Merge pull request #3 from schmiedc/newswitches

Newswitches

spim_registration/timelapse/Snakefile

@@ -6,9 +6,13 @@ JOBDIR=os.path.abspath(os.path.curdir)
 if JOBDIR[-1] != "/": # this checks if jobdir ends with slash if not it adds a slash
    JOBDIR+="/"
 
-#data specific config file, expected to be inside JOBDIR
-# configfile: "tomancak_test_cluster.json"
-configfile: "tomancak_test_cluster.yaml"
+# Test config file single Channel:
+# configfile: "single_test.yaml"
+# Test config file dual channel one channel contains beads:
+configfile: "dual_OneChannel.yaml"
+
+# data specific config file, expected to be inside JOBDIR
+# configfile: "tomancak_test_cluster.yaml"
 
 
 padding_format = "{0:0"+str(padding_of_file_id(int(config["common"]["ntimepoints"])))+"d}"
@@ -179,9 +183,15 @@ rule registration:
 	-Dreg_radius_1={reg_radius_1} \
 	-Dreg_radius_2={reg_radius_2} \
         -Dreg_threshold={reg_threshold} \
-        -Dinitial_sigma={initial_sigma} \
+        -Dsigma={sigma} \
         -Dthreshold_gaussian={threshold_gaussian} \
-        -Dregistration_algorithm={algorithm} \
+        -Dcompute_on={compute_on} \
+	-Ddirectory_cuda={directory_cuda} \
+	-Dseparableconvolution={separableconvolution} \
+	-Ddownsample_detection={downsample_detection} \
+	-Ddownsample_xy={downsample_xy} \
+	-Ddownsample_z={downsample_z} \
+	-Dregistration_algorithm={algorithm} \
         -Dreg_interest_points_channel={reg_interest_points_channel} \
         -Dfix_tiles={fix_tiles} \
         -Dmap_back_tiles={map_back_tiles} \
@@ -254,10 +264,10 @@ rule timelapse:
         cmd_string += " > {log} 2>&1 && touch {output}"
         shell(cmd_string)
 
-rule dublicate_transformations:
+rule duplicate_transformations:
     input: rules.timelapse.output, merged_xml="{xml_base}_merge.xml"
-    output: rules.timelapse.output[0] + "_dublicate"
-    log: "{xml_base}_dublicate_transformations.log"
+    output: rules.timelapse.output[0] + "_duplicate"
+    log: "{xml_base}_duplicate_transformations.log"
     run:
         cmd_string = produce_string(
         	"""{fiji-prefix} {fiji-app} \
@@ -296,7 +306,6 @@ rule fusion:
     	-Dprocess_illumination={process_illumination} \
     	-Dprocess_angle={process_angle} \
     	-Dxml_output={xml_output} \
-    	-Dfused_image={fused_image} \
     	-Dminimal_x={minimal_x} \
     	-Dminimal_y={minimal_y} \
     	-Dminimal_z={minimal_z} \
@@ -380,7 +389,9 @@ rule deconvolution:
         -Dosem_acceleration={osem_acceleration} \
         -DTikhonov_parameter={Tikhonov_parameter} \
         -Dcompute={compute} \
-        -Dpsf_estimation={psf_estimation} \
+        -Dcompute_on={compute_on} \
+        -Dcudafourierconvolution={cudafourierconvolution} \
+	-Dpsf_estimation={psf_estimation} \
         -Ddirectory_cuda={directory_cuda} \
         -Ddetections_to_extract_psf_for_channel={detections_to_extract_psf_for_channel} \
         -Dpsf_size_x={psf_size_x} \

spim_registration/timelapse/cluster.json

@@ -4,7 +4,12 @@
 	"lsf_extra" : "-R \"span[hosts=1]\"",
 	"lsf_q" : "short"	
     },
- 
+
+    "resave_hdf5" :	
+    {
+ 	"lsf_extra" : "-n 7 -R \"span[hosts=1] rusage[mem=50000]\""
+    },
+
     "registration" :
     {
         "lsf_extra" : "-R \"span[hosts=1] rusage[mem=100000]\""
@@ -20,6 +25,11 @@
         "lsf_extra" : "-R \"span[hosts=1] rusage[mem=10000]\""
     },
 
+    "fusion" : 
+    {
+        "lsf_extra" : "-n 12 -R \"span[hosts=1] rusage[mem=100000]\""
+    },
+
     "deconvolution" :
     {
         "lsf_extra" : "-n 7 -R \"span[hosts=1] rusage[mem=50000]\"",

spim_registration/timelapse/deconvolution_GPU.bsh → spim_registration/timelapse/deconvolution.bsh

@@ -4,11 +4,11 @@ import ij.Prefs; 	// calls imagej settings
 import java.lang.Runtime;
 import java.io.File;
 import java.io.FilenameFilter;
- 
+
 runtime = Runtime.getRuntime();
 System.out.println(runtime.availableProcessors() + " cores available for multi-threading");
 
-Prefs.setThreads(7); 	// defines the number of threads allowed 
+Prefs.setThreads(7); 	// defines the number of threads allowed
 print("Threads: "+Prefs.getThreads()); // prints thread setting in output
 
 System.out.println( "Start to load Parameters:" );
@@ -27,13 +27,12 @@ int parallel_timepoints = Integer.parseInt(System.getProperty( "parallel_timepoi
 process_timepoint = System.getProperty( "process_timepoint" );
 process_channel = System.getProperty( "process_channel" );
 process_illumination = System.getProperty( "process_illumination" );
-process_angle = System.getProperty( "process_angle" ); 
-
+process_angle = System.getProperty( "process_angle" );
 
 System.out.println( "-------------------------------------------------------" );
 System.out.println( "General parameters: " );
 System.out.println( "timepoint_processed = " + parallel_timepoints );
-System.out.println( "process_timepoints = " + process_timepoint ); 
+System.out.println( "process_timepoints = " + process_timepoint );
 System.out.println( "process_channel = " + process_channel );
 System.out.println( "process_illumination = " + process_illumination );
 System.out.println( "process_angle = " + process_angle );
@@ -66,7 +65,6 @@ psf_estimation = System.getProperty( "psf_estimation" );
 iterations = System.getProperty( "iterations" );
 deco_output_file_directory = System.getProperty( "deco_output_file_directory" );
 
-
 System.out.println( "-------------------------------------------------------" );
 System.out.println( "Deconvolution settings: " );
 System.out.println( "imglib2_container = " + imglib2_container_deco );
@@ -78,12 +76,6 @@ System.out.println( "psf_estimation = " + psf_estimation );
 System.out.println( "number_of_iterations = " + iterations );
 System.out.println( "deco_output_file_directory = " + deco_output_file_directory );
 
-// Search for CUDA
-System.out.println( "-------------------------------------------------------" );
-System.out.println( "Loading CUDA directory: " );
-directory_cuda = System.getProperty( "directory_cuda" );
-System.out.println( "directory_cuda = " + directory_cuda );
-
 // PSF Parameters
 psf_size_x = System.getProperty( "psf_size_x" );
 psf_size_y = System.getProperty( "psf_size_y" );
@@ -101,24 +93,24 @@ System.out.println( "-------------------------------------------------------" );
 System.out.println( "Channel Settings: " );
 // Channel setting for Deconvolution
 // parses channels and takes from there the number of channels
-// parses detections_to_extract_psf_for_channel 
+// parses detections_to_extract_psf_for_channel
 channels = System.getProperty( "channels" );
-System.out.println( "Channels = " + channels ); 
+System.out.println( "Channels = " + channels );
 
 detections_to_extract_psf_for_channel = System.getProperty( "detections_to_extract_psf_for_channel" );
 System.out.println( "PSF: " + detections_to_extract_psf_for_channel );
 
-// Splits channels and detections_to_extract_psf_for_channel 
+// Splits channels and detections_to_extract_psf_for_channel
 String delims = "[,]";
 String[] channel_token = channels.split(delims);
 String[] psf_token = detections_to_extract_psf_for_channel.split(delims);
-		
-// Assembles channel_string 
+
+// Assembles channel_string
 StringBuilder channel_string = new StringBuilder();
 
 for (int channel=0; channel < channel_token.length; channel++ )
 
-{	
+{
 	String channel_part = "detections_to_extract_psf_for_channel_" + channel_token[channel] + "=" + psf_token[channel] + " ";
 	channel_string.append( channel_part );
 	channel_string.append(" ");
@@ -126,6 +118,45 @@ for (int channel=0; channel < channel_token.length; channel++ )
 
 System.out.println( channel_string );
 
+// GPU/CPU setting
+System.out.println( "-------------------------------------------------------" );
+System.out.println( "GPU/CPU setting: " );
+
+compute_on = System.getProperty( "compute_on" );
+directory_cuda = System.getProperty( "directory_cuda" );
+cudafourierconvolution = System.getProperty( "cudafourierconvolution" );
+
+System.out.println( "compute_on = " + compute_on );
+System.out.println( "directory_cuda = " + directory_cuda  );
+System.out.println( "cudafourierconvolution = " + cudafourierconvolution );
+
+String compute_string = "";
+String cuda_settings = "";
+
+if (compute_on.equalsIgnoreCase( "GPU (Nvidia CUDA via JNA)" ) )
+{
+	System.out.println( "GPU deconvoultion selected" );
+	compute_string = "compute_on=[GPU (Nvidia CUDA via JNA)] ";
+	cuda_settings = "cuda_directory=" + directory_cuda + " " +
+			"select_native_library_for_cudafourierconvolution=" + cudafourierconvolution + " " +
+			"gpu_1 ";
+}
+
+else if (compute_on.equalsIgnoreCase( "CPU (Java)" ) )
+{
+	System.out.println( "CPU deconvoultion selected" );
+	compute_string = "compute_on=[" + compute_on + "] ";
+	cuda_settings  = "";
+}
+			
+else 
+{
+	System.out.println( "Deconvolution GPU/CPU selection bad" );
+}
+					
+System.out.println( "compute_string=" + compute_string );
+System.out.println( "cuda_settings=" + cuda_settings );
+
 // Execute Fiji Plugin
 System.out.println( "=======================================================" );
 System.out.println( "Starting Deconvolution" );
@@ -154,24 +185,21 @@ IJ.run("Fuse/Deconvolve Dataset",
 	"use_tikhonov_regularization " +
 	"tikhonov_parameter=" + Tikhonov_parameter + " " +
 	"compute=[" + compute + "] " +
-	"compute_on=[GPU (Nvidia CUDA via JNA)] " +
+	compute_string +
 	"psf_estimation=[" + psf_estimation + "] " +
 	"psf_display=[Do not show PSFs] " +
 	"output_file_directory=" + deco_output_file_directory + " " +
-	"cuda_directory=[" + directory_cuda + "] " +
-	"select_native_library_for_cudafourierconvolution=libFourierConvolutionCUDALib.so " + 
-	"gpu_1 " +
+	cuda_settings +
 	channel_string +
 	"psf_size_x=" + psf_size_x + " " +
 	"psf_size_y=" + psf_size_y + " " +
 	"psf_size_z=" + psf_size_z + "");
 }
-catch ( e ) { 
+catch ( e ) {
 
     print( "[deconvolution-GPU] caught exception: "+e );
     //important to fail the process if exception occurs
     runtime.exit(1);
-    
 }
 
 /* shutdown */

spim_registration/timelapse/define_czi.bsh

@@ -48,7 +48,6 @@ String angle_part;
 		angle_part = "angle_" + num_angles + "=" + angle_token[angle];
 		angle_string.append(angle_part);
 		angle_string.append(" ");
-			
 		}
 
 System.out.println( angle_string );
@@ -76,9 +75,7 @@ String channel_part;
 		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("---------------------------------------------------------");
@@ -104,7 +101,6 @@ String illum_part;
 		illum_part = "_______illumination_" + num_illum + "=" + illum_token[illum];
 		illum_string.append(illum_part);
 		illum_string.append(" ");
-			
 		}
 
 System.out.println( illum_string );

spim_registration/timelapse/dual_OneChannel.yaml

+common: {
+  # directory that contains the bean shell scripts and Snakefile
+  bsh_directory: "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/", 
+  # Directory that contains the cuda libraries
+  directory_cuda: "/sw/users/schmied/cuda/",                                                          
+  # Directory that contains the current working Fiji
+  #fiji-app: "/sw/users/schmied/packages/2015-06-08_Fiji.app.cuda/ImageJ-linux64",
+  fiji-app: "/sw/users/schmied/packages/2015-05-29_Fiji_2.3.9_SNAP.app.cuda/ImageJ-linux64",          
+  fiji-prefix: "/sw/bin/xvfb-run -a",       # calls xvfb for Fiji headless mode
+  # xml file names without .xml suffix
+  first_xml_filename: "Dual_Channel",       # Name of the xml file for the .czi or .tif files
+  hdf5_xml_filename: '"hdf5_Dual_Channel"', # Name of .xml file for the hdf5 data after resave_hdf5
+  merged_xml: "hdf5_Dual_Channel_merge",    # Name of .xml file after merge
+  # Describe the dataset
+  ntimepoints: 2,               # number of timepoints of dataset
+  angles: "0,72,144,216,288",   # angles          
+  channels: "green,red",        # channels
+  illumination: "0",            # illuminations
+  pixel_distance_x: '0.28590',  # Manual calibration x
+  pixel_distance_y: '0.28590',  # Manual calibration y
+  pixel_distance_z: '1.50000',  # Manual calibration z
+  pixel_unit: "um",             # unit of manual calibration
+  # Use switches to decide which processing steps you need:
+  # transformation_switch: "timelapse" standard processing
+  # after timelapse registration directly goes into fusion, timelapse_duplicate
+  # "timelapse_duplicate" for dual channel processing one channel contains the beads
+  # duplicates transformations
+  transformation_switch: "timelapse_duplicate", 
+  # Switches between content based fusion and deconvoltion
+  # "deconvolution" > for deconvolution
+  # "fusion" > for content based fusion
+  fusion_switch: "fusion"
+  }
+
+define_xml_czi: {
+  first_czi: "2015-02-20_LZ2_Stock48_Stock58.czi", # master .czi file
+  rotation_around: "X-Axis",                       # axis of acquistion
+  bsh_file: "define_czi.bsh"                       # .bsh script for defining .czi file
+  }
+          
+define_xml_tif: {
+  # file pattern of .tif files
+  # for multi channel give spim_TL{tt}_Angle{a}_Channel{c}.tif
+  # # SPIM file pattern: for padded zeros use tt 
+  image_file_pattern: 'img_TL{{t}}_Angle{{a}}.tif', 
+  # Settings for ImageJ Opener
+  type_of_dataset: '"Image Stacks (ImageJ Opener)"',
+  multiple_timepoints: '"YES (one file per time-point)"', # or NO (one time-point)
+  multiple_angles: '"YES (one file per angle)"',          # or NO (one angle)
+  multiple_channels: '"NO (one channel)"',                # or "\"NO (one channel)\""
+  multiple_illumination_directions: '"NO (one illumination direction)"', # or YES (one file per illumination direction)
+  imglib_container: '"ArrayImg (faster)"',        # '"ArrayImg (faster)"'
+  bsh_file: "define_tif_zip.bsh"  
+  }
+  
+resave_hdf5: {
+  # Resaves .tif or .czi data into hdf5
+  # Subsampling and resolution settings for hdf5: data dependent
+  hdf5_chunk_sizes: '"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}"', 
+  subsampling_factors: '"{{ {{1,1,1}}, {{2,2,1}}, {{4,4,1}}, {{8,8,1}} }}"',  
+  # Standard settings for cluster processing
+  setups_per_partition: '0',
+  timepoints_per_partition: '1',
+  resave_timepoint: '"All Timepoints"',  
+  resave_angle: '"All angles"',
+  resave_channel: '"All channels"',
+  resave_illumination: '"All illuminations"',
+  bsh_file: "export.bsh"
+  }
+
+registration: {
+  # reg_process_channel:
+  # # Single Channel:  '"All channels"'
+  # Dual Channel: '"All channels"'
+  # Dual Channel one Channel contains beads: '"Single channel (Select from List)"'
+  reg_process_channel: '"Single channel (Select from List)"',
+  # reg_processing_channel:
+  # Dual Channel setting for 1 Channel contains the beads
+  reg_processing_channel: '"red"',      
+  # reg_interest_points_channel:
+  # Single Channel: '"beads"'
+  # Dual Channel: '"beads,beads"'
+  # Dual Channel: Channel does not contain the beads '"[DO NOT register this channel],beads"'
+  reg_interest_points_channel: '"beads"',
+  # type of detection: '"Difference-of-Mean (Integral image based)"' or '"Difference-of-Gaussian"'
+  type_of_detection: '"Difference-of-Mean (Integral image based)"',  
+  # Settings for Difference-of-Mean
+  # For multiple channels 'value1,value2' delimiter is ,
+  reg_radius_1: '2',          
+  reg_radius_2: '3',            
+  reg_threshold: '0.005',
+  # Settings for Difference-of-Gaussian
+  # For multiple channels 'value1,value2' delimiter is ,
+  sigma: '1.8',         
+  threshold_gaussian: '0.0080',   
+  # Processing setting for Difference-of-Gaussian detection
+  # compute_on:
+  compute_on: '"GPU accurate (Nvidia CUDA via JNA)"',
+  separableconvolution: '"libSeparableConvolutionCUDALib.so"',
+  # Downsampling settings
+  downsample_detection: "No", # "No" or "Yes"
+  downsample_xy: '"Match Z Resolution (less downsampling)"',
+  downsample_z: "1x",
+  # Standard Settings for bead based registration
+  label_interest_points: '"beads"',              
+  reg_process_timepoint: '"Single Timepoint (Select from List)"',
+  reg_process_angle: '"All angles"',
+  reg_process_illumination: '"All illuminations"',
+  subpixel_localization: '"3-dimensional quadratic fit"',
+  detection_min_max: "find_maxima",
+  type_of_registration: '"Register timepoints individually"',
+  algorithm: '"Fast 3d geometric hashing (rotation invariant)"',
+  transformation_model: "Affine",
+  allowed_error_for_ransac: '5',
+  significance: '10',
+  fix_tiles: '"Fix first tile"',
+  map_back_tiles: '"Map back to first tile using rigid model"',
+  model_to_regularize_with: "Rigid",
+  lambda: '0.10',
+  imglib_container: '"ArrayImg (faster)"',
+  bsh_file: "registration.bsh"  # .bsh script for registration
+  }
+
+xml_merge: {
+  bsh_file: "xml_merge.bsh"
+  }
+  
+timelapse: {
+  reference_timepoint: '0',   # Reference timepoint
+  # Standard settings for timelapse registration
+  type_of_registration_timelapse: '"Match against one reference timepoint (no global optimization)"',
+  timelapse_process_timepoints: '"All Timepoints"',
+  bsh_file: "timelapse_registration.bsh"
+  }
+  
+dublicate_transformations: {
+  # If dual channel processing and only one channel contains beads
+  # this allows you to dublicate the transformation for the 
+  # channel that does not contain beas
+  source_dublication: "red",  # source channel
+  target_dublication: "green", # target channel
+  duplicate_which_transformations: '"Replace all transformations"', # mode of dublication
+  bsh_file: "dublicate_transformations.bsh" # .bsh script for dublication
+  }
+  
+fusion: {
+  # content based multiview fusion
+  # supports multi channel without new settings
+  downsample: '1',  # set downsampling
+  # Cropping parameters of full resolution
+  minimal_x: '220', 
+  minimal_y: '40',  
+  minimal_z: '-290',  
+  maximal_x: '976',   
+  maximal_y: '1892',    
+  maximal_z: '472',   
+  # fused_image: '"Append to current XML Project"', does not work yet
+  process_timepoint: '"Single Timepoint (Select from List)"',
+  process_angle: '"All angles"',
+  process_channel: '"All channels"',
+  process_illumination: '"All illuminations"',
+  imglib2_container_fusion: '"ArrayImg"',
+  interpolation: '"Linear Interpolation"',
+  pixel_type: '"16-bit unsigned integer"',
+  imglib2_data_container: '"ArrayImg (faster)"',
+  process_views_in_paralell: '"All"',
+  xml_output: '"Save every XML with user-provided unique id"',
+  bsh_file: "fusion.bsh"
+  }
+
+external_transform: {
+  # Downsamples for deconvolution
+  # BUG: external transformation breaks .xml file
+  # channel setting: '"all_channels"'
+  channel_setting: '"green,red"',
+  transform_timepoint: '"All Timepoints"',
+  transform_angle: '"All angles"',
+  transform_channel: '"All channels"',
+  transform_illumination: '"All illuminations"',
+  apply_transformation: '"Current view transformations (appends to current transforms)"',
+  define_mode_transform: '"Matrix"',
+  # Matrix for downsampling
+  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"', 
+  transformation: '"Rigid"',
+  bsh_file: "transform.bsh"
+  }
+
+deconvolution: {
+  iterations: '1', # number of iterations
+  # Cropping parameters: take downsampling into account
+  minimal_x_deco: '190', 
+  minimal_y_deco: '-16', 
+  minimal_z_deco: '-348', 
+  maximal_x_deco: '1019', 
+  maximal_y_deco: '1941', 
+  maximal_z_deco: '486', 
+  # Channel settings for deconvolution
+  # Single Channel: '"beads"'
+  # Dual Channel: '"beads,beads"'
+  # Dual Channel one channel contains beads: '"[Same PSF as channel red],beads"'
+  detections_to_extract_psf_for_channel: '"[Same PSF as channel red],beads"',
+  # Settings for GPU or CPU processing 
+  # '"CPU (Java)"' or '"GPU (Nvidia CUDA via JNA)"'
+  compute_on: '"GPU (Nvidia CUDA via JNA)"',
+  cudafourierconvolution: "libFourierConvolutionCUDALib.so", # GPU processing name of cuda library
+  # Standard settings for deconvolution
+  process_timepoint: '"Single Timepoint (Select from List)"',
+  process_angle: '"All angles"',
+  process_channel: '"All channels"',
+  process_illumination: '"All illuminations"',
+  type_of_iteration: '"Efficient Bayesian - Optimization I (fast, precise)"',
+  Tikhonov_parameter: '0.0006',
+  compute: '"in 512x512x512 blocks"',
+  osem_acceleration: '"1 (balanced)"',
+  psf_estimation: '"Extract from beads"',
+  psf_size_x: '19',
+  psf_size_y: '19',
+  psf_size_z: '25',
+  imglib2_container: '"ArrayImg"',
+  bsh_file: "deconvolution.bsh"
+  }
+  
+hdf5_output: {
+  # writes new hdf5 dataset for fusion output: will be obsolete
+  # Naming pattern of output
+  # Single Channel: TP{t}_Chgreen_Ill0_Ang0,72,144,216,288.tif > Ch{name} is added here
+  # Dual Channel: TP{t}_Ch{0}_Ill0_Ang0,72,144,216,288.tif > Ch{name} is added here
+  output_image_file_pattern: 'TP{{t}}_Ch{{c}}_Ill0_Ang0,72,144,216,288.tif',
+  # channel setting
+  output_multiple_channels: '"YES (one file per channel)"', # '"YES (one file per channel)"' or  '"NO (one channel)"'
+  output_channels: "green,red",
+  # .xml file names
+  output_xml: '"fused_Dual_Channel"',
+  output_hdf5_xml: '"hdf5_fused_Dual_Channel"',
+  output_timepoints: '0-1', # Timepoints format: '1-2'
+  # pixel size of output: take downsampling into account!
+  output_pixel_distance_x: 0.28590, 
+  output_pixel_distance_y: 0.28590,
+  output_pixel_distance_z: 0.28590,
+  output_pixel_unit: 'um',
+  # give if 16Bit data or 32Bit data 
+  # output of fusion is 16Bit, of deconvolution it is 32Bit
+  output_data_type: "16Bit", # "32Bit" or "16Bit"
+  # if data is 32Bit then the data is converted into 16Bit data
+  convert_32bit: '"[Use min/max of first image (might saturate intenities over time)]"',
+  # subsampling and chunk size settings: dataset dependent
+  subsampling_output: '"{{ {{1,1,1}}, {{2,2,2}}, {{4,4,4}}, {{8,8,8}} }}"', # data dependent
+  chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}}, {{16,16,16}}, {{16,16,16}} }}"', # data dependent
+  # subsampling_output: '"{{ {{1,1,1}}, {{2,2,2}} }}"',
+  # chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}} }}"',
+  # Standard settings for hdf5_output
+  output_type_of_dataset: '"Image Stacks (ImageJ Opener)"',
+  output_multiple_timepoints: '"YES (one file per time-point)"',
+  output_multiple_angles: '"NO (one angle)"',
+  output_illumination_directions: '"NO (one illumination direction)"',
+  output_imglib_container: '"ArrayImg (faster)"',
+  bsh_file_define: "define_output.bsh", # .bsh script for defining the dataset
+  bsh_file_hdf5: "export_output.bsh"    # .bsh script for resaving into hdf5
+  }
+

spim_registration/timelapse/SingleChannel.yaml → spim_registration/timelapse/single_test.yaml

 common: {
-  # directory that contains the bean shell scripts
-  bsh_directory: "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/",
-  directory_cuda: "/sw/users/schmied/packages/2015-06-08_Fiji.app.cuda/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",
-  hdf5_xml_filename: '"hdf5_test_unicore"',
-  merged_xml: "hdf5_test_unicore_merge",
-  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",
-  # transformation_switch: "timelapse_dublicate",
-  transformation_switch: "timelapse",
-  # fusion_switch: "deconvolution"
+  # directory that contains the bean shell scripts and Snakefile
+  bsh_directory: "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/", 
+  # Directory that contains the cuda libraries
+  directory_cuda: "/sw/users/schmied/cuda/",                                                          
+  # Directory that contains the current working Fiji
+  fiji-app: "/sw/users/schmied/packages/2015-06-30_Fiji.app.cuda/ImageJ-linux64",        
+  fiji-prefix: "/sw/users/schmied/packages/xvfb-run -a",       # calls xvfb for Fiji headless mode
+  # xml file names without .xml suffix
+  first_xml_filename: 'single',       # Name of the xml file for the .czi or .tif files
+  hdf5_xml_filename: '"hdf5_single"', # Name of .xml file for the hdf5 data after resave_hdf5
+  merged_xml: 'hdf5_single_merge',    # Name of .xml file after merge
+  # Describe the dataset
+  ntimepoints: 2,               # number of timepoints of dataset
+  angles: "0,72,144,216,288",   # angles          
+  channels: "green",        # channels
+  illumination: "0",            # illuminations
+  pixel_distance_x: '0.28590106964',  # Manual calibration x
+  pixel_distance_y: '0.28590106964',  # Manual calibration y
+  pixel_distance_z: '1.50000',  # Manual calibration z
+  pixel_unit: "um",             # unit of manual calibration
+  # Use switches to decide which processing steps you need:
+  # transformation_switch: "timelapse" standard processing
+  # after timelapse registration directly goes into fusion, timelapse_duplicate
+  # "timelapse_duplicate" for dual channel processing one channel contains the beads
+  # duplicates transformations
+  transformation_switch: "timelapse", 
+  # Switches between content based fusion and deconvoltion
+  # "deconvolution" > for deconvolution
+  # "fusion" > for content based fusion
   fusion_switch: "fusion"
   }
-              
+
 define_xml_czi: {
-  first_czi: "2015-04-11_LZ2_Stock68_3.czi",
-  rotation_around: "X-Axis",
-  bsh_file: "define_czi.bsh"
+  first_czi: "2015-02-21_LZ1_Stock68_3.czi", # master .czi file
+  rotation_around: "X-Axis",                       # axis of acquistion
+  bsh_file: "define_czi.bsh"                       # .bsh script for defining .czi file
   }
           
 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)"',
+  # file pattern of .tif files
+  # for multi channel give spim_TL{tt}_Angle{a}_Channel{c}.tif
+  # # SPIM file pattern: for padded zeros use tt 
+  image_file_pattern: 'img_TL{{t}}_Angle{{a}}.tif', 
+  # Settings for ImageJ Opener
   type_of_dataset: '"Image Stacks (ImageJ Opener)"',
-  bsh_file: "define_tif_zip.bsh"
+  multiple_timepoints: '"YES (one file per time-point)"', # or NO (one time-point)
+  multiple_angles: '"YES (one file per angle)"',          # or NO (one angle)
+  multiple_channels: '"NO (one channel)"',                # or "\"NO (one channel)\""
+  multiple_illumination_directions: '"NO (one illumination direction)"', # or YES (one file per illumination direction)
+  imglib_container: '"ArrayImg (faster)"',        # '"ArrayImg (faster)"'
+  bsh_file: "define_tif_zip.bsh"  
   }
   
 resave_hdf5: {
-  hdf5_chunk_sizes: '"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}"',
+  # Resaves .tif or .czi data into hdf5
+  # Subsampling and resolution settings for hdf5: data dependent
+  hdf5_chunk_sizes: '"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}"', 
+  subsampling_factors: '"{{ {{1,1,1}}, {{2,2,1}}, {{4,4,1}}, {{8,8,1}} }}"',  
+  # Standard settings for cluster processing
+  setups_per_partition: '0',
+  timepoints_per_partition: '1',
+  resave_timepoint: '"All Timepoints"',  
   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',
   bsh_file: "export.bsh"
   }
 
 registration: {
-  # "Single Channel" is not a valid choice for "Process_channel"
-  reg_process_channel: '"All channels"', 
-  reg_processing_channel: '"green"',
+  # reg_process_channel:
+  # # Single Channel:  '"All channels"'
+  # Dual Channel: '"All channels"'
+  # Dual Channel one Channel contains beads: '"Single channel (Select from List)"'
+  reg_process_channel: '"All channels"',
+  # reg_processing_channel:
+  # Dual Channel setting for 1 Channel contains the beads
+  reg_processing_channel: '"green"',      
+  # reg_interest_points_channel:
+  # Single Channel: '"beads"'
+  # Dual Channel: '"beads,beads"'
+  # Dual Channel: Channel does not contain the beads '"[DO NOT register this channel],beads"'
   reg_interest_points_channel: '"beads"',
-  reg_radius_1: '2',
-  reg_radius_2: '3',
+  # type of detection: '"Difference-of-Mean (Integral image based)"' or '"Difference-of-Gaussian"'
+  type_of_detection: '"Difference-of-Mean (Integral image based)"',  
+  # Settings for Difference-of-Mean
+  # For multiple channels 'value1,value2' delimiter is ,
+  reg_radius_1: '2',          
+  reg_radius_2: '3',            
   reg_threshold: '0.005',
-  initial_sigma: '1.8',
-  threshold_gaussian: '0.0080',
-  type_of_detection: '"Difference-of-Mean (Integral image based)"',
-  label_interest_points: '"beads"',
+  # Settings for Difference-of-Gaussian
+  # For multiple channels 'value1,value2' delimiter is ,
+  sigma: '1.8',         
+  threshold_gaussian: '0.0080',   
+  # Processing setting for Difference-of-Gaussian detection
+  # compute_on:
+  compute_on: '"GPU accurate (Nvidia CUDA via JNA)"',
+  separableconvolution: '"libSeparableConvolutionCUDALib.so"',
+  # Downsampling settings
+  downsample_detection: "No", # "No" or "Yes"
+  downsample_xy: '"Match Z Resolution (less downsampling)"',
+  downsample_z: "1x",
+  # Standard Settings for bead based registration
+  label_interest_points: '"beads"',              
   reg_process_timepoint: '"Single Timepoint (Select from List)"',
   reg_process_angle: '"All angles"',
   reg_process_illumination: '"All illuminations"',
@@ -77,7 +117,7 @@ registration: {
   model_to_regularize_with: "Rigid",
   lambda: '0.10',
   imglib_container: '"ArrayImg (faster)"',
-  bsh_file: "registration.bsh"
+  bsh_file: "registration.bsh"  # .bsh script for registration
   }
 
 xml_merge: {
@@ -85,105 +125,135 @@ xml_merge: {
   }
   
 timelapse: {
-  reference_timepoint: '0',
+  reference_timepoint: '0',   # Reference timepoint
+  # Standard settings for timelapse registration
   type_of_registration_timelapse: '"Match against one reference timepoint (no global optimization)"',
   timelapse_process_timepoints: '"All Timepoints"',
   bsh_file: "timelapse_registration.bsh"
   }
   
-Dublicate_transformations: {
-  source_dublication: "red",
-  target_dublication: "green",
-  duplicate_which_transformations: '"Replace all transformations"',
-  bsh_file: "Dublicate_transformations.bsh"
+dublicate_transformations: {
+  # If dual channel processing and only one channel contains beads
+  # this allows you to dublicate the transformation for the 
+  # channel that does not contain beas
+  source_dublication: "red",  # source channel
+  target_dublication: "green", # target channel
+  duplicate_which_transformations: '"Replace all transformations"', # mode of dublication
+  bsh_file: "dublicate_transformations.bsh" # .bsh script for dublication
   }
   
 fusion: {
-  bsh_file: "fusion.bsh",
-  downsample: '4',
-  fused_image: '"Append to current XML Project"',
-  imglib2_container_fusion: '"ArrayImg"',
-  imglib2_data_container: '"ArrayImg (faster)"',
-  interpolation: '"Linear Interpolation"',
-  minimal_x: '190',
-  minimal_y: '-16',
-  minimal_z: '-348',
-  maximal_x: '1019',
-  maximal_y: '1941',
-  maximal_z: '486',
-  pixel_type: '"16-bit unsigned integer"',
+  # content based multiview fusion
+  # supports multi channel without new settings
+  downsample: '2',  # set downsampling
+  # Cropping parameters of full resolution
+  minimal_x: '190', 
+  minimal_y: '-16',  
+  minimal_z: '-348',  
+  maximal_x: '1019',   
+  maximal_y: '1941',    
+  maximal_z: '486',   
+  # fused_image: '"Append to current XML Project"', does not work yet
+  process_timepoint: '"Single Timepoint (Select from List)"',
   process_angle: '"All angles"',
   process_channel: '"All channels"',
   process_illumination: '"All illuminations"',
-  process_timepoint: '"Single Timepoint (Select from List)"',
+  imglib2_container_fusion: '"ArrayImg"',
+  interpolation: '"Linear Interpolation"',
+  pixel_type: '"16-bit unsigned integer"',
+  imglib2_data_container: '"ArrayImg (faster)"',
   process_views_in_paralell: '"All"',
-  xml_output: '"Save every XML with user-provided unique id"'
+  xml_output: '"Save every XML with user-provided unique id"',
+  bsh_file: "fusion.bsh"
   }
 
 external_transform: {
+  # Downsamples for deconvolution
+  # BUG: external transformation breaks .xml file
   # channel setting: '"all_channels"'
   channel_setting: '"green"',
   transform_timepoint: '"All Timepoints"',
   transform_angle: '"All angles"',
   transform_channel: '"All channels"',
-  # illumination setting only one illumination side
   transform_illumination: '"All illuminations"',
   apply_transformation: '"Current view transformations (appends to current transforms)"',
   define_mode_transform: '"Matrix"',
-  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"',
+  # Matrix for downsampling
+  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"', 
   transformation: '"Rigid"',
   bsh_file: "transform.bsh"
   }
 
 deconvolution: {
-  iterations: '1',
-  minimal_x_deco: '190',
-  minimal_y_deco: '-16',
-  minimal_z_deco: '-348',
-  maximal_x_deco: '1019',
-  maximal_y_deco: '1941',
-  maximal_z_deco: '486',
-  detections_to_extract_psf_for_channel: '"beads"',
+  iterations: '5', # number of iterations
+  # Cropping parameters: take downsampling into account
+  minimal_x_deco: '190', 
+  minimal_y_deco: '-16', 
+  minimal_z_deco: '-348', 
+  maximal_x_deco: '1019', 
+  maximal_y_deco: '1941', 
+  maximal_z_deco: '486', 
+  # Channel settings for deconvolution
+  # Single Channel: '"beads"'
+  # Dual Channel: '"beads,beads"'
+  # Dual Channel one channel contains beads: '"[Same PSF as channel red],beads"'
+  detections_to_extract_psf_for_channel: '"[Same PSF as channel red],beads"',
+  # Settings for GPU or CPU processing 
+  # '"CPU (Java)"' or '"GPU (Nvidia CUDA via JNA)"'
+  compute_on: '"GPU (Nvidia CUDA via JNA)"',
+  cudafourierconvolution: "libFourierConvolutionCUDALib.so", # GPU processing name of cuda library
+  # Standard settings for deconvolution
   process_timepoint: '"Single Timepoint (Select from List)"',
   process_angle: '"All angles"',
   process_channel: '"All channels"',
   process_illumination: '"All illuminations"',
+  type_of_iteration: '"Efficient Bayesian - Optimization I (fast, precise)"',
   Tikhonov_parameter: '0.0006',
   compute: '"in 512x512x512 blocks"',
-  compute_on: '"GPU (Nvidia CUDA via JNA)"',
-  imglib2_container: '"ArrayImg"',
   osem_acceleration: '"1 (balanced)"',
   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)"',
-  bsh_file: "deconvolution_GPU.bsh"
+  imglib2_container: '"ArrayImg"',
+  bsh_file: "deconvolution.bsh"
   }
   
 hdf5_output: {
-  output_image_file_pattern: 'TP{{t}}_Chgreen_Ill0_Ang0,72,144,216,288.tif',
-  output_xml: '"fused_Single_Channel"',
-  output_hdf5_xml: '"hdf5_fused_Single_Channel"',
-  output_multiple_channels: '"NO (one channel)"',
-  output_timepoints: '0-4',
-  output_pixel_distance_x: 0.5718,
-  output_pixel_distance_y: 0.5718,
-  output_pixel_distance_z: 0.5718,
-  output_pixel_unit: 'um',
+  # writes new hdf5 dataset for fusion output: will be obsolete
+  # Naming pattern of output
+  # Single Channel: TP{{t}}_Chgreen_Ill0_Ang0,72,144,216,288.tif > Ch{name} is added here
+  # Dual Channel: TP{{t}}_Ch{{0}}_Ill0_Ang0,72,144,216,288.tif > Ch{name} is added here
+  output_image_file_pattern: '"TP{{t}}_Chgreen_Ill0_Ang0,72,144,216,288.tif"',
+  # channel setting
+  output_multiple_channels: '"NO (one channel)"', # '"YES (one file per channel)"' or  '"NO (one channel)"'
   output_channels: "green",
-  output_data_type: "32Bit",
+  # .xml file names
+  output_xml: '"fused_Single"',
+  output_hdf5_xml: '"hdf5_fused_Single"',
+  output_timepoints: '0-1', # Timepoints format: '1-2'
+  # pixel size of output: take downsampling into account!
+  output_pixel_distance_x: 0.28590106964, 
+  output_pixel_distance_y: 0.28590106964,
+  output_pixel_distance_z: 0.28590106964,
+  output_pixel_unit: 'um',
+  # give if 16Bit data or 32Bit data 
+  # output of fusion is 16Bit, of deconvolution it is 32Bit
+  output_data_type: "16Bit", # "32Bit" or "16Bit"
+  # if data is 32Bit then the data is converted into 16Bit data
   convert_32bit: '"[Use min/max of first image (might saturate intenities over time)]"',
+  # subsampling and chunk size settings: dataset dependent
+  subsampling_output: '"{{ {{1,1,1}}, {{2,2,2}}, {{4,4,4}}, {{8,8,8}} }}"', # data dependent
+  chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}}, {{16,16,16}}, {{16,16,16}} }}"', # data dependent
+  # subsampling_output: '"{{ {{1,1,1}}, {{2,2,2}} }}"',
+  # chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}} }}"',
+  # Standard settings for hdf5_output
   output_type_of_dataset: '"Image Stacks (ImageJ Opener)"',
   output_multiple_timepoints: '"YES (one file per time-point)"',
   output_multiple_angles: '"NO (one angle)"',
   output_illumination_directions: '"NO (one illumination direction)"',
   output_imglib_container: '"ArrayImg (faster)"',
-  subsampling_output: '"{{ {{1,1,1}}, {{2,2,2}}, {{4,4,4}}, {{8,8,8}} }}"',
-  chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}}, {{16,16,16}}, {{16,16,16}} }}"',
-  # subsampling_output: '"{{ {{1,1,1}}, {{2,2,2}} }}"',
-  # chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}} }}"',
-  bsh_file_define: "define_output.bsh",
-  bsh_file_hdf5: "export_output.bsh"
+  bsh_file_define: "define_output.bsh", # .bsh script for defining the dataset
+  bsh_file_hdf5: "export_output.bsh"    # .bsh script for resaving into hdf5
   }
 

spim_registration/timelapse/tomancak.json

-{
-    "common" :
-    {
-	"fiji-app" : "/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/ImageJ-linux64",
-	"fiji-prefix" : "/sw/bin/xvfb-run -a",
-	"directory_cuda" : "/lustre/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/lib/",
-	"merged_xml" : "hdf5_test_unicore_merge"
-    },
-    
-    "registration" :
-    {
-	"timepoint" : "\"Single Timepoint (Select from List)\"",
-	"illuminations" : "\"All illuminations\"",
-	"angle" : "\"All angles\"",
-	"channel" : "\"All channels\"",
-	"proc-ch" : "\"channel 1\"",
-	"algorithm" : "\"Fast 3d geometric hashing (rotation invariant)\"",
-	"label_interest_points" : "\"beads\"",
-	"type_of_registration" : "\"Register timepoints individually\"",
-	"type_of_registration_timelapse" : "\"Match against one reference timepoint (no global optimization)\"",
-	"type_of_detection" : "\"Difference-of-Mean (Integral image based)\"" ,
-	"subpixel_localization" : "\"3-dimensional quadratic fit\"",
-	"imglib_container" : "\"ArrayImg (faster)\"",
-	"radius_1" : "2",
-	"radius_2" : "3",
-	"threshold" : "0.005",
-	"interest_points_channel_0" : "\"[DO NOT register this channel]\"" ,
-	"interest_points_channel_1" : "\"beads\"",
-	"fix_tiles" : "\"Fix first tile\""	,
-	"map_back_tiles" : "\"Map back to first tile using rigid model\"",
-	"transformation_model" : "Affine",
-	"model_to_regularize_with" : "Rigid",
-	"lambda" : "0.10" ,
-	"allowed_error_for_ransac" : "5",
-	"detection_min_max" : "find_maxima",
-	"initial_sigma" : "1.8",
-	"threshold_gaussian" : "0.0080",
-	"bsh_file" : "registration.bsh"
-    },
- 
-    "xml_merge" :
-    {
-	"bsh_file" : "xml_merge.bsh"
-    },
-
-    "external_transform" :
-    {
-	"bsh_file" : "transform.bsh",
-	"angle" : "\"All angles\"",
-	"channel" : "\"All channels\"",
-	"illumination" : "\"All illuminations\"",
-	"timepoint" : "\"All Timepoints\"",
-	"transformation" : "\"Rigid\"",
-	"apply_transformation" : "\"Current view transformations (appends to current transforms)\"",
-	"define_mode_transform" : "\"Matrix\"",
-	"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\""
-    },
-
-    "deconvolution" :
-    {
-
-	"bsh_file" : "deconvolution_GPU.bsh",
-	"process_timepoint" : "\"Single Timepoint (Select from List)\"",
-	"process_channel" : "\"All channels\"",
-	"process_illumination" : "\"All illuminations\"",
-	"process_angle" : "\"All angles\"",
-	"minimal_x" : "76",
-	"minimal_y" : "4",
-	"minimal_z" : "-192",
-	"maximal_x" : "488",
-	"maximal_y" : "956",
-	"maximal_z" : "214",
-	"imglib2_container" : "\"ArrayImg \"",
-	"type_of_iteration" : "\"Efficient Bayesian - Optimization I (fast, precise)\"",
-	"osem_acceleration" : "\"1 (balanced)\"",
-	"Tikhonov_parameter" : "0.0006",
-	"compute" : "\"in 512x512x512 blocks\"",
-	"compute_on" : "\"GPU (Nvidia CUDA via JNA)\"",
-	"psf_estimation" : "\"Extract from beads\"",
-	"iterations" : "5",
-	"detections_to_extract_psf_for_channel_0" : "\"beads\"",
-	"detections_to_extract_psf_for_channel_1" : "\"beads\"",
-	"psf_size_x" : "19",
-	"psf_size_y" : "19",
-	"psf_size_z" : "25"
-    }
-    
-}

spim_registration/timelapse/tomancak_czi.json

-{
-    "common" :
-    {
-	"fiji-app" : "/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/ImageJ-linux64",
-	"fiji-prefix" : "/sw/bin/xvfb-run -a",
-	"directory_cuda" : "/lustre/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/lib/",
-	"merged_xml" : "hdf5_test_unicore_merge",
-	"bsh_directory" : "/home/steinbac/development/cschmied-snakemake-workflows/spim_registration/timelapse/",
-	"first_xml_filename" : "test_unicore",
-	"hdf5_xml_filename" : "\"hdf5_test_unicore\"",
-	"fusion_switch" : "deconvolution",
-	"ntimepoints" : 3
-    },
-    
-    "define_xml_czi" :
-    {
-    	    "pixel_distance_x" : "0.2875535786151886",
-    	    "pixel_distance_y" : "0.2875535786151886",
-    	    "pixel_distance_z" : "1.50000", 
-    	    "pixel_unit" : "um",				    
-    	    "first_czi" : "2015-02-21_LZ1_Stock68_3.czi",
-    	    "channel_1" : "green",		
-    	    "channel_2" : "red",
-    	    "angle_1" : "0",
-    	    "angle_2" : "72",
-    	    "angle_3" :"144",
-    	    "angle_4" :"216",
-    	    "angle_5" : "288",
-    	    "illumination_1" : "0",
-    	    "rotation_around" : "X-Axis",
-    	    "bsh_file" : "define_czi.bsh" 
-    },
-    
-    "define_xml_tif" :
-    {
-	"timepoints" : "0-1",
-	"acquisition_angles" : "0,72,144,216,288",
-	"channels" : "0",
-	"image_file_pattern" : "img_TL{{t}}_Angle{{a}}.tif",
-	"pixel_distance_x"  : "0.2875535786151886",
-	"pixel_distance_y" : "0.2875535786151886",
-	"pixel_distance_z" : "1.50000",
-	"pixel_unit" : "um",
-	"multiple_timepoints" : "\"YES (one file per time-point)\"",
-	"multiple_channels" : "\"NO (one channel)\"",
-	"multiple_illumination_directions" : "\"NO (one illumination direction)\"",
-	"multiple_angles" : "\"YES (one file per angle)\"",
-	"type_of_dataset" : "\"Image Stacks (ImageJ Opener)\"",
-	"imglib_container" : "\"ArrayImg (faster)\"",
-	"bsh_file" : "define_tif_zip.bsh" 
-    },
-    
-    "resave_hdf5" :
-    {
-    	    "parallel_timepoints" : "3",
-    	    "resave_angle" : "\"All angles\"",
-    	    "resave_channel" : "\"All channels\"",
-    	    "resave_illumination" : "\"All illuminations\"",
-    	    "resave_timepoint" : "\"All Timepoints\"",
-    	    "subsampling_factors" : "\"{{ {{1,1,1}}, {{2,2,1}}, {{4,4,1}}, {{8,8,1}} }}\"",
-    	    "hdf5_chunk_sizes" : "\"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}\"",
-    	    "timepoints_per_partition" : "1",
-    	    "setups_per_partition" : "0",
-    	    "bsh_file" : "export.bsh"
-    },
-    
-    "registration" :
-    {
-	"timepoint" : "\"Single Timepoint (Select from List)\"",
-	"illuminations" : "\"All illuminations\"",
-	"angle" : "\"All angles\"",
-	"channel" : "\"All channels\"",
-	"proc-ch" : "\"channel 0\"",
-	"algorithm" : "\"Fast 3d geometric hashing (rotation invariant)\"",
-	"label_interest_points" : "\"beads\"",
-	"type_of_registration" : "\"Register timepoints individually\"",
-	"type_of_detection" : "\"Difference-of-Mean (Integral image based)\"" ,
-	"subpixel_localization" : "\"3-dimensional quadratic fit\"",
-	"imglib_container" : "\"ArrayImg (faster)\"",
-	"radius_1" : "2",
-	"radius_2" : "3",
-	"threshold" : "0.005",
-	"interest_points_channel_0" : "\"beads\"",
-	"interest_points_channel_1" : "\"beads\"",
-	"fix_tiles" : "\"Fix first tile\"",
-	"map_back_tiles" : "\"Map back to first tile using rigid model\"",
-	"transformation_model" : "Affine",
-	"model_to_regularize_with" : "Rigid",
-	"lambda" : "0.10" ,
-	"allowed_error_for_ransac" : "5",
-	"significance" : "10",
-	"detection_min_max" : "find_maxima",
-	"initial_sigma" : "1.8",
-	"threshold_gaussian" : "0.0080",
-	"bsh_file" : "registration.bsh"
-    },
- 
-    "xml_merge" :
-    {
-	"bsh_file" : "xml_merge.bsh"
-    },
-    
-    "timelapse" : 
-    {
-    	  "reference_timepoint" : "0",
-    	  "timelapse_process_timepoints" : "\"All Timepoints\"",
-    	  "type_of_registration_timelapse" : "\"Match against one reference timepoint (no global optimization)\"",
-    	  "bsh_file" : "timelapse_registration.bsh"
-    },
-
-    "external_transform" :
-    {
-	"bsh_file" : "transform.bsh",
-	"angle" : "\"All angles\"",
-	"channel" : "\"All channels\"",
-	"illumination" : "\"All illuminations\"",
-	"timepoint" : "\"All Timepoints\"",
-	"transformation" : "\"Rigid\"",
-	"apply_transformation" : "\"Current view transformations (appends to current transforms)\"",
-	"define_mode_transform" : "\"Matrix\"",
-	"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\""
-    },
-    
-    "fusion" :
-    {
-    	    "minimal_x" : "128",	
-    	    "minimal_y" : "-13",
-    	    "minimal_z" : "-407",
-    	    "maximal_x" : "986",
-    	    "maximal_y" : "1927",
-    	    "maximal_z" : "498",
-    	    "downsample" : "1",
-    	    "process_timepoint" : "\"Single Timepoint (Select from List)\"",
-    	    "process_channel" : "\"All channels\"",
-    	    "process_illumination" : "\"All illuminations\"",
-    	    "process_angle" : "\"All angles\"",
-    	    "xml_output" : "\"Save every XML with user-provided unique id\"", 
-    	    "fused_image" : "\"Append to current XML Project\"",
-    	    "pixel_type" : "\"16-bit unsigned integer\"",
-    	    "imglib2_container_fusion" : "\"ArrayImg\"",
-    	    "process_views_in_paralell" : "\"All\"",
-    	    "interpolation" : "\"Linear Interpolation\"",
-    	    "imglib2_data_container" : "\"ArrayImg (faster)\"",
-    	    "bsh_file" : "fusion.bsh"
-    },
-
-    "deconvolution" :
-    {
-
-	"bsh_file" : "deconvolution_GPU.bsh",
-	"process_timepoint" : "\"Single Timepoint (Select from List)\"",
-	"process_channel" : "\"All channels\"",
-	"process_illumination" : "\"All illuminations\"",
-	"process_angle" : "\"All angles\"",
-	"minimal_x" : "76",
-	"minimal_y" : "4",
-	"minimal_z" : "-192",
-	"maximal_x" : "488",
-	"maximal_y" : "956",
-	"maximal_z" : "214",
-	"imglib2_container" : "\"ArrayImg \"",
-	"type_of_iteration" : "\"Efficient Bayesian - Optimization I (fast, precise)\"",
-	"osem_acceleration" : "\"1 (balanced)\"",
-	"Tikhonov_parameter" : "0.0006",
-	"compute" : "\"in 512x512x512 blocks\"",
-	"compute_on" : "\"GPU (Nvidia CUDA via JNA)\"",
-	"psf_estimation" : "\"Extract from beads\"",
-	"iterations" : "5",
-	"detections_to_extract_psf_for_channel_0" : "\"beads\"",
-	"detections_to_extract_psf_for_channel_1" : "\"beads\"",
-	"psf_size_x" : "19",
-	"psf_size_y" : "19",
-	"psf_size_z" : "25"
-    },
-    
-    "hdf5_output" :
-    {
-    	    "output_image_file_pattern" : "TP{{t}}_Ch{{c}}_Ill0_Ang0,72,144,216,288.tif",
-    	    "output_data_type" : "32Bit",
-    	    "output_xml" : "\"fused_Dual_Channel\"",
-    	    "output_hdf5_xml" : "\"hdf5_fused_Stock68\"",
-    	    "output_multiple_channels" : "\"NO (one channel)\"",	
-    	    "output_timepoints" : "0-1",
-    	    "output_channels" : "green",
-    	    "output_pixel_distance_x" : "0.5718", 	
-    	    "output_pixel_distance_y" : "0.5718", 	
-    	    "output_pixel_distance_z" : "0.5718", 	
-    	    "output_pixel_unit" : "um",			
-    	    "output_multiple_timepoints" : "\"YES (one file per time-point)\"",   	
-    	    "output_illumination_directions" : "\"NO (one illumination direction)\"",	
-    	    "output_multiple_angles" : "\"NO (one angle)\"",					
-    	    "output_type_of_dataset" : "\"Image Stacks (ImageJ Opener)\"", 		
-    	    "output_imglib_container" : "\"ArrayImg (faster)\"",
-    	    "bsh_file_define" : "/define_output.bsh",
-    	    "bsh_file_hdf5" : "/export_output.bsh", 	
-    	    "convert_32bit" : "\"[Use min/max of first image (might saturate intenities over time)]\""
-    	    
-    }
-
-    
-    
-    
-    
-}

spim_registration/timelapse/tomancak_test_cluster.json

-{
-    "common" :
-    {
-	"fiji-app" : "/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/ImageJ-linux64",
-	"fiji-prefix" : "/sw/bin/xvfb-run -a",
-	"directory_cuda" : "/lustre/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/lib/",
-	"merged_xml" : "hdf5_test_unicore_merge",
-	"bsh_directory" : "/home/steinbac/development/schmied-snakemake-workflows/spim_registration/timelapse/",
-	"first_xml_filename" : "test_unicore",
-	"hdf5_xml_filename" : "\"hdf5_test_unicore\"",
-	"fusion_switch" : "deconvolution",
-	"ntimepoints" : 5
-    },
-    
-    "define_xml_czi" :
-    {
-    	    "pixel_distance_x" : "0.28590106964",
-    	    "pixel_distance_y" : "0.28590106964",
-    	    "pixel_distance_z" : "1.50000", 
-    	    "pixel_unit" : "um",				    
-    	    "first_czi" : "2015-04-11_LZ2_Stock68_3.czi",
-    	    "channel_1" : "green",		
-    	    "channel_2" : "red",
-    	    "angle_1" : "0",
-    	    "angle_2" : "72",
-    	    "angle_3" : "144",
-    	    "angle_4" : "216",
-    	    "angle_5" : "288",
-    	    "illumination_1" : "0",
-    	    "rotation_around" : "X-Axis",
-    	    "bsh_file" : "define_czi.bsh" 
-    },
-    
-    "define_xml_tif" :
-    {
-	"acquisition_angles" : "0,72,144,216,288",
-	"channels" : "0",
-	"image_file_pattern" : "img_TL{{t}}_Angle{{a}}.tif",
-	"pixel_distance_x" : "0.28590106964",
-	"pixel_distance_y" : "0.28590106964",
-	"pixel_distance_z" : "1.50000",
-	"pixel_unit" : "um",
-	"multiple_timepoints" : "\"YES (one file per time-point)\"",
-	"multiple_channels" : "\"NO (one channel)\"",
-	"multiple_illumination_directions" : "\"NO (one illumination direction)\"",
-	"multiple_angles" : "\"YES (one file per angle)\"",
-	"type_of_dataset" : "\"Image Stacks (ImageJ Opener)\"",
-	"imglib_container" : "\"ArrayImg (faster)\"",
-	"bsh_file" : "define_tif_zip.bsh" 
-    },
-    
-    "resave_hdf5" :
-    {
-    	    "resave_angle" : "\"All angles\"",
-    	    "resave_channel" : "\"All channels\"",
-    	    "resave_illumination" : "\"All illuminations\"",
-    	    "resave_timepoint" : "\"All Timepoints\"",
-    	    "subsampling_factors" : "\"{{ {{1,1,1}}, {{2,2,1}}, {{4,4,1}}, {{8,8,1}} }}\"",
-    	    "hdf5_chunk_sizes" : "\"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}\"",
-    	    "timepoints_per_partition" : "1",
-    	    "setups_per_partition" : "0",
-    	    "bsh_file" : "export.bsh"
-    },
-    
-    "registration" :
-    {
-	"timepoint" : "\"Single Timepoint (Select from List)\"",
-	"illuminations" : "\"All illuminations\"",
-	"angle" : "\"All angles\"",
-	"channel" : "\"All channels\"",
-	"proc-ch" : "\"channel 0\"",
-	"algorithm" : "\"Fast 3d geometric hashing (rotation invariant)\"",
-	"label_interest_points" : "\"beads\"",
-	"type_of_registration" : "\"Register timepoints individually\"",
-	"type_of_detection" : "\"Difference-of-Mean (Integral image based)\"" ,
-	"subpixel_localization" : "\"3-dimensional quadratic fit\"",
-	"imglib_container" : "\"ArrayImg (faster)\"",
-	"radius_1" : "2",
-	"radius_2" : "3",
-	"threshold" : "0.005",
-	"interest_points_channel_0" : "\"beads\"",
-	"interest_points_channel_1" : "\"beads\"",
-	"fix_tiles" : "\"Fix first tile\"",
-	"map_back_tiles" : "\"Map back to first tile using rigid model\"",
-	"transformation_model" : "Affine",
-	"model_to_regularize_with" : "Rigid",
-	"lambda" : "0.10" ,
-	"allowed_error_for_ransac" : "5",
-	"significance" : "10",
-	"detection_min_max" : "find_maxima",
-	"initial_sigma" : "1.8",
-	"threshold_gaussian" : "0.0080",
-	"bsh_file" : "registration.bsh"
-    },
- 
-    "xml_merge" :
-    {
-	"bsh_file" : "xml_merge.bsh"
-    },
-    
-    "timelapse" : 
-    {
-    	  "reference_timepoint" : "0",
-    	  "timelapse_process_timepoints" : "\"All Timepoints\"",
-    	  "type_of_registration_timelapse" : "\"Match against one reference timepoint (no global optimization)\"",
-    	  "bsh_file" : "timelapse_registration.bsh"
-    },
-
-    "external_transform" :
-    {
-	"bsh_file" : "transform.bsh",
-	"angle" : "\"All angles\"",
-	"channel" : "\"All channels\"",
-	"illumination" : "\"All illuminations\"",
-	"timepoint" : "\"All Timepoints\"",
-	"transformation" : "\"Rigid\"",
-	"apply_transformation" : "\"Current view transformations (appends to current transforms)\"",
-	"define_mode_transform" : "\"Matrix\"",
-	"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\""
-    },
-    
-    "fusion" :
-    {
-    	    "minimal_x" : "190",	
-    	    "minimal_y" : "-16",
-    	    "minimal_z" : "-348",
-    	    "maximal_x" : "1019",
-    	    "maximal_y" : "1941",
-    	    "maximal_z" : "486",
-    	    "downsample" : "1",
-    	    "process_timepoint" : "\"Single Timepoint (Select from List)\"",
-    	    "process_channel" : "\"All channels\"",
-    	    "process_illumination" : "\"All illuminations\"",
-    	    "process_angle" : "\"All angles\"",
-    	    "xml_output" : "\"Save every XML with user-provided unique id\"", 
-    	    "fused_image" : "\"Append to current XML Project\"",
-    	    "pixel_type" : "\"16-bit unsigned integer\"",
-    	    "imglib2_container_fusion" : "\"ArrayImg\"",
-    	    "process_views_in_paralell" : "\"All\"",
-    	    "interpolation" : "\"Linear Interpolation\"",
-    	    "imglib2_data_container" : "\"ArrayImg (faster)\"",
-    	    "bsh_file" : "fusion.bsh"
-    },
-
-    "deconvolution" :
-    {
-
-	"bsh_file" : "deconvolution_GPU.bsh",
-	"process_timepoint" : "\"Single Timepoint (Select from List)\"",
-	"process_channel" : "\"All channels\"",
-	"process_illumination" : "\"All illuminations\"",
-	"process_angle" : "\"All angles\"",
-	"minimal_x" : "95",
-	"minimal_y" : "-8",
-	"minimal_z" : "-174",
-	"maximal_x" : "509",
-	"maximal_y" : "970",
-	"maximal_z" : "243",
-	"imglib2_container" : "\"ArrayImg \"",
-	"type_of_iteration" : "\"Efficient Bayesian - Optimization I (fast, precise)\"",
-	"osem_acceleration" : "\"1 (balanced)\"",
-	"Tikhonov_parameter" : "0.0006",
-	"compute" : "\"in 512x512x512 blocks\"",
-	"compute_on" : "\"GPU (Nvidia CUDA via JNA)\"",
-	"psf_estimation" : "\"Extract from beads\"",
-	"iterations" : "5",
-	"detections_to_extract_psf_for_channel_0" : "\"beads\"",
-	"detections_to_extract_psf_for_channel_1" : "\"beads\"",
-	"psf_size_x" : "19",
-	"psf_size_y" : "19",
-	"psf_size_z" : "25"
-    },
-    
-    "hdf5_output" :
-    {
-    	    "output_image_file_pattern" : "TP{{t}}_Ch{{c}}_Ill0_Ang0,72,144,216,288.tif",
-    	    "output_data_type" : "32Bit",
-    	    "output_xml" : "\"fused_Dual_Channel\"",
-    	    "output_hdf5_xml" : "\"hdf5_fused_Stock68\"",
-    	    "output_multiple_channels" : "\"NO (one channel)\"",	
-    	    "output_timepoints" : "0-4",
-    	    "output_channels" : "green",
-    	    "output_pixel_distance_x" : "0.5718", 	
-    	    "output_pixel_distance_y" : "0.5718", 	
-    	    "output_pixel_distance_z" : "0.5718", 	
-    	    "output_pixel_unit" : "um",			
-    	    "output_multiple_timepoints" : "\"YES (one file per time-point)\"",   	
-    	    "output_illumination_directions" : "\"NO (one illumination direction)\"",	
-    	    "output_multiple_angles" : "\"NO (one angle)\"",					
-    	    "output_type_of_dataset" : "\"Image Stacks (ImageJ Opener)\"", 		
-    	    "output_imglib_container" : "\"ArrayImg (faster)\"",
-    	    "bsh_file_define" : "/define_output.bsh",
-    	    "bsh_file_hdf5" : "/export_output.bsh", 	
-    	    "convert_32bit" : "\"[Use min/max of first image (might saturate intenities over time)]\""
-    	    
-    }
-
-    
-    
-    
-    
-}

spim_registration/timelapse/tomancak_test_cluster.yaml

 common: {
-  # directory that contains the bean shell scripts
-  bsh_directory: "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/",
-  directory_cuda: "/sw/users/schmied/packages/cuda/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: "Dual_Channel",
-  hdf5_xml_filename: '"hdf5_Dual_Channel"',
-  merged_xml: "hdf5_Dual_Channel_merge",
-  ntimepoints: 2,
-  angles: "0,72,144,216,288",
-  channels: "green,red",
-  illumination: "0",
-  pixel_distance_x: '0.28590',
-  pixel_distance_y: '0.28590',
-  pixel_distance_z: '1.50000',
-  pixel_unit: "um",
-  transformation_switch: "timelapse_dublicate",
-  # transformation_switch: "timelapse",
-  # fusion_switch: "deconvolution"
-  fusion_switch: "fusion"
+  # directory that contains the bean shell scripts and Snakefile
+  bsh_directory: "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/", 
+  # Directory that contains the cuda libraries
+  directory_cuda: "/sw/users/schmied/cuda/",                                                          
+  # Directory that contains the current working Fiji
+  #fiji-app: "/sw/users/schmied/packages/2015-06-08_Fiji.app.cuda/ImageJ-linux64",
+  fiji-app: "/sw/users/schmied/packages/2015-05-29_Fiji_2.3.9_SNAP.app.cuda/ImageJ-linux64",          
+  fiji-prefix: "/sw/bin/xvfb-run -a",       # calls xvfb for Fiji headless mode
+  # xml file names without .xml suffix
+  first_xml_filename: "Dual_Channel",       # Name of the xml file for the .czi or .tif files
+  hdf5_xml_filename: '"hdf5_Dual_Channel"', # Name of .xml file for the hdf5 data after resave_hdf5
+  merged_xml: "hdf5_Dual_Channel_merge",    # Name of .xml file after merge
+  # Describe the dataset
+  ntimepoints: 2,               # number of timepoints of dataset
+  angles: "0,72,144,216,288",   # angles          
+  channels: "green,red",        # channels
+  illumination: "0",            # illuminations
+  pixel_distance_x: '0.28590',  # Manual calibration x
+  pixel_distance_y: '0.28590',  # Manual calibration y
+  pixel_distance_z: '1.50000',  # Manual calibration z
+  pixel_unit: "um",             # unit of manual calibration
+  # Use switches to decide which processing steps you need:
+  # transformation_switch: "timelapse" standard processing
+  # after timelapse registration directly goes into fusion, timelapse_duplicate
+  # "timelapse_duplicate" for dual channel processing one channel contains the beads
+  # duplicates transformations
+  transformation_switch: "timelapse_duplicate", 
+  # Switches between content based fusion and deconvoltion
+  # "deconvolution" > for deconvolution
+  # "fusion" > for content based fusion
+  fusion_switch: "deconvolution"
   }
-              
+
 define_xml_czi: {
-  first_czi: "2015-02-20_LZ2_Stock48_Stock58.czi", # essential
-  rotation_around: "X-Axis",
-  bsh_file: "define_czi.bsh"
+  first_czi: "2015-02-20_LZ2_Stock48_Stock58.czi", # master .czi file
+  rotation_around: "X-Axis",                       # axis of acquistion
+  bsh_file: "define_czi.bsh"                       # .bsh script for defining .czi file
   }
           
 define_xml_tif: {
-  image_file_pattern: 'img_TL{{t}}_Angle{{a}}.tif', # essential
-  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)"',
+  # file pattern of .tif files
+  # for multi channel give spim_TL{tt}_Angle{a}_Channel{c}.tif
+  # # SPIM file pattern: for padded zeros use tt 
+  image_file_pattern: 'img_TL{{t}}_Angle{{a}}.tif', 
+  # Settings for ImageJ Opener
   type_of_dataset: '"Image Stacks (ImageJ Opener)"',
-  bsh_file: "define_tif_zip.bsh"
+  multiple_timepoints: '"YES (one file per time-point)"', # or NO (one time-point)
+  multiple_angles: '"YES (one file per angle)"',          # or NO (one angle)
+  multiple_channels: '"NO (one channel)"',                # or "\"NO (one channel)\""
+  multiple_illumination_directions: '"NO (one illumination direction)"', # or YES (one file per illumination direction)
+  imglib_container: '"ArrayImg (faster)"',        # '"ArrayImg (faster)"'
+  bsh_file: "define_tif_zip.bsh"  
   }
   
 resave_hdf5: {
-  hdf5_chunk_sizes: '"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}"', # data dependent
-  subsampling_factors: '"{{ {{1,1,1}}, {{2,2,1}}, {{4,4,1}}, {{8,8,1}} }}"',  # data dependent
+  # Resaves .tif or .czi data into hdf5
+  # Subsampling and resolution settings for hdf5: data dependent
+  hdf5_chunk_sizes: '"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}"', 
+  subsampling_factors: '"{{ {{1,1,1}}, {{2,2,1}}, {{4,4,1}}, {{8,8,1}} }}"',  
+  # Standard settings for cluster processing
+  setups_per_partition: '0',
+  timepoints_per_partition: '1',
+  resave_timepoint: '"All Timepoints"',  
   resave_angle: '"All angles"',
   resave_channel: '"All channels"',
   resave_illumination: '"All illuminations"',
-  resave_timepoint: '"All Timepoints"',
-  setups_per_partition: '0',
-  timepoints_per_partition: '1',
   bsh_file: "export.bsh"
   }
 
 registration: {
-  reg_process_channel: '"Single channel (Select from List)"', # essential '"All channels"'; '"Single channel (Select from List)"'
-  reg_processing_channel: '"red"',      # essential
-  reg_interest_points_channel: '"beads"', # essential
-  reg_radius_1: '2',           # essential
-  reg_radius_2: '3',            # essential
-  reg_threshold: '0.005',       # essential
-  initial_sigma: '1.8',         # essetial
-  threshold_gaussian: '0.0080',   # essential
-  type_of_detection: '"Difference-of-Mean (Integral image based)"', # switch
-  label_interest_points: '"beads"',               
+  # reg_process_channel:
+  # # Single Channel:  '"All channels"'
+  # Dual Channel: '"All channels"'
+  # Dual Channel one Channel contains beads: '"Single channel (Select from List)"'
+  reg_process_channel: '"Single channel (Select from List)"',
+  # reg_processing_channel:
+  # Dual Channel setting for 1 Channel contains the beads
+  reg_processing_channel: '"red"',      
+  # reg_interest_points_channel:
+  # Single Channel: '"beads"'
+  # Dual Channel: '"beads,beads"'
+  # Dual Channel: Channel does not contain the beads '"[DO NOT register this channel],beads"'
+  reg_interest_points_channel: '"beads"',
+  # type of detection: '"Difference-of-Mean (Integral image based)"' or '"Difference-of-Gaussian"'
+  type_of_detection: '"Difference-of-Mean (Integral image based)"',  
+  # Settings for Difference-of-Mean
+  # For multiple channels 'value1,value2' delimiter is ,
+  reg_radius_1: '2',          
+  reg_radius_2: '3',            
+  reg_threshold: '0.005',
+  # Settings for Difference-of-Gaussian
+  # For multiple channels 'value1,value2' delimiter is ,
+  sigma: '1.8',         
+  threshold_gaussian: '0.0080',   
+  # Processing setting for Difference-of-Gaussian detection
+  # compute_on:
+  compute_on: '"GPU accurate (Nvidia CUDA via JNA)"',
+  separableconvolution: '"libSeparableConvolutionCUDALib.so"',
+  # Downsampling settings
+  downsample_detection: "No", # "No" or "Yes"
+  downsample_xy: '"Match Z Resolution (less downsampling)"',
+  downsample_z: "1x",
+  # Standard Settings for bead based registration
+  label_interest_points: '"beads"',              
   reg_process_timepoint: '"Single Timepoint (Select from List)"',
   reg_process_angle: '"All angles"',
   reg_process_illumination: '"All illuminations"',
@@ -76,7 +118,7 @@ registration: {
   model_to_regularize_with: "Rigid",
   lambda: '0.10',
   imglib_container: '"ArrayImg (faster)"',
-  bsh_file: "registration.bsh"
+  bsh_file: "registration.bsh"  # .bsh script for registration
   }
 
 xml_merge: {
@@ -84,107 +126,135 @@ xml_merge: {
   }
   
 timelapse: {
-  reference_timepoint: '0',   # essential
+  reference_timepoint: '0',   # Reference timepoint
+  # Standard settings for timelapse registration
   type_of_registration_timelapse: '"Match against one reference timepoint (no global optimization)"',
   timelapse_process_timepoints: '"All Timepoints"',
   bsh_file: "timelapse_registration.bsh"
   }
   
 dublicate_transformations: {
-  source_dublication: "red",  # essential for 1 usecase
-  target_dublication: "green", # essential for 1 usecase
-  duplicate_which_transformations: '"Replace all transformations"',
-  bsh_file: "dublicate_transformations.bsh"
+  # If dual channel processing and only one channel contains beads
+  # this allows you to dublicate the transformation for the 
+  # channel that does not contain beas
+  source_dublication: "red",  # source channel
+  target_dublication: "green", # target channel
+  duplicate_which_transformations: '"Replace all transformations"', # mode of dublication
+  bsh_file: "dublicate_transformations.bsh" # .bsh script for dublication
   }
   
 fusion: {
-  downsample: '1',  # essential
-  minimal_x: '220', # essential maybe automate
-  minimal_y: '40',  # essential maybe automate
-  minimal_z: '-290',  # essential maybe automate
-  maximal_x: '976',   # essential maybe automate
-  maximal_y: '1892',  # essential maybe automate  
-  maximal_z: '472',   # essential maybe automate
-  fused_image: '"Append to current XML Project"',
-  imglib2_container_fusion: '"ArrayImg"',
-  imglib2_data_container: '"ArrayImg (faster)"',
-  interpolation: '"Linear Interpolation"',
-  pixel_type: '"16-bit unsigned integer"',
+  # content based multiview fusion
+  # supports multi channel without new settings
+  downsample: '1',  # set downsampling
+  # Cropping parameters of full resolution
+  minimal_x: '220', 
+  minimal_y: '40',  
+  minimal_z: '-290',  
+  maximal_x: '976',   
+  maximal_y: '1892',    
+  maximal_z: '472',   
+  # fused_image: '"Append to current XML Project"', does not work yet
+  process_timepoint: '"Single Timepoint (Select from List)"',
   process_angle: '"All angles"',
   process_channel: '"All channels"',
   process_illumination: '"All illuminations"',
-  process_timepoint: '"Single Timepoint (Select from List)"',
+  imglib2_container_fusion: '"ArrayImg"',
+  interpolation: '"Linear Interpolation"',
+  pixel_type: '"16-bit unsigned integer"',
+  imglib2_data_container: '"ArrayImg (faster)"',
   process_views_in_paralell: '"All"',
   xml_output: '"Save every XML with user-provided unique id"',
   bsh_file: "fusion.bsh"
   }
 
 external_transform: {
-  # BUG
+  # Downsamples for deconvolution
+  # BUG: external transformation breaks .xml file
   # channel setting: '"all_channels"'
   channel_setting: '"green,red"',
   transform_timepoint: '"All Timepoints"',
   transform_angle: '"All angles"',
   transform_channel: '"All channels"',
-  # illumination setting only one illumination side
   transform_illumination: '"All illuminations"',
   apply_transformation: '"Current view transformations (appends to current transforms)"',
   define_mode_transform: '"Matrix"',
-  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"',  # essential
+  # Matrix for downsampling
+  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"', 
   transformation: '"Rigid"',
   bsh_file: "transform.bsh"
   }
 
 deconvolution: {
-  iterations: '1', # essential
-  minimal_x_deco: '190', # essential maybe automate
-  minimal_y_deco: '-16', # essential maybe automate
-  minimal_z_deco: '-348', # essential maybe automate
-  maximal_x_deco: '1019', # essential maybe automate
-  maximal_y_deco: '1941', # essential maybe automate
-  maximal_z_deco: '486', # essential maybe automate
-  detections_to_extract_psf_for_channel: '"beads"',
+  iterations: '1', # number of iterations
+  # Cropping parameters: take downsampling into account
+  minimal_x_deco: '190', 
+  minimal_y_deco: '-16', 
+  minimal_z_deco: '-348', 
+  maximal_x_deco: '1019', 
+  maximal_y_deco: '1941', 
+  maximal_z_deco: '486', 
+  # Channel settings for deconvolution
+  # Single Channel: '"beads"'
+  # Dual Channel: '"beads,beads"'
+  # Dual Channel one channel contains beads: '"[Same PSF as channel red],beads"'
+  detections_to_extract_psf_for_channel: '"[Same PSF as channel red],beads"',
+  # Settings for GPU or CPU processing 
+  # '"CPU (Java)"' or '"GPU (Nvidia CUDA via JNA)"'
+  compute_on: '"GPU (Nvidia CUDA via JNA)"',
+  cudafourierconvolution: "libFourierConvolutionCUDALib.so", # GPU processing name of cuda library
+  # Standard settings for deconvolution
   process_timepoint: '"Single Timepoint (Select from List)"',
   process_angle: '"All angles"',
   process_channel: '"All channels"',
   process_illumination: '"All illuminations"',
+  type_of_iteration: '"Efficient Bayesian - Optimization I (fast, precise)"',
   Tikhonov_parameter: '0.0006',
   compute: '"in 512x512x512 blocks"',
-  compute_on: '"GPU (Nvidia CUDA via JNA)"',
-  imglib2_container: '"ArrayImg"',
   osem_acceleration: '"1 (balanced)"',
   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)"',
-  bsh_file: "deconvolution_GPU.bsh"
+  imglib2_container: '"ArrayImg"',
+  bsh_file: "deconvolution.bsh"
   }
   
 hdf5_output: {
-  # Will be obsolete
+  # writes new hdf5 dataset for fusion output: will be obsolete
+  # Naming pattern of output
+  # Single Channel: TP{t}_Chgreen_Ill0_Ang0,72,144,216,288.tif > Ch{name} is added here
+  # Dual Channel: TP{t}_Ch{0}_Ill0_Ang0,72,144,216,288.tif > Ch{name} is added here
   output_image_file_pattern: 'TP{{t}}_Ch{{c}}_Ill0_Ang0,72,144,216,288.tif',
+  # channel setting
+  output_multiple_channels: '"YES (one file per channel)"', # '"YES (one file per channel)"' or  '"NO (one channel)"'
+  output_channels: "green,red",
+  # .xml file names
   output_xml: '"fused_Dual_Channel"',
   output_hdf5_xml: '"hdf5_fused_Dual_Channel"',
-  output_multiple_channels: '"YES (one file per channel)"', # "\"YES (one file per channel)\"" or  "\"NO (one channel)\""
-  output_timepoints: '0-1',
-  output_pixel_distance_x: 0.28590,
+  output_timepoints: '0-1', # Timepoints format: '1-2'
+  # pixel size of output: take downsampling into account!
+  output_pixel_distance_x: 0.28590, 
   output_pixel_distance_y: 0.28590,
   output_pixel_distance_z: 0.28590,
   output_pixel_unit: 'um',
-  output_channels: "green,red",
-  output_data_type: "16Bit",
+  # give if 16Bit data or 32Bit data 
+  # output of fusion is 16Bit, of deconvolution it is 32Bit
+  output_data_type: "16Bit", # "32Bit" or "16Bit"
+  # if data is 32Bit then the data is converted into 16Bit data
   convert_32bit: '"[Use min/max of first image (might saturate intenities over time)]"',
+  # subsampling and chunk size settings: dataset dependent
+  subsampling_output: '"{{ {{1,1,1}}, {{2,2,2}}, {{4,4,4}}, {{8,8,8}} }}"', # data dependent
+  chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}}, {{16,16,16}}, {{16,16,16}} }}"', # data dependent
+  # subsampling_output: '"{{ {{1,1,1}}, {{2,2,2}} }}"',
+  # chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}} }}"',
+  # Standard settings for hdf5_output
   output_type_of_dataset: '"Image Stacks (ImageJ Opener)"',
   output_multiple_timepoints: '"YES (one file per time-point)"',
   output_multiple_angles: '"NO (one angle)"',
   output_illumination_directions: '"NO (one illumination direction)"',
   output_imglib_container: '"ArrayImg (faster)"',
-  subsampling_output: '"{{ {{1,1,1}}, {{2,2,2}}, {{4,4,4}}, {{8,8,8}} }}"', # data dependent
-  chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}}, {{16,16,16}}, {{16,16,16}} }}"', # data dependent
-  # subsampling_output: '"{{ {{1,1,1}}, {{2,2,2}} }}"',
-  # chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}} }}"',
-  bsh_file_define: "define_output.bsh",
-  bsh_file_hdf5: "export_output.bsh"
+  bsh_file_define: "define_output.bsh", # .bsh script for defining the dataset
+  bsh_file_hdf5: "export_output.bsh"    # .bsh script for resaving into hdf5
   }