Running Ilastik Multicut classifier from Fiji?

Hi

I trained Ilastik pixel-based and multicut classifiers for boundary based segmentation as described in: https://www.ilastik.org/documentation/multicut/multicut#superpixels--dt-watershed and got very good results. I want to include this in a Fiji macro that will apply the classifier to an image and then use the results for further processing within Fiji.
Is it possible to run the Ilastik multicut classifier directly from Fiji ? using IJ macro language ? using another scripting language ?

Thanks
Ofra

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Hello @Ofra_Golani,

cool that you like the results you get with multicut!

Right now it is not possible to automate the mutlicut workflow via a fiji macro (or even run it from fiji). However, you can batch process images using the headless mode. The headless mode for multicut itself is not documented there yet, however here is an example invocation that should do it:

./run_ilastik.sh
  --headless \
  --project="/path/to/project/MyProject.ilp" \
  --raw_data="/path/to/raw/data.h5" \
  --probabilities="/path/to/boundary/probability/data.h5" \
  --export_source="Multicut Segmentation" \
  --output_filename_format="/path/to/results/{nickname}_results.h5"
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