Note: the following examples use linux shell syntax, but the options are the same for all platforms. \ilastik.exe -headless -project=MyProject.ilp my_next_image1.png my_next_image2.png Those should always be given as the last arguments to the command line.įor example, this command will run your classifier over 2 additional images (here we assume your classifier was trained on 2D images): One or more files to be processed as a batch.ilp project file, via the -project argument (e.g. The -headless flag, to trigger headless operation.When running ilastik in headless mode, you must specify at least: Once you’re done with the training, save your project and quit ilastik. Pixel Classification Workflow or Object Classification Workflow for instructions on how to train your classifier). In order to run ilastik in headless mode, you will need to use the graphical user interface to create a project and train a classifier by manually drawing annotations as usual (see, e.g. Still, if you wish to run ilastik from inside your automation scripts or in environments with no graphical capabilities (e.g.: HPC clusters), then you can use the “headless” mode, which will allow you to run ilastik as a command line tool.Įxcept for the Carving Workflow, all workflows are able to run in headless mode. Once you’re happy with your classifier, you may wish to apply it to several other images using the Batch Processing Applet. Ilastik has an interactive graphical user interface for training a classifier and refining your results. Headless Mode Operation - Using ilastik as a command line tool General
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