//Macro for automatic counting of calyptras in RGB images in a black background//
//Ibáñez et al. CBGG//
//Batch process of all the jpg images in the supplied directory//
//The following macro code provides a macro version of the BATCH PROCESS command//
dir1 = getDirectory("Choose Source Directory ");
//format = getFormat();
format="jpeg";
dir2 = getDirectory("Choose Destination Directory ");
list = getFileList(dir1);
setBatchMode(true);
for (i=0; i<list.length; i++) {
showProgress(i+1, list.length);
open(dir1+list[i]);
//Batch: Macro for counting calyptras//
//print (list[i]);//
run("Split Channels");
selectWindow(list[i] + " (red)");
setAutoThreshold("Default");
//run("Threshold...");
call("ij.plugin.frame.ThresholdAdjuster.setMode", "B&W");
setThreshold(50, 255);
//setThreshold(0, 50);
setOption("BlackBackground", false);
run("Convert to Mask");
run("Fill Holes");
run("Watershed");
run("Erode");
run("Analyze Particles...", "size=200-1000 show=[Overlay Masks] display exclude clear include summarize");
saveAs(format, dir2+list[i] + " (red).jpg");
//run("Close All");//
}