batch mode

Hi all.

Today I tried to start KNIME workflows without the GUI (batch mode) and I encountered a problem with the ImageJ Macro nodes.

So I made a workflow were I read images in and then do some processing. The workflow works in KNIME without any error messages. But in batch mode (starting with the console) suddenly it doesn’t work anymore.

I found out that in batch mode the ImageJ Macro nodes don’t work properly. So without them everything works fine in batch mode. With the ImageJ Macro nodes included it stops working in batch mode. I am just doing watershed and subtract backround with the ImageJ Macro nodes. In batch mode they give out a rows with -> “?”

What am I doing wrong ?

Any help would be gread.

Kind regards,


Hi Flo,

thanks for reporting the problem!

It might be that ImageJ somehow calls some gui-functionality despite being in headless mode. Because in ImageJ1 the gui and the logic itself is not separated very well.

Anyway, we will have a look into it as soon as possible.



Good morning,


I encountered a lot of problems in batch mode and I just want to know whether it’s just not working or it’s my own dumb fault :)

For example XLS Writer works in batch mode but the “auto opening file” feature does not :(

Or if I place a Plate Heatmap Viewer and let’s say I want to save that Heatmap image (Image to Table, Image Column Writer) it does not work (even without the saving feature the whole workflow does not work anymore).


Kind regards,


Hi Flo,

it's almost certain that this is not your fault. The according nodes are presambly using gui functionality that is not available in headless mode.

Regarding the headless-problem with the ImageJ-Macro we'll try to figure out how to work around it (but unfortunately we can't promise to find a solution).

The XLS-Writer node: do you mean with "auto opening file" that the file is opened automatically after execution, e.g. with Excel? If so, than it actually makes sense, that this feature doesn't work in headless mode. Because the headless mode assumes that there is no display, mouse and keyboard. But the "External Tool"-node of the "External Tool Support"-extension is probably a good workaround for that (let us know, if you need more help with it).

In the case of the "Plate Heatmap Viewer"-node a can't tell much and the HCS-Tool-guys can give you more advice.



I have made an example workflow. Like I said it doesn’t work with the heatmap node (just delete it to test the workflow in batch mode).

workflow =

Images for the Image Reader =

So were exactly do I have to put the external Tool node ? :D




Hi Flo,

a added the node to your workflow and configured it such that it opens libre-office with a certain file specifed in the command line arguments in the configure dialog of the External Tool-node. You have to adopt them accordingly, e.g. to open Excel

I'm not sure if this is the best way to do it, but it works ;)

Does it also work for you?

It works :-)


Thanks a lot again for the effort.


Kind regards,