Multiple timepoints:  YES (one file per timepoint) or (all time-points in one file)
Multiple channels:  YES (one file per timepoint) or (all time-points in one file)
Multiple illumination directions: YES (one file per illumination direction)
Multiple angles: YES (one file per angle)

Multiple timepoints: YES (one file per timepoint) or (all time-points in one file)
Multiple channels: YES (one file per timepoint) or (all time-points in one file)
Multiple illumination directions: YES (one file per illumination direction) => not tested yet
Multiple angles: YES (one file per angle)

Multiple timepoints: YES (one file per timepoint)
Multiple channels: YES (one file per channel)
Multiple illumination directions: YES (one file per illumination direction) => not tested yet
Multiple angles: YES (one file per angle)

/path/to/repo/timelapse
├── single_test.yaml
├── dual_OneChannel.yaml
├── Snakefile
├── cluster.json
├── define_tif_zip.bsh
├── define_czi.bsh
├── registration.bsh
├── deconvolution.bsh
├── transform.bsh	 		
├── registration.bsh 		
└── xml_merge.bsh	 		

/path/to/data
├── dataset.czi
├── dataset(1).czi
├── dataset(2).czi
├── dataset(3).czi
├── dataset(4).czi
└── dataset.yaml	 		# copied/symlinked from this repo

/path/to/repo/tools
├── master_preprocessing.sh
├── czi_resave
    ├── create-resaving-jobs.sh
    ├── resaving.bsh
    └── submit-jobs

common: {
  # ============================================================================
  #
  # yaml example file for single channel processing
  #
  # General settings for processing
  #
  # ============================================================================
  # 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
  sysconfcpus: "sysconfcpus -n",
  # ============================================================================
  # Processing switches
  # Description: Use switches to decide which processing steps you need:
  #
  # Options:
  #           transformation_switch: "timelapse",
  #           goes directly into fusion after timelapse registration
  #
  #           transformation_switch: "timelapse_duplicate",
  #           for dual channel processing one channel contains the beads
  #           dublicates the transformation from the source channel to the 
  #           target channel
  #
  #           Switches between content based fusion and deconvoltion
  #           fusion_switch: "deconvolution", > for deconvolution
  #           fusion_switch: "fusion", > for content based fusion
  # ============================================================================
  # Transformation switch:
  transformation_switch: "timelapse",
  # Fusion switch:
  fusion_switch: "deconvolution",
  # ============================================================================
  # xml file name
  # 
  # Description: xml file name without .xml suffix
  # ============================================================================
  hdf5_xml_filename: '"single"', 
  # ============================================================================
  # Describe the dataset
  #
  # Options: number of timepoints
  #          angles
  #          channels
  #          illuminations
  #          Settings for .czi or .tif files
  # ============================================================================
  ntimepoints: 90,        # number of timepoints of dataset
  angles: "0,72,144,216,288",   # format e.g.: "0,72,144,216,288",
  channels: "green",     # format e.g.: "green,red", IMPORTANT: for tif numeric!
  illumination: "0",     # format e.g.: "0,1",
  # ----------------------------------------------------------------------------
  # Settings for .czi files
  first_czi: "2015-02-21_LZ1_Stock68_3.czi", 
  # ----------------------------------------------------------------------------
  # Settings for .tif datasets
  # Options: 
  #          file pattern of .tif files:
  #          multi channel with one file per channel: 
  #          spim_TL{tt}_Angle{a}_Channel{c}.tif
  #          for padded zeros use tt 
  image_file_pattern: 'img_TL{{t}}_Angle{{a}}.tif',
  multiple_channels: '"NO (one channel)"',         # '"YES (all channels in one file)"' or '"YES (one file per channel)"' or '"NO (one channel)"'
  # ============================================================================
  # Detection and registration
  #
  # Description: settings for interest point detection and registration
  # Options: Single channel and dual channel processing
  #          Source and traget for dual channel one channel contains the beads
  #          Interestpoints label
  #          Difference-of-mean or difference-of-gaussian detection
  # ============================================================================
  # 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"',
  #
  # Dual channel 1 Channel contains the beads: which channel contains the beads?
  # Ignore if Single Channel or Dual Channel both channels contain beads
  source_channel: "red", # channel that contains the beads
  target_channel: "green", # channel without beads
  # 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-Gaussian"',
  # 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: '1.3',
  threshold_gaussian: '0.025',
  # ============================================================================
  # Timelapse registration
  #
  # Description: settings for timelapse registration
  # Options: reference timepoint
  # ============================================================================
  reference_timepoint: '1',   # Reference timepoint
  # ============================================================================
  # Content-based multiview fusion
  #
  # Description: settings for content-based multiview fusion
  # Options: downsampling
  #          Cropping parameters based on full resolution
  # ============================================================================
  downsample: '2',    # set downsampling
  minimal_x: '190',   # Cropping parameters of full resolution
  minimal_y: '-16',
  minimal_z: '-348',
  maximal_x: '1019',
  maximal_y: '1941',
  maximal_z: '486',
  # ============================================================================
  # External transformation switch
  #
  # Description: Allows downsampling prior deconvolution
  # Options: no downsampling 
  #          external_trafo_switch: "_transform",
  #
  #          downsampling
  #          external_trafo_switch: "external_trafo",
  #          IMPORTANT: boundingbox needs to reflect this downsampling. 
  #
  #          Matrix for downsampling
  # ============================================================================
  # External transformation switch:
  external_trafo_switch: "_transform",
  #
  # 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"',
  # ============================================================================
  # Multiview deconvolution
  #
  # Description: settings for multiview deconvolution
  # Options: 
  #          number of iterations
  #          Cropping parameters taking downsampling into account!
  #          Channel settings for deconvolution
  # ============================================================================
  iterations: '20',        # number of iterations
  minimal_x_deco: '95',  # Cropping parameters: take downsampling into account
  minimal_y_deco: '-8',
  minimal_z_deco: '-174',
  maximal_x_deco: '509',
  maximal_y_deco: '970',
  maximal_z_deco: '243',
  # 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: '"beads"'
  }

/path/to/snakemake/snakemake -j2 -d /path/to/data/ --cluster-config ./cluster.json --drmaa " -q {cluster.lsf_q} {cluster.lsf_extra}"

/path/to/snakemake/snakemake -j2 -d /path/to/data/ --cluster-config ./cluster.json --cluster "bsub -q {cluster.lsf_q} {cluster.lsf_extra}"

/path/to/snakemake/snakemake -j2 -d /path/to/data/ --cluster-config ./cluster.json --drmaa " -q {cluster.lsf_q} {cluster.lsf_extra} -o test.out -e test.err"

/path/to/snakemake/snakemake -j2 -d /path/to/data/ --cluster-config ./cluster.json --cluster "bsub -q {cluster.lsf_q} {cluster.lsf_extra} -o test.out -e test.err"