Added the ImageJ Fiji macro script for the alignment of images in a folder

Image Alignment/Sift_reg.ijm

+// visit all subfolders and run sift alignment
+// on all images in a folder
+//
+// Paul Wuerzberg
+
+requires("1.37e")
+setBatchMode(true);
+call("java.lang.System.gc");
+dir = getDirectory( "Choose the Directory" );
+openfolders(dir);
+
+function openfolders(dir){
+	list = getFileList( dir );
+	x=0;
+	for ( i=0; i<list.length; i++ ) {
+    		if (endsWith(list[i], "/"))
+    		{
+    			openfolders(dir + list[i]);
+    		}
+		else{
+			x=1;
+		}
+    		
+	}
+	if (x==1){processFiles(dir);}
+}
+
+
+function processFiles(dir) {
+	list = getFileList( dir );
+for ( i=0; i<list.length; i++ ) {
+    open( dir + list[i] ); 
+	}
+	run("Images to Stack", "name=Stack title=[] use");
+	run("Linear Stack Alignment with SIFT", "initial_gaussian_blur=1.60 steps_per_scale_octave=3 minimum_image_size=64 maximum_image_size=1024 feature_descriptor_size=4 feature_descriptor_orientation_bins=8 closest/next_closest_ratio=0.92 maximal_alignment_error=25 inlier_ratio=0.05 expected_transformation=Rigid interpolate");
+	run("Stack to Images");
+	//myDir = some_dir+"align"+File.separator;
+	//File.makeDirectory(myDir);
+	for ( i = list.length - 1; i>=0; i-- ) 
+		{
+		//saveAs("Jpeg", some_dir + "align/" + list[i]);
+		saveAs("Jpeg", dir + "_alin_" + list[i]);
+		close();
+	}
+	close();
+	// gc after each round may be overkill
+	call("java.lang.System.gc");
+}
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