diff --git a/spim_registration/timelapse/dual_OneChannel.yaml b/spim_registration/timelapse/dual_OneChannel.yaml
deleted file mode 100644
index 239f9dfd3b117367df8297cf56f13414c695f349..0000000000000000000000000000000000000000
--- a/spim_registration/timelapse/dual_OneChannel.yaml
+++ /dev/null
@@ -1,260 +0,0 @@
-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
- }
-
diff --git a/spim_registration/timelapse/single.yaml b/spim_registration/timelapse/single.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..fdd6ccd39a1b26f5081b67cbbbfc43d04a50c51d
--- /dev/null
+++ b/spim_registration/timelapse/single.yaml
@@ -0,0 +1,4 @@
+Unstaged changes after reset:
+M spim_registration/timelapse/dual_OneChannel.yaml
+M spim_registration/timelapse/single.yaml
+M spim_registration/timelapse/single_test.yaml
diff --git a/spim_registration/timelapse/single_test.yaml b/spim_registration/timelapse/single_test.yaml
deleted file mode 100644
index 3171fb1cfc1a09b4422865dfb382d7a003661149..0000000000000000000000000000000000000000
--- a/spim_registration/timelapse/single_test.yaml
+++ /dev/null
@@ -1,335 +0,0 @@
-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
- # ============================================================================
- # Processing switches
- # Description: Use switches to decide which processing steps you need:
- #
- # Options:
- # 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
- #
- # Switches between content based fusion and deconvoltion
- # "deconvolution" > for deconvolution
- # "fusion" > for content based fusion
- # ============================================================================
- #
- # Transformation switch:
- transformation_switch: "timelapse",
- # Fusion switch:
- fusion_switch: "fusion",
- # ============================================================================
- # xml file names
- #
- # 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
- #
- # Options: number of timepoints
- # angles
- # channels
- # illuminations
- # pixel size
- # ============================================================================
- 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
- # ----------------------------------------------------------------------------
- # For .czi datasets
- # master .czi file
- first_czi: "2015-02-21_LZ1_Stock68_3.czi",
- # ----------------------------------------------------------------------------
- # For .tif datasets
- # file pattern of .tif files:
- # for multi channel give spim_TL{tt}_Angle{a}_Channel{c}.tif
- # for padded zeros use tt
- image_file_pattern: 'img_TL{{t}}_Angle{{a}}.tif',
- # ============================================================================
- # Detection and registration
- #
- # Description: settings for interest point detection and registration
- # Options: Single channel and dual channel processing
- # 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?
- 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"',
- #
- # 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',
- # ============================================================================
- # Timelapse registration
- #
- # Description: settings for timelapse registration
- # Options: reference timepoint
- # ============================================================================
- reference_timepoint: '0', # 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',
- # ============================================================================
- # Multiview deconvolution
- #
- # Description: settings for multiview deconvolution
- # Options: number of iterations
- # Cropping parameters taking downsampling into account
- # Channel settings for deconvolution
- # ============================================================================
- iterations: '5', # number of iterations
- minimal_x_deco: '190', # Cropping parameters: take downsampling into account
- 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"',
- #
- # ============================================================================
- # Resave output
- #
- # Description: writes new hdf5 dataset for fusion output
- # Options: Naming pattern of output based on channel number
- # Channel settings
- # File name for resaving output into hdf5
- # Pixel size > isotropic resolution
- # Image type (16Bit from content-based fusion, 32Bit from deconvolution)
- # ============================================================================
- # Number of timepoints
- output_timepoints: '0-1', # Timepoints format: '1-2'
- #
- # Naming pattern:
- # 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:
- # Single channel: '"NO (one channel)"'
- # Dual channel: '"YES (one file per channel)"'
- output_multiple_channels: '"NO (one channel)"',
- output_channels: "green",
- #
- # .xml file names
- output_xml: '"fused_Single"',
- output_hdf5_xml: '"hdf5_fused_Single"',
- #
- # 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',
- #
- # File type
- output_data_type: "16Bit" # "32Bit" or "16Bit"
- }
-
-define_xml_czi: {
- rotation_around: "X-Axis", # axis of acquistion
- bsh_file: "define_czi.bsh" # .bsh script for defining .czi file
- }
-
-define_xml_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: {
- # 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: {
- # 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: {
- # 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"',
- 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: {
- # 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: {
- # 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
- }
-