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.

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

The grout looks really tiny and the scale bar is very thin The suggested grout sizes work well for 400x400 images. If you have 1000x1000 images the suggested grouts will look thin when imported into a figure, adjust accordingly. As a guide, a 600x600 image that has two panels and one merge with a grout of 8 pixels will be 1816 pixels wide. At 300 dpi this is a final size of 155 mm. A full size figure is usually 170 mm, so the figure will be ~91% of the full width of the figure. If you shrink it to half size, now the grout will be 4 pixels or 0.34 mm which will look quite thin. A rule of thumb is grout should be 1/50th of the image width, but ultimately, test it out!