When I try to use the "Analyze particles" function of the Imagej Macro Node, I get the following error message:
Error in row 20151005 SafO_P3M4_5x_2ms_2 crop.tif: Encountered duplicate row ID "20151005 SafO_P3M4_5x_2ms crop.tif#0" at row number 9
ERROR ImageJ Macro 0:116 Execute failed: org.knime.core.util.DuplicateKeyException: Encountered duplicate row ID "20151005 SafO_P3M4_5x_2ms crop.tif#0" at row number 9
I don't get what this means because the Row IDs are clearly distinct and besides that, it has worked before with the exact same settings (I tried to delete one node, but added it afterwards so nothing was changed after all).
If I just don't load this image in the beginning, the same error message occurs again with the new first row...
Unfortunately, the zip file of the workflow is way too big to attach it here, but maybe somebody can tell me why this message generally occurs.
actually, I don't know why this error message occurs. Seems like something weird in ImageJ1 changed recently. I really don't encourage people to use the ImageJ1 macro node, if there also exists a solution within KNIME. ImageJ1 is a great tool, however its close to impossible to integrate it into other tools like KNIME (thanks god there is ImageJ2).
So what I suggest instead of the analyze particles macro: Global Thresholder (with your preferred settings) -> Connected Component Analysis -> Image Segment Feature Node.
There are several example workflows on knime.imagej.net demonstrating how to do that (e.g. the HCS workflow, which is also explained in our youtube video).
Let me know if this works out.
PS: We will have a look at the IJ1 problem anyway and try to reproduce and fix it! Thanks for reporting this stuff, this is super helpful!!!
If I use Global Thresholder -> (inverter)-> Connected Component Analysis -> Labeling filter -> Labeling Properties it works out. But if I try to use Image Segment Features instead of Labeling Properties, I get the error message "No column in spec compatible to "ImgPlusValue" if I try to configure the node...
You can try the `Segment Feature` node instead of `Image Segment Features`, if you only want to calculate geometric properties.