I am very new to KNIME, so maybe this is straightforward, but I couldn't figure it out even after several hours of trying..
I need to use the Fiji Plugin "Find connected regions", so I recorded a Macro in Fiji and copied the code to use it in the ImageJ Macro Node. However the following error occured:
"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"
Then I tried to install the plugin by changing the plugins folder from
...plugins/org.knime.knip.imagej1_0.9.1.201501182101/plugins ...plugins/org.knime.knip.imagej1_0.9.201407021502/plugins to the plugin folder
plugins/org.knime.knip.imagej1_0.9.1.201501182101/plugins of fiji (Fiji.app/plugins) as it is described here but that didn't work out either. I then realized that I couldn't even find the .jar file of the "Find connected regions" plugin in the plugin folder although fiji (and therefore the plugin) works perfectly fine and that there is no folder named "Process" as it is supposed to according to this Plugin description
Thanks very much in advance for any help !!
Ok sorry I don't know why this path was posted three times instead of once like I wrote it... but anyway I think I made my point
is the macro part of the ImageJ standard distribution? I will try to find out why this isn't working tomorrow.
Please note, that the ImageJ1 Macro should really just be used if there is no alterantive way to do it in KNIME. This has several reasons, but especially it is that IJ1 is really hard to integrate, so we have to copy images between KNIME and IJ1 which is not really performant. So if you like, I can offer my help to set up a workflow with native KNIME or ImageJ2 nodes (this also helps understanding the concepts behind KNIME Image Processing). For example, the find connected regions plugin looks similar to the `Connected Component Analysis` in KNIP in combination with the `Global Thresholder Node` or so. If you provide me some more details (or even your script + example images) I can try to help you out!
Anyway, the IJ Macro should also work as expected. I will try to find a solution and let you know right here.
PS: Could you provide me the workflow + one image you are using for testing the macro and the .jar via e-mail (firstname.lastname@example.org). Would make my debugging life much easier ;-)