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:


Chiming in to say that this is still an issue for me. Happens randomly when using the “ImageJ Macro” node with substract background. It does not happen on the same images reproducible and I have yet been able to figure out an underlying cause. It happens on Knime 4.2 as well as 4.3.