subtract Background as well as the custom macro described by @Elisabet_T:

My operation system is Windows 10 Pro. I gave a try to your workflow and no window popping up, but then I try the following code that is mostly the one I have in the ImageJ macro node:

run("Set Measurements...", "bounding fit redirect=None decimal=3");
run("Set Scale...", "distance=0 known=0 pixel=1 unit=pixel");
angle = getResult("Angle", nResults-1);
run("Select None");
run("Rotate... ", "angle="+angle+" grid=1 interpolation=Bilinear enlarge");
run("Make Binary");

and I can reproduce the dialog window popping up.

Thank you for the macro, @Elisabet_T. I still wasn’t able to reproduce the issue within 10000 runs of the macro that you have provided.

I guess I’ll have to investigate an operating system dependency. Which does make sense, because there are a couple of fixes with regards to batch mode in ImageJ1 between the two versions (the one from 3.7.2 and 4.1.0) and some are OS-specific.

@Manuel Can you try to reproduce the issue with Elisabet’s macro in the workflow? Thank you!

Hi @stelfrich,

I got some mixed results. I wasn’t able to reproduce with your workflow initially, nor with the code provided by @Elisabet_T. Choosing only ‘subtract background’ however produced the dialog once, but not in the following executions :confused: