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config_example.toml
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[input_output]
file_or_directory = "dir"
image_conf = "two-in-one"
path = "/Users/testuser/Documents/GitHub/DARTS/Data"
results_dir = "/Users/testuser/Documents/GitHub/DARTS/results"
excel_filename_microdomain_data = "microdomain_data.xlsx"
[properties_of_measurement]
used_microscope = "test"
scale = 0.0
frame_rate = 3.0
resolution = 3
cell_type = "test1"
cell_types_options = ["jurkat", "primary", "NK", "test1", "test2"]
day_of_measurement = "2024-03-20"
user = "test"
experiment_name = "test"
imaging_local_or_global = "local"
bead_contact = true
duration_of_measurement = 48.0
wavelength_1 = 488
wavelength_2 = 561
time_of_measurement_before_starting_point = 1.0
time_of_measurement_after_starting_point = 15.0
[properties_of_measurement.calibration_parameters_cell_types]
[properties_of_measurement.calibration_parameters_cell_types.jurkat]
[properties_of_measurement.calibration_parameters_cell_types.NK]
[properties_of_measurement.calibration_parameters_cell_types.primary]
[properties_of_measurement.calibration_parameters_cell_types.test1]
"KD value (of Ca2+ dye)" = 1.0
"minimum ratio" = 1.0
"maximum ratio" = 1.0
"minimum fluorescence intensity" = 1.0
"maximum fluorescence intensity" = 1.0
"spot Height Ca2+ microdomains" = 1.0
[properties_of_measurement.calibration_parameters_cell_types.test2]
"KD value (of Ca2+ dye)" = 2.0
"minimum ratio" = 2.0
"maximum ratio" = 2.0
"minimum fluorescence intensity" = 2.0
"maximum fluorescence intensity" = 2.0
"spot Height Ca2+ microdomains" = 2.0
[processing_pipeline]
[processing_pipeline.postprocessing]
channel_alignment_in_pipeline = true
channel_alignment_each_frame = false
registration_method = "SITK"
background_sub_in_pipeline = true
cell_segmentation_tracking_in_pipeline = true
deconvolution_in_pipeline = true
deconvolution_algorithm = "LR"
TDE_lambda = ""
TDE_lambda_t = ""
bleaching_correction_in_pipeline = true
bleaching_correction_algorithm = "additiv no fit"
ratio_images = true
median_filter_kernel = 3
[processing_pipeline.postprocessing.psf]
type = "confocal"
lambdaEx_ch1 = 488
lambdaEm_ch1 = 520
lambdaEx_ch2 = 488
lambdaEm_ch2 = 600
numAper = 1.4
magObj = 100
rindexObj = 1.518
ccdSize = 6450
dz = 0
nslices = 1
depth = 0
rindexSp = 1.518
nor = 0
xysize = 150
[processing_pipeline.shape_normalization]
shape_normalization = true
[processing_pipeline.analysis]
hotspot_detection = true
dartboard_projection = true