I have Fiji (ImageJ 1.51w) installed and use the ImageJ Macro node, which comes with the KNIME Image Processing - ImageJ Integration (Beta) package. I also have an ImageJ plugin installed called “Log 3D”, which works very well, both in manual mode and when used in a macro.
Now when I want to run this this plugin within KNIME, the node fails with the following error message:
WARN ImageJ Macro 0:148 Problem occured in rowWellF12_Seq0006.nd2_27 : 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
WARN ImageJ Macro 0:148 ImageJ Macro Error: Unrecognized command: “LoG 3D”
What can I do to get this working?
Btw, this is the link to the Log 3D plugin: BIG>Daniel Sage>LoG 3D
what directory is configured for ImageJ1 plugin directory in File > Preferences, in the KNIME > Image Processing Plugin > ImageJ1 Preferences section?
This should point to the
./plugins/ directory of your Fiji installation where the plugin in installed.
It is configured correctly: C:\Fiji\plugins
Though, the LoG 3D plugin is in C:\Fiji\plugins\LoG3D
I will look into why this plugin is not loading correctly next week, did you know you we have a native LoG implementation in KNIME Image Processing? You can find it in the Convolution Kernel Creator and also supports three (and more) dimenstions .
Once created you can apply this kernel using the Convolver node.
Good morning @gab1one ,
that would be awesome if you could take a look into that. It would be fantastic if I had a solution by Wednesday, because I have got an appointment with a collaborator where we need that.
I did not know about the native LoG implementation! This is amazing and would be way better than using the macro. I will try this, thanks!
The settings for the LoG 3D ImageJ plugins are the following:
> run("LoG 3D", "sigmax=3 sigmay=3 sigmaz=0 displaykernel=0 volume=0");
What are the equivalent settings for the Convolution Kernel Creator node settings? I must confess, I know nothing about it, I just wanted to get the macro running (which is from someone else).
This translates to a sigma of 3 and a two dimensional kernel, in our implementation. Take a look at the configuration of the Kernel Creator node in the attached example workflow: LoG example.knwf (8.3 KB)
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