parameters.ini

[Input]
data_path                  : /home/eric/Data/Pictures/people/carole-rovere/complete-20W/hypothalamus-priority/TIF/CO8_pos1.tif
#./data/DIO_6H_6_1.70bis_2.2_3.tif
#./data/TO5_2_12W_pos1.tif
#/home/eric/Pictures/carole-rovere/CHO_1H_D_1.70_3.3_8.tif
#/home/eric/Pictures/carole-rovere/clara-test/TO5_2_12W_pos1.tif
#/home/eric/Pictures/carole-rovere/clara-test/ST8_1.tif

channel                    : G
size_voxel_in_micron       : [0.07099799999999999, 0.07099799999999999, 0.49972500000000003] ; [X,Y,Z]
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
dilatation_erosion         : True
; 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
statistical_analysis       : False

[Somas]
soma_low_c                 :    0.15
; this is a coefficient => not in micron
soma_high_c                :    0.7126
; this is a coefficient => not in micron
soma_selem_micron_c        :    0.481
; below, area correspond to a volume
soma_min_area_c            :    116
# 58 if ToPixel (0,1)
soma_max_area_c            :    1160
# 580 if ToPixel (0,1)

[Extensions]
adapt_hist_equalization    :    False
; for hysteresis
ext_low_c                  :    10
ext_high_c                 :    0.6
; for morphological cleaning
ext_selem_micron_c         :    0.2405
;below, area correspond to a volume
ext_min_area_c             :    11.568
# 5.7840 if ToPixel (0,1)

[Connexions]
max_straight_sq_dist_c     :    217
max_weighted_length_c      :    5

[Frangi]
; Values can be adapted to the image with the interface of frangi3gui.py
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

[Features Extraction]
; histograms of extensions lengths
hist_min_length
#:    0
; in micron
; by default, 0
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)


[Program Running]
with_plot                  :    False
interactive                :    False
in_parallel                :    False