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.
At any time, use the
--help option to show help about a steinbock command, e.g.:
> steinbock --help Usage: steinbock [OPTIONS] COMMAND [ARGS]... Options: --version Show the version and exit. --help Show this message and exit. Commands: 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
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:
- Copy the raw directory to your steinbock data/working directory
- Place the panel.csv into the
rawdirectory in your steinbock data/working directory
- 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.