name = getTitle()
run("Duplicate...", "title=[multichannel]");
run("Split Channels");
selectWindow("multichannel (green)");
run("16-bit");
run("Set Scale...", "distance=0 known=0 pixel=1 unit=pixel");
run("Invert");
run("Duplicate...", "title=[name_1]");
run("Duplicate...", "title=[name_3]");
selectWindow("name_3");



selectWindow("multichannel (red)");
//run("Threshold...");
setThreshold(5, 255);
run("Make Binary", "thresholded remaining black");


run("Create Selection")
selectWindow("name_3");
run("Restore Selection");

run("Enhance Contrast...", "saturated=10");
run("Select None");
run("Subtract Background...", "rolling=3 light");
run("Smooth");
run("Smooth");
run("Smooth");
run("Restore Selection");
run("Enhance Contrast...", "saturated=.5");
run("Make Binary");
run("Fill Holes");

selectWindow("name_1");
run("Find Maxima...", "noise=30 output=[Single Points] light");
run("Create Selection");
run("Enlarge...", "enlarge=5");
selectWindow("name_3");
run("Invert");
run("Restore Selection");
run("Clear", "slice");
run("Select None");

selectWindow("name_1");
setOption("BlackBackground", false);
run("Make Binary");
run("Erode");
run("Erode");
run("Erode");
run("Dilate");
run("Dilate");
run("Dilate");
run("Dilate");
run("Dilate");
run("Dilate");
run("Create Selection");
selectWindow("name_3");
run("Restore Selection");
run("Clear", "slice");
run("Select None");
run("Invert");

run("Skeletonize");
run("Canvas Size...", "width=1020 height=1020 position=Center");
run("Make Binary")
run("Analyze Skeleton (2D/3D)", "prune=none calculate");
close("Tagged skeleton");
close("Longest shortest paths");

// ***********************************************************************
// ***********************************************************************
// Replace the following directory with desired location for .csv files
// Note the presence of '\\' rather than the convetional '/'

saveAs("Results", "C:\\Example\\File\\Path\\" + name + ".csv");

// ***********************************************************************
// ***********************************************************************
run("Close");