Ilastik Integration output

Dear KNIME community,

I would like to use the ILASTIK headless pixel classification in KNIME. I established an ilastik project (two labels) and could also run my images in the node. Using the image viewer node the only output seems to be the two images of the probabilities, which should be the default output. However, my desired output would be the simple segmentation. Is there any option within KNIME or ILASTIK to change the default output of the headless mode? Using the GUI, it is possible to export the simple segmentation image, which can then be loaded into KNIME with the image reader node. However, I need an automated solution…

Thank you very much in advance!

Best regards


Hi @diddi,

There is currently no way to directly obtain the simple segmentation image from ilastik for subsequent use in a KNIME workflow. You can, however, apply a manual threshold on all the channels using a Global Thresholder node. Change the “Method” to “Manual” and set the “Threshold Value” to e.g. 0.95. Subsequently, you can use a Connected Component Analysis node to re-generate a labeling for you input images to e.g. do measurements on your labels…


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Dear Stefan,

thank you very much for your solution and opening of the issue!


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