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Ilastik offers the possibility (both in the UI and from the CLI) to provide a mask in addition to the raw data to reduce the data blocks to be processed when providing sparse data.
Citing @stuarteberg from the ilastik mailing list:
If you have, say, three raw data images to process, and three
corresponding masks, provide the lists of filenames preceded by --raw_data
and --prediction_mask, like this:./run_ilastik.sh --headless \ --project=MyProject.ilp \ --raw_data my_raw_data_1.png my_raw_data_2.png my_raw_data_3.png \ --prediction_mask mask_1.png mask_2.png mask_3.png
I suggest adding an optional input to the Ilastik Headless (Pixel classification) node, allowing to choose an image column that contains a prediction mask.
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