// Measurement of fibre area and axon area in pixels
open();
// setBatchMode
bm=false; // true;     // false;
id=getImageID();
na1=getTitle();
di=getDirectory("image");
na=substring(na1,0,lengthOf(na1)-4);
setBatchMode(bm);
// Create mask of fibers (myelin)
run("8-bit");
setAutoThreshold();
run("Convert to Mask");
setTool(3);
if (bm) setBatchMode(false);
run("Wait For User","");
if (bm) setBatchMode(true);
selectImage(id);
run("Select None");
setThreshold(1,255);
run("Convert to Mask");
// Create ROIs for each connected fiber
run("Set Measurements...", "  redirect=None decimal=0");
run("Analyze Particles...", "size=500-Infinity circularity=0.00-1.00 show=Nothing clear include add");
// Create inverted Mask with pixel values 1
run("Divide...", "value=255.000");
// Measure Area: fibre area, Intden: axon area
setThreshold(1,255);
run("Set Measurements...", "area integrated redirect="+na1+" decimal=0");
roiManager("Measure");
// Store results
selectWindow("Results");
saveAs("text", di+na+".xls");
if (bm) {
	roiManager("reset");
	runMacro("Close_All_Windows");
}