Command line

QuPath is mostly designed to be an interactive application, and this remains the main priority.

However, v0.2.0 introduces a new command line, which makes it possible to:

  • Launch QuPath with specific options (e.g. a logging level)

  • Run scripts headlessly

  • Convert images to OME-TIFF

Tip

The order in which command line arguments are passed can be important. See this forum post.

Viewing command line options

The general way to view the command line options is with:

QuPath-0.2.0 --help

However, there are some platform-specific details on Windows and Mac.

Windows

On Windows, there are two executable files for QuPath. It is necessary to use “QuPath (console).exe” here to be able to view the output, e.g.

"QuPath-0.2.0 (console).exe" --help
../../_images/command_line_win.png

Mac

On macOS, the executable is buried inside the .app file and therefore you need something like:

./QuPath-0.2.0.app/Contents/MacOS/QuPath-0.2.0 --help
../../_images/command_line_mac.png

Subcommands

Some of the command line functionality is available via subcommands, such as script. Help is available for these separately.

QuPath-0.2.0 script --help
../../_images/command_line_mac_script.png