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The input and output files and directories of all steinbock CLI commands can be controlled via command-line options. However, without explicitly specifying input/output arguments, the following typical directory structure is assumed when working with the steinbock CLI:

steinbock data/working directory
├── raw                       (user-provided, when starting from raw data)
├── img                       (user-provided, when not starting from raw data)
├── panel.csv                 (user-provided, when not starting from raw data)
├── images.csv
├── ilastik_img
├── ilastik_crops
├── pixel_classifier.ilp
├── ilastik_probabilities
├── cell_segmentation.cppipe
├── masks
├── intensities
├── regionprops
└── neighbors

Depending on the choice of preprocessing approaches, either the raw directory containing the raw data, or the img directory containing the images and a panel.csv file must be provided by the user. All other files and directories are generated by the steinbock Docker container when following a supported workflow.