I’ve stared running batch analysis in Qupath by x11 forwarding on a HPC cluster, but it doesnt like GUI drop down menus(to “run script for project”)
Is there a script that I can use in my existing script to effectively run the same command?
Hi @James_Monkman, not exactly but I can think of two options:
- Write a script that loops through all images in your project, opens them, does something, and then writes the image data as the result (some hints here).
- Call the script from the command line (some docs here)
The first approach takes a bit more code and is awkward if you then want to use the same script without Run for project.
If you take the second approach, note there is a related bug – described here with its workaround.