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


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.


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


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

./ --help


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