diff --git a/ch.psi.fda/src/main/java/ch/psi/fda/AcquisitionMain.java b/ch.psi.fda/src/main/java/ch/psi/fda/AcquisitionMain.java
index 299e3ef..6c93e67 100644
--- a/ch.psi.fda/src/main/java/ch/psi/fda/AcquisitionMain.java
+++ b/ch.psi.fda/src/main/java/ch/psi/fda/AcquisitionMain.java
@@ -26,7 +26,6 @@ import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
 import java.io.File;
 import java.io.PrintWriter;
-import java.util.HashMap;
 import java.util.concurrent.Executors;
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.logging.Level;
@@ -91,8 +90,6 @@ public class AcquisitionMain {
 		boolean nogui = false;
 		String files[] = null;
 		
-		HashMap<String,String> varTable = new HashMap<String,String>();
-		
 		// Iterations option
 		OptionBuilder.hasArg();
         OptionBuilder.withArgName("iterations");
@@ -100,19 +97,11 @@ public class AcquisitionMain {
         OptionBuilder.withType(new Integer(1));
         Option o_iterations = OptionBuilder.create( "iterations");
         
-        // Variables option
-        OptionBuilder.hasArg();
-        OptionBuilder.withArgName("variables");
-        OptionBuilder.withDescription("Scan variables - variables are specified in the form var=value,var2=value2");
-        OptionBuilder.withType(new Integer(1));
-        Option o_variables = OptionBuilder.create( "variables");
-        
         Option o_autoclose = new Option( "autoclose", "Close down application after scan" );
         Option o_init = new Option( "initialize", "Initialize application directories and configuration files" );
         Option o_nogui = new Option( "nogui", "Do not show scan GUI" );
         
         Options options = new Options();
-        options.addOption(o_variables);
         options.addOption(o_iterations);
         options.addOption(o_autoclose);
         options.addOption(o_init);
@@ -142,19 +131,6 @@ public class AcquisitionMain {
             	iterations = Integer.parseInt(line.getOptionValue(o_iterations.getOpt()));
             }
 		
-			// Variables
-			if( line.hasOption(o_variables.getOpt()) ){
-				String variables = line.getOptionValue(o_variables.getOpt() );
-				String[] vars = variables.split(",");
-				for(String varp:vars){
-					String[] pair = varp.split("=");
-					if(pair.length!=2){
-						throw new ParseException("Variables are not specified the correct way. -variables var1=val1,var2=val2");
-					}
-					varTable.put(pair[0], pair[1]);
-				}
-			}
-			
 			// Autoclose option
             if( line.hasOption( o_autoclose.getOpt() ) ) {
                 autoclose = true;
@@ -175,7 +151,7 @@ public class AcquisitionMain {
         // Run application
         try{
         	for(String file: files){
-        		run(new File(file), iterations, autoclose, nogui, varTable);
+        		run(new File(file), iterations, autoclose, nogui);
         	}
         	
     		// Close application automatically if autoclose option is set (and visualizations are specified)
@@ -200,7 +176,7 @@ public class AcquisitionMain {
 	 * @param nogui			Flag whether to run the scan with a GUI
 	 * @param variables		Table of scan variables
 	 */
-	public static void run(File file, Integer iterations, boolean autoclose, boolean nogui, HashMap<String,String> variables){
+	public static void run(File file, Integer iterations, boolean autoclose, boolean nogui){
 		
 		// Initialize application
 		ApplicationConfigurator ac = new ApplicationConfigurator();