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The following sections document the usage of the steinbock command-line interface (CLI).


From this point onwards, it is assumed that the steinbock command alias was configured correctly.

Getting help

At any time, use the --help option to show help about a steinbock command, e.g.:

> steinbock --help

Usage: steinbock [OPTIONS] COMMAND [ARGS]...

--version  Show the version and exit.
--help     Show this message and exit.

preprocess  Extract and preprocess images from raw data
classify    Perform pixel classification to extract probabilities
segment     Perform image segmentation to create object masks
measure     Extract object data from segmented images
export      Export data to third-party formats
utils       Various utilities and tools
apps        Third-party applications

Directory structure

By default, all steinbock command options follow to the default directory structure.

Trying it out

To try out steinbock, the IMC mock dataset can be used as follows:

  1. Copy the raw directory to your steinbock data/working directory
  2. Place the panel.csv into the raw directory in your steinbock data/working directory
  3. Continue with Imaging Mass Cytometry (IMC) preprocessing and subsequent steps


Existing Ilastik training data (Ilastik pixel classification project, Ilastik crops) can be used for the classification step.