// For all images in a folder, extract the middle slice and save it into a
// subfolder.
//
// Written 2017 by Volker Baecker, Montpellier Ressource Imagerie


var _FILE_EXTENSION = ".tif";

setBatchMode(true);
dir = getDirectory("Select the input folder!");
files = getFileList(dir);
File.makeDirectory(dir + "/out");
print("\\Clear");
print("started extracting middle slices");
for(i=0; i<files.length; i++) {
	print("\\Update1:extracting image " + (i+1) + " of " + files.length);
	file = files[i];
	if (endsWith(file, _FILE_EXTENSION)) {
		open(dir + "/" + file);
		middleSlice = floor(nSlices / 2);
		setSlice(middleSlice);
		run("Duplicate...", " ");
		resetMinAndMax();
		save(dir + "/out/" + file);
		close();
		close();
	}
}
print("finished extracting middle slices");