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sa_params.jsonc
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{
"use_csv": true,
// Format of droplet images
"img_format":".tif",
// 6.45/5 5x lens sweetnam fluorescent camera
"img_pixel_size": "1.816",
// pixel size of intensity for concentration converter
"cvt_pixel_size": "1.816",
// depth of wells for the calibration not droplets
"cvt_depth": "100",
// image of droplets Directory
"img_dir":"./",
// Background images for droplet images
"bkg_dir": "./calibration",
// luminescence correction images folder
"lumi_dir":"./calibration",
// luminescence correction bkg images (noise) folder
"lumi_bkg_dir": "./calibration",
// dir of images for cvt, using the same bkgs in bkg_dir
"int_conc_cvt_dir": "./calibration",
// Channel names, in order. /calibration/546 647
"channels": ["488","647"],
// Channel name for detecting droplet shapes
"ch_detect": "647",
// Channel name for detecting features (condensates)
"ch_feature": "488",
// Channel name for uniform check (removing overlapping and smearing)
"ch_uniform": "647",
// bkg file names in bkg_dir. This is for droplet images. Same order as channels.
"bkg_names": ["500ms_bkg.tif", "500ms_bkg.tif"],
// luminescence correction images in lumi_dir. Same order as channels
"lumi_corr_img_names" : ["488_illum_bkg.tif", "647_illum_bkg_500ms.tif"],
// lumi corr background images in lumi_dir. Same order channels.
"lumi_corr_bkg_names" : ["500ms_bkg.tif", "500ms_bkg.tif"],
// File processing options
// Plot channels
"ch_plot" : [0, 1],
// Training channels for boundary fitting
"ch_train": [0, 1],
// use data after cvt for training
"train_on_cvt": true,
// Map the concentration in the cvt image names to some other values.
// List must be in the same length as the channels. If not needed, put None for the channel.
// Otherwise, put [concentration_in_cvt, new_value]
// Note this option is used by cvt_int_conc.py, which means the cvt.pickle file is not affected.
// It is not necessary to redo the cvt generation after changing this option
// "cvt_map" : [null, [6.4 100]],
"cvt_map" : {
"dye" : [ 6.76, 6.4, 6.25], // barcode concentrations for channel 0, 1, 2 (fluorescent flows 1, 2, 3)
"component" : [[6.76, 0, 0 ], // Component 1 concentration for corresponding dye concentration
[150, 250, 100 ], // Component 2 concentration for corresponding dye concentration
[0, 0, 0 ]], // Component 3 concentration for corresponding dye concentration
"background": [0, // Component 1 in buffer
300, // Component 2 in buffer
400] // Component 3 in buffer
},
// if set to false, masked regions of each circle not plotted
"verbose_plot": false,
"plot_text_scale" : 1,
"plot_line_thickness" : 1,
"parallel": true,
// Scan a number of stddev_tolerance settings. Scan only support process mode. Only use process mode when scan_enabled set to true
"stddev_scan": {
"scan_enabled" : false,
"stddev_min": 4,
"stddev_max": 9,
"scan_num": 24
},
// Analyser
"analyser": "SphereAnalyser5",
// kwargs for optional analyser settings
"kwargs": {
// minimum radius in px
"min_size": 15,
// maximum radius in px. Note this has an effect on detection
"max_size": 45,
// limit min size, mean minus min_size * standard deviation
"min_size_stddev":3,
// limit max size, mean plus max_size * standard deviation
"max_size_stddev":3,
// cut cut_size * radius of detected circle for uneven detection (uniform and feature check)
"cut_side": 0,
// cut cut_centre * radius of detected circle for uneven detection. If cut_centre > 1, cut_centre is in px
"cut_centre": 0,
// ignore a number of the brightest pixels for uneven detection
"ignore_bright_pixels": 5,
// remove dark droplets for correct detection, in intensity per unit pixel area. Those below this value will be
// labelled as dark [channels] e.g., [488,647]
// remove dark droplets for correct detection, in intensity per unit pixel area. Those below this value will be
// labelled as dark
"dark_thresholds": [100,100],
// how much deviates from the sphere setting. 1 means 100% deviation from the fitted sphere model
"uneven_threshold": 0.05,
// how much pixel can deviates from the background for condensate check. Deprecated for v5
"stddev_tolerance": 3,
// Below for v5 only
// feature threshold (for intensity thresholding)
"feature_threshold": 5,
// number of padding pixels for convolution
"feature_padding_pixels":5,
// percentage of brightness below which the pixels will be ignored in padding processed (replaced by padding)
"feature_padding_threshold":20,
// Sigma value for bilateral filtering
"feature_smooth_sigma":11,
// Minimum of connected pixels to be regarded as feature
"feature_connected_pixels":2,
// Minimum number of clusters in a droplet to be considered as feature
"feature_min_cluster_num": 1,
// enhancement mode 1: the conventional method adapted for the CoH microscope, 2: adapted for high
// signal-noise ratio camera
"enhance_mode": 1,
},
// Configs for intensity concentration conversion
"cvt_kwargs": {
// If there is no zero concentration, padding zero concentration and zero intensity
"padding_zero": false,
// Use linear mode, instead of inter- and extrapolation
"linear": true,
// Fix zero concentration if it exists
"fix_zero": true,
// Suppress warning for not finding corresponding background
"suppress_no_bkg_warning": false,
// Background suffix for individual background searching
"bg_suffix":"_bkg"
}
}