run("Close All");
input = getDirectory("/Users/ranjith.papareddy/Downloads/seed_size/onlytiffs/8bit_converted");
output = getDirectory("/Users/ranjith.papareddy/Downloads/seed_size/onlytiffs/8bit_converted");
suffix = ".tif"; //you only want to apply to tiff images, no need to ask
processFolder(input);
function processFolder(input) {
list = getFileList(input);
for (i = 0; i < list.length; i++) {
if(File.isDirectory(input + list[i])) //if it's a directory, go to subfolder
processFolder("" + input + list[i]);
if(endsWith(list[i], suffix)) //if it's a tiff image, process it
processFile(input, output, list[i]);
//if it's neither a tiff nor a directory, do nothing
}
}
function processFile(input, output, file) {
print("Processing: " + input + file);
open(input + file);
run("Set Scale...", "distance=0 known=0 pixel=1 unit=pixel global");
run("Median...", "radius=3");
setAutoThreshold("Otsu dark");
setOption("BlackBackground", true);
run("Convert to Mask");
run("Analyze Particles...", "size=1950-3750 display exclude");
saveAs("results", output + file + "_results.csv");
print("Saved to: " + output);
close();
}