Troubleshooting

Most problems are solved by allowing Fiji's updater to install the latest code from the quantixed ImageJ Update Site.

Still not working? All routines use a number of custom functions which get loaded when Fiji starts up. Errors in running these routines usually traceback to third party code that modifies StartupMacros.fiji.ijm. Which can be found in the macros directory. Specifically, if the third party has deleted this code block, then none of the autorun functions happen at startup.

macro "AutoRun" {
	// run all the .ijm scripts provided in macros/AutoRun/
	autoRunDirectory = getDirectory("imagej") + "/macros/AutoRun/";
	if (File.isDirectory(autoRunDirectory)) {
		list = getFileList(autoRunDirectory);
		// make sure startup order is consistent
		Array.sort(list);
		for (i = 0; i < list.length; i++) {
			if (endsWith(list[i], ".ijm")) {
				runMacro(autoRunDirectory + list[i]);
			}
		}
	}
}

If you can't bear to uninstall the third-party code (or don't know which update site causes the problem), just paste that code block into StatupMacros.fiji.ijm and things will start to work again.

Filenames Note that usage of RGB images has a limitation of a filename length of 59 characters.