diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
old mode 100644
new mode 100755
index 7d20dad47afc6e667ccf51e711464dd3cdd4bed9..7f7804b17d1d1c868355faae5c309f9b0f7d9be5
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -7,8 +7,8 @@ if JOBDIR[-1] != "/": # this checks if jobdir ends with slash if not it adds a s
    JOBDIR+="/"
 
 #data specific config file, expected to be inside JOBDIR
-configfile: "tomancak_test_cluster.json"
-# configfile: "tomancak_test_cluster.yaml"
+# configfile: "tomancak_test_cluster.json"
+configfile: "tomancak_test_cluster.yaml"
 
 
 padding_format = "{0:0"+str(padding_of_file_id(int(config["common"]["ntimepoints"])))+"d}"
@@ -34,20 +34,15 @@ rule define_xml_czi:
         cmd_string = produce_string("""{fiji-prefix} {fiji-app} \
         -Dimage_file_directory={jdir} \
            -Dfirst_czi={first_czi} \
-           -Dangle_1={angle_1} \
-           -Dangle_2={angle_2} \
-           -Dangle_3={angle_3} \
-           -Dangle_4={angle_4} \
-           -Dangle_5={angle_5} \
-           -Dchannel_1={channel_1} \
-           -Dchannel_2={channel_2} \
-           -Dillumination_1={illumination_1} \
-           -Drotation_around={rotation_around} \
+           -Dangles={angles} \
+           -Dchannels={channels} \
+           -Dillumination={illumination} \
            -Dpixel_distance_x={pixel_distance_x} \
            -Dpixel_distance_y={pixel_distance_y} \
            -Dpixel_distance_z={pixel_distance_z} \
            -Dpixel_unit={pixel_unit} \
            -Dfirst_xml_filename={first_xml_filename} \
+           -Drotation_around={rotation_around} \
            -- --no-splash {path_bsh}""",
                                        config["common"],
                                        config["define_xml_czi"],
@@ -68,8 +63,9 @@ rule define_xml_tif:
         	"""{fiji-prefix} {fiji-app} \
         -Dimage_file_directory={jdir} \
         -Dtimepoints={timepoints} \
-        -Dacquisition_angles={acquisition_angles} \
+        -Dangles={angles} \
         -Dchannels={channels} \
+        -Dillumination={illumination} \
         -Dimage_file_pattern={image_file_pattern} \
         -Dpixel_distance_x={pixel_distance_x} \
         -Dpixel_distance_y={pixel_distance_y} \
diff --git a/spim_registration/timelapse/define_czi.bsh b/spim_registration/timelapse/define_czi.bsh
old mode 100644
new mode 100755
index 74afeb13157ffa770376eed588bc2f6681682238..6432e33bceaf9895d442df2539d977470c9e4829
--- a/spim_registration/timelapse/define_czi.bsh
+++ b/spim_registration/timelapse/define_czi.bsh
@@ -26,25 +26,93 @@ System.out.println( "first_czi_path = " + image_file_directory + first_czi );
 
 // Dataset settings
 System.out.println("---------------------------------------------------------");
-System.out.println("Dataset:");
-angle_1 = System.getProperty( "angle_1" );
-angle_2 = System.getProperty( "angle_2" );
-angle_3 = System.getProperty( "angle_3" );
-angle_4 = System.getProperty( "angle_4" );
-angle_5 = System.getProperty( "angle_5" );
-channel_1 = System.getProperty( "channel_1" );
-channel_2 = System.getProperty( "channel_2" );
-illumination_1 = System.getProperty( "illumination_1" );
-rotation_around = System.getProperty( "rotation_around" );
+System.out.println("Angle Settings:");
+
+// Angle settings
+// Parses angles and determines the number of angles
+// uses tokens of string angles to assemble the string for angle_string
+// via StringBuilder
+angles = System.getProperty( "angles" );
+System.out.println( "Angles = " + angles );
+
+// Parses string angles
+String delims = "[,]";
+String[] angle_token = angles.split(delims);
+
+// Builds string using the number of tokens and inserts the tokens in the string
+StringBuilder angle_string = new StringBuilder();
+String angle_part;
+
+	for ( int angle = 0; angle < angle_token.length; angle++) {
+		int num_angles = angle + 1;
+		angle_part = "angle_" + num_angles + "=" + angle_token[angle];
+		angle_string.append(angle_part);
+		angle_string.append(" ");
+			
+		}
+
+System.out.println( angle_string );
+
+System.out.println("---------------------------------------------------------");
+System.out.println("Channel Settings:");
+
+// Channel settings
+// This parses channels and determines the number of channels
+// then uses the tokens of channels to assemble the necessary string
+// for channel_string via StringBuilder
+channels = System.getProperty( "channels" );
+System.out.println( "Channel Names = " + channels );
+
+// Parses string channel_names
+String delims = "[,]";
+String[] channel_token = channels.split(delims);
+
+// Builds string using the number of tokens and inserts the tokens in the string
+StringBuilder channel_string = new StringBuilder();
+String channel_part;
+
+	for ( int channel = 0; channel < channel_token.length; channel++) {
+		int num_channel = channel + 1;
+		channel_part = "channel_" + num_channel + "=" + channel_token[channel];
+		channel_string.append(channel_part);
+		channel_string.append(" ");
+			
+		}
+			
+System.out.println( "Channel String = " + channel_string );
+
+System.out.println("---------------------------------------------------------");
+System.out.println("Illumination Settings:");
+
+// Illuminatin settings
+// This parses illumination and determines the number of illuminations
+// then uses the tokens of illuminations to assemble the string for 
+// illum_string via StringBuilder
+illumination = System.getProperty( "illumination" );
+System.out.println( "Illumination = " + illumination );
+
+// Parses string illumination
+String delims = "[,]";
+String[] illum_token = illumination.split(delims);
+
+// Builds string using the number of tokens and inserts the tokens in the string
+StringBuilder illum_string = new StringBuilder();
+String illum_part;
 
-System.out.println( "angle_1 = " + angle_1 );
-System.out.println( "angle_2 = " + angle_2 );
-System.out.println( "angle_3 = " + angle_3 );
-System.out.println( "angle_4 = " + angle_4 );
-System.out.println( "angle_5 = " + angle_5 );
-System.out.println( "channel_1 = " + channel_1 );
-System.out.println( "channel_2 = " + channel_2 );
-System.out.println( "illumination_1 = " + illumination_1 );
+	for ( int illum= 0; illum< illum_token.length; illum++) {
+		int num_illum = illum + 1;
+		illum_part = "_______illumination_" + num_illum + "=" + illum_token[illum];
+		illum_string.append(illum_part);
+		illum_string.append(" ");
+			
+		}
+
+System.out.println( illum_string );
+
+System.out.println("---------------------------------------------------------");
+System.out.println("Rotation setting:");
+
+rotation_around = System.getProperty( "rotation_around" );
 System.out.println( "rotation_around = " + rotation_around );
 
 // Calibaration
@@ -63,19 +131,29 @@ System.out.println( "pixel_unit = " + pixel_unit );
 // Executes Fiji plugin
 System.out.println("=========================================================");
 System.out.println("Start plugin:");
+System.out.println("Define Multi-View Dataset type_of_dataset=[Zeiss Lightsheet Z.1 Dataset (LOCI Bioformats)] " +
+	"xml_filename=" + first_xml_filename + ".xml " +
+	"browse=" + image_file_directory + first_czi + " " + 
+	"first_czi=" + image_file_directory + first_czi + " " + 
+	angle_string +
+	channel_string + 
+ 	illum_string +
+	"modify_calibration " + 
+	"modify_rotation_axis " +
+	"pixel_distance_x=" + pixel_distance_x + " " + 
+	"pixel_distance_y=" + pixel_distance_y + " " + 
+	"pixel_distance_z=" + pixel_distance_z + " " +
+	"pixel_unit=" + pixel_unit + " " +
+	"rotation_around=" + rotation_around + "");
+
 IJ.run("Define Multi-View Dataset", 
 	"type_of_dataset=[Zeiss Lightsheet Z.1 Dataset (LOCI Bioformats)] " +
 	"xml_filename=" + first_xml_filename + ".xml " +
 	"browse=" + image_file_directory + first_czi + " " + 
 	"first_czi=" + image_file_directory + first_czi + " " + 
-	"angle_1=" + angle_1 + " " +
-	"angle_2=" + angle_2 + " " + 
-	"angle_3=" + angle_3 + " " +
-	"angle_4=" + angle_4 + " " + 
-	"angle_5=" + angle_5 + " " +
-	"channel_1=" + channel_1 + " " +
-//	"channel_2=" + channel_2 + " " + // for dual channel comment out if single channel
- 	"_______illumination_1=" + illumination_1 + " " +
+	angle_string +
+	channel_string + 
+	illum_string +
 	"modify_calibration " + 
 	"modify_rotation_axis " +
 	"pixel_distance_x=" + pixel_distance_x + " " + 
diff --git a/spim_registration/timelapse/define_tif_zip.bsh b/spim_registration/timelapse/define_tif_zip.bsh
old mode 100644
new mode 100755
index f03b52fec9445b4a3408983a8ade1af437162245..37f129b732c30616f6a8ff7cbbad92bf0b078716
--- a/spim_registration/timelapse/define_tif_zip.bsh
+++ b/spim_registration/timelapse/define_tif_zip.bsh
@@ -24,28 +24,91 @@ System.out.println( "xml_filename = " + xml_filename );
 // Dataset settings
 System.out.println("=========================================================");
 System.out.println("Dataset:");
-timepoints = System.getProperty( "timepoints" );
-channels = System.getProperty( "channels" ); 
-acquisition_angles = System.getProperty( "acquisition_angles" );
 image_file_pattern = System.getProperty( "image_file_pattern" );
 type_of_dataset = System.getProperty( "type_of_dataset" );
+timepoints = System.getProperty( "timepoints" );
+angles = System.getProperty( "angles" );
+
+System.out.println( "image_file_pattern = " + image_file_pattern );
+System.out.println( "type_of_dataset = " + type_of_dataset );
+System.out.println( "timepoints = " + timepoints );
+System.out.println( "angles = " + angles );
+
 multiple_timepoints = System.getProperty( "multiple_timepoints" );
 multiple_channels = System.getProperty( "multiple_channels" );
 multiple_illumination_directions = System.getProperty( "multiple_illumination_directions" );
 multiple_angles = System.getProperty( "multiple_angles" );
 imglib_container = System.getProperty( "imglib_container" );
 
-System.out.println( "timepoints = " + timepoints );
-System.out.println( "channels = " + channels );
-System.out.println( "acquisition_angles = " + acquisition_angles );
-System.out.println( "image_file_pattern = " + image_file_pattern );
-System.out.println( "type_of_dataset = " + type_of_dataset );
 System.out.println( "multiple_timepoints = " + multiple_timepoints );
 System.out.println( "multiple_channels = " + multiple_channels );
 System.out.println( "multiple_illumination_directions = " + multiple_illumination_directions );
 System.out.println( "multiple_angles = " + multiple_angles );
 System.out.println( "imglib_container = " + imglib_container );
 
+System.out.println("---------------------------------------------------------");
+System.out.println("Channel setting:");
+
+// Channel switch: parses channels and determines if Single or Multi Channel
+// assembles the appropriate string for the channel setting
+channels = System.getProperty( "channels" ); 
+
+String channel_string = null;
+		
+String delims = "[,]";
+String[] channel_token = channels.split(delims);
+		
+if (channels.equalsIgnoreCase(""))
+	{
+	System.out.println("Warning: There are no channels set");
+	}
+			
+else if ( channel_token.length == 1  )
+	{
+	channel_string="";
+	System.out.println("Single Channel");
+	}
+		
+	else if ( channel_token.length > 1)
+	{
+	channel_string = "channels_=" + channels + " ";
+	System.out.println("Multi Channel");
+	}
+		
+System.out.println( "Channels = " + channel_string );
+
+
+System.out.println("---------------------------------------------------------");
+System.out.println("Illumination setting:");
+// Illuminatin switch: parses illumination and determines if there is a single
+// or multiple illumination sides and then assembles the illum_string
+
+illumination = System.getProperty( "illumination" );
+
+String illum_string = null;
+		
+String delims = "[,]";
+String[] illum_token = illumination.split(delims);
+		
+if (illumination.equalsIgnoreCase(""))
+	{
+	System.out.println("Warning: There are no illuminations set");
+	}
+			
+	else if ( illum_token.length == 1  )
+	{
+	illum_string="";
+	System.out.println("One illumination side or fused illumination");
+	}
+		
+	else if ( illum_token.length > 1)
+	{
+	illum_string = "illumination_=" + illumination + " ";
+	System.out.println("Dual Illumination sides");
+	}
+		
+System.out.println( "Illuminations = " + illum_string );
+
 // Calibaration
 System.out.println("=========================================================");
 System.out.println("Calibration:");
@@ -59,6 +122,26 @@ System.out.println( "pixel_distance_y = " + pixel_distance_y );
 System.out.println( "pixel_distance_z = " + pixel_distance_z );
 System.out.println( "pixel_unit = " + pixel_unit );
 
+
+System.out.println("Define Multi-View Dataset , type_of_dataset=[" + type_of_dataset + "] " +
+	"xml_filename=[" + xml_filename + ".xml] " +
+	"multiple_timepoints=[" + multiple_timepoints + "] " +
+	"multiple_channels=[" + multiple_channels + "] " +
+	"_____multiple_illumination_directions=[" + multiple_illumination_directions + "] " + 
+	"multiple_angles=[" + multiple_angles + "] " +
+	"image_file_directory=" + image_file_directory + " " +
+	"image_file_pattern=" + image_file_pattern + " " + 
+	"timepoints_=" + timepoints + " " +
+	channel_string +
+	illum_string +
+	"acquisition_angles_=" + acquisition_angles + " " +  
+	"calibration_type=[Same voxel-size for all views] calibration_definition=[User define voxel-size(s)]" + " " + 
+	"imglib2_data_container=[" + imglib_container + "] " + 
+	"pixel_distance_x=" + pixel_distance_x + " " + 
+	"pixel_distance_y=" + pixel_distance_y + " " + 
+	"pixel_distance_z=" + pixel_distance_z + " " +
+	"pixel_unit=" + pixel_unit + "");
+
 // Executes Fiji plugin
 System.out.println("=========================================================");
 System.out.println("Start plugin:");
@@ -72,8 +155,9 @@ IJ.run("Define Multi-View Dataset",
 	"image_file_directory=" + image_file_directory + " " +
 	"image_file_pattern=" + image_file_pattern + " " + 
 	"timepoints_=" + timepoints + " " +
-//	"channels_=" + channels	+ " " +		// for dual channel comment out if single channel
-	"acquisition_angles_=" + acquisition_angles + " " +  
+	channel_string +
+	illum_string +
+	"acquisition_angles_=" + angles + " " +  
 	"calibration_type=[Same voxel-size for all views] calibration_definition=[User define voxel-size(s)]" + " " + 
 	"imglib2_data_container=[" + imglib_container + "] " + 
 	"pixel_distance_x=" + pixel_distance_x + " " + 
diff --git a/spim_registration/timelapse/tomancak_test_cluster.yaml b/spim_registration/timelapse/tomancak_test_cluster.yaml
old mode 100644
new mode 100755
index fa7788278a9544938599cef4df97a171c7445811..975904f3ff5e851da35dec321762d84fb969f732
--- a/spim_registration/timelapse/tomancak_test_cluster.yaml
+++ b/spim_registration/timelapse/tomancak_test_cluster.yaml
@@ -1,95 +1,91 @@
-common:
-  {
+common: {
   # directory that contains the bean shell scripts
-  bsh_directory: "/home/steinbac/development/schmied-snakemake-workflows/spim_registration/timelapse/",
-  directory_cuda: "/lustre/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/lib/",
-  fiji-app: "/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/ImageJ-linux64",
+  bsh_directory: "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/",
+  directory_cuda: "/sw/users/schmied/packages/2015-06-08_Fiji.app.cuda/lib/lib/",
+  fiji-app: "/sw/users/schmied/packages/2015-06-08_Fiji.app.cuda/ImageJ-linux64",
   fiji-prefix: "/sw/bin/xvfb-run -a",
   first_xml_filename: "test_unicore",
-  fusion_switch: "deconvolution",
   hdf5_xml_filename: '"hdf5_test_unicore"',
   merged_xml: "hdf5_test_unicore_merge",
-  ntimepoints: 5
-  }
-      
-deconvolution:
-  {
-  Tikhonov_parameter: '0.0006',
-  bsh_file: "deconvolution_GPU.bsh",
-  compute: '"in 512x512x512 blocks"',
-  compute_on: '"GPU (Nvidia CUDA via JNA)"',
-  detections_to_extract_psf_for_channel_0: '"beads"',
-  detections_to_extract_psf_for_channel_1: '"beads"',
-  imglib2_container: '"ArrayImg"',
-  iterations: '5',
-  maximal_x: '509',
-  maximal_y: '970',
-  maximal_z: '243',
-  minimal_x: '95',
-  minimal_y: '-8',
-  minimal_z: '-174',
-  osem_acceleration: '"1 (balanced)"',
-  process_angle: '"All angles"',
-  process_channel: '"All channels"',
-  process_illumination: '"All illuminations"',
-  process_timepoint: '"Single Timepoint (Select from List)"',
-  psf_estimation: '"Extract from beads"',
-  psf_size_x: '19',
-  psf_size_y: '19',
-  psf_size_z: '25',
-  type_of_iteration: '"Efficient Bayesian - Optimization I (fast, precise)"'
-  }
-        
-define_xml_czi:
-  {
-  angle_1: '0',
-  angle_2: '72',
-  angle_3: '144',
-  angle_4: '216',
-  angle_5: '288',
-  bsh_file: "define_czi.bsh",
-  channel_1: "green",
-  channel_2: "red",
-  first_czi: "2015-04-11_LZ2_Stock68_3.czi",
-  illumination_1: '0',
+  ntimepoints: 5,
+  angles: "0,72,144,216,288",
+  channels: "green",
+  illumination: "0",
   pixel_distance_x: '0.28590106964',
   pixel_distance_y: '0.28590106964',
   pixel_distance_z: '1.50000',
   pixel_unit: "um",
-  rotation_around: "X-Axis"
+  fusion_switch: "deconvolution"
+  }
+              
+define_xml_czi: {
+  first_czi: "2015-04-11_LZ2_Stock68_3.czi",
+  rotation_around: "X-Axis",
+  bsh_file: "define_czi.bsh"
   }
           
-define_xml_tif:
-  {
-  acquisition_angles: '0,72,144,216,288',
-  bsh_file: "define_tif_zip.bsh",
-  channels: '0',
+define_xml_tif: {
   image_file_pattern: 'img_TL{{t}}_Angle{{a}}.tif',
   imglib_container: '"ArrayImg (faster)"',
   multiple_angles: '"YES (one file per angle)"',
   multiple_channels: '"NO (one channel)"',
   multiple_illumination_directions: '"NO (one illumination direction)"',
   multiple_timepoints: '"YES (one file per time-point)"',
-  pixel_distance_x: '0.28590106964',
-  pixel_distance_y: '0.28590106964',
-  pixel_distance_z: '1.50000',
-  pixel_unit: "um",
-  type_of_dataset: '"Image Stacks (ImageJ Opener)"'
+  type_of_dataset: '"Image Stacks (ImageJ Opener)"',
+  bsh_file: "define_tif_zip.bsh"
+  }
+  
+resave_hdf5: {
+  bsh_file: "export.bsh",
+  hdf5_chunk_sizes: '"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}"',
+  resave_angle: '"All angles"',
+  resave_channel: '"All channels"',
+  resave_illumination: '"All illuminations"',
+  resave_timepoint: '"All Timepoints"',
+  setups_per_partition: '0',
+  subsampling_factors: '"{{ {{1,1,1}}, {{2,2,1}}, {{4,4,1}}, {{8,8,1}} }}"',
+  timepoints_per_partition: '1'
   }
 
-        
-external_transform:
-  {
+registration: {
+  algorithm: '"Fast 3d geometric hashing (rotation invariant)"',
+  allowed_error_for_ransac: '5',
   angle: '"All angles"',
-  apply_transformation: '"Current view transformations
-  (appends to current transforms)"',
-  bsh_file: "transform.bsh",
+  bsh_file: "registration.bsh",
   channel: '"All channels"',
-  define_mode_transform: '"Matrix"',
-  illumination: '"All illuminations"',
-  matrix_transform: '"0.5, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0"',
-  timepoint: '"All Timepoints"',
-  transformation: '"Rigid"'
+  detection_min_max: "find_maxima",
+  fix_tiles: '"Fix first tile"',
+  illuminations: '"All illuminations"',
+  imglib_container: '"ArrayImg (faster)"',
+  initial_sigma: '1.8',
+  interest_points_channel_0: '"beads"',
+  interest_points_channel_1: '"beads"',
+  label_interest_points: '"beads"',
+  lambda: '0.10',
+  map_back_tiles: '"Map back to first tile using rigid model"',
+  model_to_regularize_with: "Rigid",
+  proc-ch: '"channel 0"',
+  radius_1: '2',
+  radius_2: '3',
+  significance: '10',
+  subpixel_localization: '"3-dimensional quadratic fit"',
+  threshold: '0.005',
+  threshold_gaussian: '0.0080',
+  timepoint: '"Single Timepoint (Select from List)"',
+  transformation_model: "Affine",
+  type_of_detection: '"Difference-of-Mean (Integral image based)"',
+  type_of_registration: '"Register timepoints individually"'
+  }
+
+xml_merge: {
+  bsh_file: "xml_merge.bsh"
+  }
+  
+timelapse: {
+  bsh_file: "timelapse_registration.bsh",
+  reference_timepoint: '0',
+  timelapse_process_timepoints: '"All Timepoints"',
+  type_of_registration_timelapse: '"Match against one reference timepoint (no global optimization)"'
   }
   
 fusion: {
@@ -113,6 +109,46 @@ fusion: {
   process_views_in_paralell: '"All"',
   xml_output: '"Save every XML with user-provided unique id"'
   }
+
+external_transform: {
+  angle: '"All angles"',
+  apply_transformation: '"Current view transformations
+  (appends to current transforms)"',
+  bsh_file: "transform.bsh",
+  channel: '"All channels"',
+  define_mode_transform: '"Matrix"',
+  illumination: '"All illuminations"',
+  matrix_transform: '"0.5, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0"',
+  timepoint: '"All Timepoints"',
+  transformation: '"Rigid"'
+  }
+
+deconvolution: {
+  Tikhonov_parameter: '0.0006',
+  bsh_file: "deconvolution_GPU.bsh",
+  compute: '"in 512x512x512 blocks"',
+  compute_on: '"GPU (Nvidia CUDA via JNA)"',
+  detections_to_extract_psf_for_channel_0: '"beads"',
+  detections_to_extract_psf_for_channel_1: '"beads"',
+  imglib2_container: '"ArrayImg"',
+  iterations: '5',
+  maximal_x: '509',
+  maximal_y: '970',
+  maximal_z: '243',
+  minimal_x: '95',
+  minimal_y: '-8',
+  minimal_z: '-174',
+  osem_acceleration: '"1 (balanced)"',
+  process_angle: '"All angles"',
+  process_channel: '"All channels"',
+  process_illumination: '"All illuminations"',
+  process_timepoint: '"Single Timepoint (Select from List)"',
+  psf_estimation: '"Extract from beads"',
+  psf_size_x: '19',
+  psf_size_y: '19',
+  psf_size_z: '25',
+  type_of_iteration: '"Efficient Bayesian - Optimization I (fast, precise)"'
+  }
   
 hdf5_output: {
   bsh_file_define: "define_output.bsh",
@@ -133,57 +169,6 @@ hdf5_output: {
   output_pixel_unit: 'um',
   output_timepoints: '0-4',
   output_type_of_dataset: '"Image Stacks (ImageJ Opener)"',
-  output_xml: '"fused_Dual_Channel"'}
-
-registration: {
-  algorithm: '"Fast 3d geometric hashing (rotation invariant)"',
-  allowed_error_for_ransac: '5',
-  angle: '"All angles"',
-  bsh_file: "registration.bsh",
-  channel: '"All channels"',
-  detection_min_max: "find_maxima",
-  fix_tiles: '"Fix first tile"',
-  illuminations: '"All illuminations"',
-  imglib_container: '"ArrayImg (faster)"',
-  initial_sigma: '1.8',
-  interest_points_channel_0: '"beads"',
-  interest_points_channel_1: '"beads"',
-  label_interest_points: '"beads"',
-  lambda: '0.10',
-  map_back_tiles: '"Map back to first tile using rigid model"',
-  model_to_regularize_with: "Rigid",
-  proc-ch: '"channel 0"',
-  radius_1: '2',
-  radius_2: '3',
-  significance: '10',
-  subpixel_localization: '"3-dimensional quadratic fit"',
-  threshold: '0.005',
-  threshold_gaussian: '0.0080',
-  timepoint: '"Single Timepoint (Select from List)"',
-  transformation_model: "Affine",
-  type_of_detection: '"Difference-of-Mean (Integral image based)"',
-  type_of_registration: '"Register timepoints individually"'
-  }
-
-resave_hdf5: {
-  bsh_file: "export.bsh",
-  hdf5_chunk_sizes: '"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}"',
-  resave_angle: '"All angles"',
-  resave_channel: '"All channels"',
-  resave_illumination: '"All illuminations"',
-  resave_timepoint: '"All Timepoints"',
-  setups_per_partition: '0',
-  subsampling_factors: '"{{ {{1,1,1}}, {{2,2,1}}, {{4,4,1}}, {{8,8,1}} }}"',
-  timepoints_per_partition: '1'}
-
-timelapse: {
-  bsh_file: "timelapse_registration.bsh",
-  reference_timepoint: '0',
-  timelapse_process_timepoints: '"All Timepoints"',
-  type_of_registration_timelapse: '"Match against one reference timepoint (no global optimization)"'
-  }
-
-xml_merge: {
-  bsh_file: "xml_merge.bsh"
+  output_xml: '"fused_Dual_Channel"'
   }