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Commit c3b1a849 authored by Christopher Schmied's avatar Christopher Schmied
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Added annotation for .yaml file

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spim_registration/timelapse/tomancak_test_cluster.yaml
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common: {
# directory that contains the bean shell scripts
bsh_directory: "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/",
directory_cuda: "/sw/users/schmied/cuda/",
# 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",
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",
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_dublicate
# "timelapse_dublicate" for dual channel processing one channel contains the beads
# dublicates transformations
transformation_switch: "timelapse_dublicate",
# Switches between content based fusion and deconvoltion
# "deconvolution" > for deconvolution
# "fusion" > for content based fusion
fusion_switch: "deconvolution"
# fusion_switch: "fusion"
}
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
# 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
type_of_detection: '"Difference-of-Mean (Integral image based)"', # Difference-of-Gaussian
reg_radius_1: '2', # essential
reg_radius_2: '3', # essential
reg_threshold: '0.005', # essential
sigma: '1.8', # essetial
threshold_gaussian: '0.0080', # essential
# 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"',
downsample_detection: "No",
# Downsampling settings
downsample_detection: "No", # "No" or "Yes"
downsample_xy: '"Match Z Resolution (less downsampling)"',
downsample_z: "1x",
label_interest_points: '"beads"',
# 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"',
......@@ -82,7 +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: {
......@@ -90,108 +125,135 @@ 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,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)"',
cudafourierconvolution: "libFourierConvolutionCUDALib.so",
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)"',
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
}
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