#YAML:1.0 # ^ do not change YAML version ################################################ # MICROBEJ SEGMENTATION CONFIGURATION SETTINGS # ################################################ # Contains all the configuration needed for running MicrobeJ_segmentation.m # Save this file as config.yml and place in the root directory of the program metadata: version: 1.6 description: "Default run configuration" #THIS FILE IS A DEFAULT TEMPLATE INTENDED REFERNCE. #Which columns from the bacteria table to use for the analysis bacteria_cols: ['FEATURE_1_count','FEATURE_2_count','SHAPE_area','SHAPE_aspectRatio','SHAPE_circularity', 'SHAPE_length','SHAPE_perimeter','SHAPE_solidity','SHAPE_width'] #Which columns from the fluorescence table to use for the analysis fluorescence_cols: ['INTENSITY','SHAPE_area','SHAPE_aspectRatio','SHAPE_circularity','SHAPE_length','SHAPE_perimeter','SHAPE_solidity','SHAPE_width'] #Which columns to remove at end (related to features, typically) removed_cols: ['FEATURE_1_count_q1','FEATURE_1_count_q3','FEATURE_1_count_v','FEATURE_2_count_q1','FEATURE_2_count_q3','FEATURE_2_count_v'] #Feature or maxima f_or_m: 'FEATURE' blur_thresholds: sw_p_val_limit: 0.008 # Match to gaussian--under 0.01 bad, -1 if unable to calculate maxima_limit: 1 # how many 'blips' are in the profile --- 1-2 is OK, 0 is ideal, -1 if unable to calculate min_mid_diff_max: 2 # how skewed the profile is --- 2 is accceptable, 0 ideal range_diff_max: 500 # difference between the ranges of the left and right side of profile -- 150 is acceptable range_min: 100 # range of profile--maximize slope_diff_max: 500 # difference in slope of each side slope_min: 100 # average of slopes of each side-->blur threshold (IMPORTANT) #CHOOSE which attributes to filter by: set to string separated by && (will be calculated by eval()) #OPTIONS: sw_p_val_match, maxima_match, range_match, range_diff_match, slope_match, min_mid_match, slope_diff_max # or set to 'true' for NO blur filtering attributes_to_check: 'sw_p_val_match && maxima_match && range_match && range_diff_match && slope_match && min_mid_match' #How many photos will be merged per point on the graph group_size: 1 #Which outputs are to be generated output: show_correlation_plot: false save: true