input = getDirectory("Input directory");
output = getDirectory("Output directory");

processFolder(input);

function processFolder(input) {
	//-- get a list of files and folders in the input
	list = getFileList(input);
	//-- DEBUG only, print the list to see what we have
	//Array.print(list);
	//-- Iterate the list
	for (i=0; i<list.length; i++) {
		//-- If the item is a directory, list the contents of the directory and pull the first alphanumerically sorted filename
		if(File.isDirectory(input + list[i])==1);{
			fileList=getFileList(input + list[i]);
			//-- Sort to get alphabetical
			fileList=Array.sort(fileList);
			fileListFirst=fileList[0];
			}
			//-- DEBUG only, make sure the path looks good
			//print(input + list[i] +fileListFirst);
		//-- Open the image sequence by specifying the first image filename in the sequence
		run("Image Sequence...", "open=["+input+list[i]+fileListFirst+"] file=.tif sort");
		//-- Do what you do
		run("Canvas Size...", "width=5000 height=5000 position=Center");
		//-- Save the file as a tif stack
		save(output+replace(list[i],"/","_")+replace(fileListFirst,".tif","_series.tif"));
		//-- Close the files
		close("*");
} //-- folder loop

} //-- close function