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Commit fdf6dafe authored by Christopher Schmied's avatar Christopher Schmied
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Set up tests for snakemake pipeline

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spim_registration/timelapse/Snakefile
+ 7
− 3
View file @ fdf6dafe
......@@ -6,8 +6,12 @@ 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"
# 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"
......@@ -260,7 +264,7 @@ 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"
......
spim_registration/timelapse/dual_OneChannel.yaml 0 → 100755
+ 260
− 0
View file @ fdf6dafe
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: "deconvolution"
}
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
+ 260
− 0
View file @ fdf6dafe
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"
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: "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: "deconvolution"
}
define_xml_czi: {
first_czi: "2015-04-11_LZ2_Stock68_3.czi",
rotation_around: "X-Axis",
bsh_file: "define_czi.bsh"
first_czi: "2015-04-11_LZ2_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 +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: {
......@@ -85,105 +126,135 @@ 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: '1', # 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_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: 0.28590106964,
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: "32Bit", # "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
}
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{
"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 deleted 100644 → 0
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{
"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)]\""
}
}
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{
"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
+ 6
− 5
View file @ fdf6dafe
......@@ -22,16 +22,16 @@ common: {
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_dublicate
# "timelapse_dublicate" for dual channel processing one channel contains the beads
# dublicates transformations
transformation_switch: "timelapse_dublicate",
# 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", # master .czi file
rotation_around: "X-Axis", # axis of acquistion
......@@ -54,6 +54,7 @@ define_xml_tif: {
}
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}} }}"',
......
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