Batch processing particle images

Batch_crop-save_macro.ijm

/*
 * Macro template to process multiple images in a folder
 */

#@ File (label = "Input directory", style = "directory") input
#@ File (label = "Output directory", style = "directory") output
#@ String (label = "File suffix", value = ".tif") suffix

// See also Process_Folder.py for a version of this code
// in the Python scripting language.

processFolder(input);

// function to scan folders/subfolders/files to find files with correct suffix
function processFolder(input) {
	setBatchMode(true)
	list = getFileList(input);
	list = Array.sort(list);
	for (i = 0; i < list.length; i++) 
		action(input, output, list[i]); 
	setBatchMode(false){
		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 action(input, output, file) {
open(input + File.separator + file);
title = getTitle();
run("Copy");
close();
newImage("Untitled", "8-bit black", 1000, 1000, 1);
selectWindow("Untitled");
run("Paste");
selectWindow("Untitled");
saveAs("Tiff", output + File.separator + "cropped_" + file);

	print("Processing: " + input + file);
	print("Saving to: " + output);
}