This macro is listed in the appendix of chapter 15 by Merrill et al. "Measuring mitochondrial shape with ImageJ" in the upcoming book "Techniques to investigate mitochondrial function in neurons" Eds.: Strack & Usachev, Series: Neuromethods, Springer, Berlin, 2017

 var ch = 0; /* channel to be analyzed for RGB images */
/*
 *	Measure mitochondrial morphology in the current selection
 *	Ctrl+Shift+O closes current and opens next image
 */

macro "Simple Morphometry [F7]" {
	title = getTitle();
	morphometry(title, false); // not batch mode
}
/*
 *	Batch-apply a set of "named" ROIs to analyze images with that file name
 */

macro "Batch Morphometry [F8]" {
	dir = getDirectory("Select an image directory");
	while (roiManager("Count") == 0)
		waitForUser("Please open named ROIs into ROI manager");
	prevName = imgName = "";
	n = roiManager("Count");
	for (i = 0; i < n; ++i) { // loop through the ROI Manager table
		prevName = imgName;
		imgName = call("ij.plugin.frame.RoiManager.getName", i);
		if (isOpen(imgName)) { // named image is open
			selectWindow(imgName);
		} else { // done with current image, close and open next
			if (isOpen(prevName)) {
				selectWindow(prevName);
				close();
			}
			open(dir + imgName);
		}
		roiManager("Select", i); 
		morphometry(imgName, true); // batch mode
	}
}

function morphometry(title, batchMode) { 
	while (ch < 1 || ch > 3) { // RGB channel not yet selected, initialize
		ch = getNumber("Analyze RGB channel(1-3):", 1);
		run("Set Measurements...", "decimal=5 area perimeter fit");
		print("image\t n\t area2\t area-weighted ff\t form factor\t aspect ratio\t length"); // header for results table
	}
	if (bitDepth == 24) // RGB image
		run("Make Composite");
	if (isOpen("Binary")) {
		selectWindow("Binary");
		close();
	} // close previous working image
	if (isOpen("Skeleton")) {
		selectWindow("Skeleton");
		close();
	} // close previous working image
	selectWindow(title);
	if (selectionType() == -1) // no selection
		run("Select All");
	if (!batchMode) {
		roiManager("Add"); // save selection to ROI Manager and rename to image name (for batch processing)
		last = roiManager("Count") - 1;
		roiManager("Select", last);
		roiManager("Rename", title);
		/* roiManager("Save", File.directory + "named_ROIs.zip"); */ // un-comment to save ROIs automatically
	}
	// copy selection to new window and clear outside
	setSlice(ch); // ignored if grayscale
	run("Duplicate...", "title=Binary");
	run("Make Inverse");
	if (selectionType != -1) { // outside of ROI is selected
		run("Duplicate...", " "); // make a mask of the background
		run("Convert to Mask");
		run("Create Selection");
		run("Make Inverse");
		roiManager("Add");
		close();
		n = roiManager("Count");
		roiManager("Select", n - 1);
		getRawStatistics(_area, backG); // mean is background
		setColor(backG);
		run("Restore Selection"); // fill outside of selection with background
		fill();
		run("Gaussian Blur...", "radius=64"); // smooth abrupt background transition
		roiManager("Delete"); // delete masking selection (ROI manager accumulates cell selections)
	}
	run("Select None");
	// subtract background and threshold
	run("Subtract Background...", "rolling=50"); // non-destructive filter even if already applied
	run("Make Binary"); 
	// also try other threshold methods included with Fiji, e.g.: run("Auto Threshold", "method=Li white");
	// create Results table of metrics, one line/particle
	run("Analyze Particles...", "size=9-Infinity circularity=0.00-1.00 show=Masks pixel clear");
	awff = ff = ar = sum_a = a2 = len = 0;
	for (i = 0; i < nResults; i++) { // for every particle in table
		a = getResult("Area", i);
		p = getResult("Perim.", i);
		ar += getResult("Major", i) / getResult("Minor", i); // aspect ratio = length / width
		sum_a += a;
		a2 += a * a; // area2 = a2 / (sum_a * sum_a)
		awff += b = (p * p) / (4 * 3.14159265358979); // awff = ff * (a / sum_area)
		ff += b / a; // ff = p^2 / (4 * pi * a)
	}
	nParticles = nResults;
	// skeletonize to get length
	selectWindow("Mask of Binary"); // created by Analyze Particles .., excludes noise (< 9 pixels)
	rename("Skeleton");
	run("Skeletonize");
	run("Analyze Particles...", "size=0-Infinity show=Nothing pixel clear");
	for (i = 0; i < nResults; i++)
		len += getResult("Area", i);
	// average and output
	a2 /= sum_a * sum_a;
	awff /= sum_a;
	ff /= nParticles;
	ar /= nParticles;
	len /= nResults;
	print(title + "\t " + nParticles + "\t " + a2 + "\t " + awff + "\t " + ff + "\t " + ar + "\t " + len);
	selectWindow(title);
}