A proposal to fix #2007. This is done by:

• Adding a installHeadless() function to QuPathExtension with a default (do-nothing) implementation.
• Calling installHeadless() of all current extensions when the script command is used when running QuPath from the command line.

Hello @Rylern,

Is installHeadless called even when QuPath is launched with a GUI ?
It looks like no. Is it the intended behaviour ? Because then the code is a bit weird since I have to put in two places the method to add the custom image servers ser/deserializers.

    @Override
    public void installExtension(QuPathGUI qupath) {
    	if (alreadyInstalled || !checkCompatibility())
			return;
		
		try {
            addWarpyImageServer();
			// Add ImageCombinerWarpy action
			var imageCombinerWarpy = ActionTools.createAction(new InteractiveImageCombinerWarpyCommand(qupath), "Interactive image combiner Warpy");
			MenuTools.addMenuItems(qupath.getMenu("Analyze", false), imageCombinerWarpy);
	    	alreadyInstalled = true;
		} catch (Throwable t) {
			logger.debug("Unable to add ImageCombinerWarpy to menu", t);
		}		
    }

    @Override
    public void installHeadless() {
        addWarpyImageServer();
    }

Is installHeadless called even when QuPath is launched with a GUI ?

No, this is mentioned in the function documentation:

This allows for more flexibility, as it means you can have some code that runs when the GUI is not present, but not when the GUI is present.