imagej macro issue

Hey! I am trying to do colour deconvolution on some images, so I copied my macro into the ImageJ Macro pure code:

run(“Stack to RGB”);
run(“Subtract Background…”, “rolling=70 light”);
run(“Colour Deconvolution”, “vectors=[User values] hide [r1]=29.831186 [g1]=66.10667 [b1]=97.59406 [r2]=40.33258 [g2]=37.12847 [b2]=13.552562 [r3]=0.44360253 [g3]=2.2902856 [b3]=1.5317869”);

However, I get the following warning:

WARN ImageJ Macro 4:2231 ImageJ Macro Error: Unrecognized command: “Colour Deconvolution”
WARN ImageJ Macro 4:2231 Problem occured in rowTMA 101 B7H4 IHC-Scene-06-ScanRegion5.czi_1 : The specified macro has thrown an error while execution. Make sure that the used plugins are available in the selected IJ1 plugin folder! See KNIME Log for details! Missing cell has been inserted

Is it because colour deconvolution can’t run headless? Or am i doing something wrong? Is there a way around it? Can it be added as an imageJ2 pluggin?



Hi @paulage,

I am sorry to tell you but it seems the “Colour Deconvolution” plugin is not supported by our ImageJ integration.

Indeed “Colour Deconvolution” seems to be not compatible with being run headless.

This would require it to be ported to ImageJ2 first. Then yes.


@gab1one, ok. How do I go about porting to ImageJ2 and then adding it as a pluggin on knime?

Thanks, Paula

Take a look at:

and feel free to ask questions here, in the imagej forum as well as the gitter channel:



1 Like

Hi @paulage,

I came across this post. We are working on a colour deconvolution plugin for IJ2.
We have now a first beta version.
I don’t know if you are still looking for a solution but maybe you can have a look at our plugin?

Let me know!


Boudewijn was talking about this release:

You can install this into Knime by following these instructions:

It’s a really new plugin, so please let us know if it works and if you have any feedback on the way it works.

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