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data_path : /home/eric/Data/Pictures/people/carole-rovere/complete-20W/hypothalamus-priority/TIF/CO/CO8_pos1.tif
channel #: G
voxel_size_in_micron : [0.0710, 0.0710, 0.4997] # Fiji>Image>Show Info> "Voxel size: 0.0710x0.0710x0.4997 micron^3"
duration : 20W
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[Soma]
soma_low : 0.15 # this is a coefficient => not in micron
soma_high : 0.7126 # this is a coefficient => not in micron
soma_selem_micron : 0.481
soma_min_area : 116 # area corresponds to a volume # 58 if ToPixel (0,1)
soma_max_area : 1160 # 580 if ToPixel (0,1)
[Extension]
adapt_hist_equalization : False
# for hysteresis
ext_low : 10
ext_high : 0.6
# for morphological cleaning
ext_selem_micron : 0.2405
ext_min_area : 11.568 # area corresponds to a volume # 5.7840 if ToPixel (0,1)
[Connection]
# Choose whether to perform erosion/dilation on the extensions during the connexion process.
# Better results are achieved with it, and doing dilatation_erosion is theoretically more rigorous
dilatation_erosion : True
max_straight_sq_dist : 217
max_weighted_length : 5
[Frangi]
scale_range : (0.1, 3.1)
# Stop at max x.1 with x <= sqrt(Z/2)
# ex: 3.1 for Z stacks < 18 and 5.1 for Z stacks < 50
scale_step : 1.0
alpha : 0.8
beta : 0.5
frangi_c : 30
diff_mode : FD11
bright_on_dark : True
method : c
[Feature]
hist_min_length #: 0 # histograms of extensions lengths # in micron
hist_step_length #: 6 # in micron
number_of_bins_length #: 5 # extensions generally do not exceed 30 microns
# If the above parameters are set to None, you can directly use the boundaries of your choice for the histogram
hist_bins_borders_length : (0, 0.5, 1, 5, 10, 50)
# histograms of extensions curvatures
hist_min_curvature #: 0
hist_step_curvature #: 6
number_of_bins_curvature #: 5
# If the above parameters are set to None, you can directly use the boundaries of your choice for the histogram
hist_bins_borders_curvature : (0, 0.05, 0.3, 1, 10, 50)
[Output]
save_images : /home/eric/Code/project/mno/nutrimorph/2-morgane/_result-SKIP # /image # MIP & graphs# None=no saving
save_csv : /home/eric/Code/project/mno/nutrimorph/2-morgane/_result-SKIP # /features # None=.tif directory
save_features_analysis : /home/eric/Code/project/mno/nutrimorph/2-morgane/_result-SKIP # /analysis
statistical_analysis : False
[Workflow]
with_plot : False
interactive : False
in_parallel : True