run("Close All");
input = getDirectory("/Users/ranjith.papareddy/Downloads/seed_size/transgenics");
output = getDirectory("/Users/ranjith.papareddy/Downloads/seed_size/transgenics");
suffix = ".czi";
processFolder(input);
// function to scan folders/subfolders/files to find files with correct suffix
function processFolder(input) {
list = getFileList(input);
list = Array.sort(list);
for (i = 0; i < list.length; i++) {
if(File.isDirectory(input + File.separator + list[i]))
processFolder(input + File.separator + list[i]);
if(endsWith(list[i], suffix))
processFile(input, output, list[i]);
}
}
function processFile(input, output, file) {
run("Bio-Formats Importer", "open=" + input + list[i] +" ");
run("8-bit");
run("Split Channels");
title = getTitle();
saveAs("Tiff", output + file + "_tl.tif");
close();
title = getTitle();
saveAs("Tiff", output + file + "_fl.tif");
close();
print(title);
print("Processing: " + input + File.separator + file);
print("Saving to: " + output);
}