run FIJI macro plugins in KNIME

KNIME Extensions
1

Hi,
I am not a KNIME user but I am interested in some of the features KNIME has.
I currently use FIJI for my image analysis and run macros that require the 3D object counter, 3D ROI manager and CLIJ. In the ImageJ integration that KNIME has, is it possible to run a macro with the plug-ins mentioned above ?

Thanks a lot

2

I know @imagejan has a lot of experience running ImageJ plugins and macros, so he can tell you more on the details.
You can configure KNIME AP to use your installation of FIJI, then the plugins from that installation are available to you in macros. Note that we only support headless plugins, I took a quick look at the 3d object counter code and it looks like it won’t work with our integration, due to the fact that it is too menu based.
Depending on your coding skills you could wrap the 3D object counter into an ImageJ2 style plugin and take advantage of our more advanced IJ2 integration. That is another topic @imagejan is experienced with.

best,
Gabriel

3

Thanks @gab1one for the info.
Both the the 3D object counter, 3D ROI manager can run without user input. Only the 3D roi manager pops up a window but it doesn’t require anything.

So I guess that should be fine then ?
Also if I understood correctly in order to use FIJI macros one needs somehow to make the output of FIJI available as an input for KNIME ? is this correct ? is there a tutorial explaining how to do it ?

Thanks a lot

4

Hi @LPUoO,
take a look at: https://www.knime.com/community/imagej
If you are using the ImageJ1 macros you need to use the ImageJ1 macro node. I do not know how well it works with 3d data though…
Once you have installed the extension, go to the preferences, search for imagej and set the path to your FIJI installation.

The node takes care of the data conversion etc. so you do not need to do that.

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