parameters.ini

# Copyright CNRS/Inria/UNS
# Contributor(s): Eric Debreuve (since 2019), Morgane Nadal (2020)
#
# eric.debreuve@cnrs.fr
#
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; -------- READ ME --- How to set parameters to None ? --------
; All the input parameters of this file are considered strings. If you write "parameter  :  None",
; you are not setting your parameter at the None value but you assigned the string 'None' to the parameter.
; In order to set the parameter to the None value, write "parameter" without anything behind (even not a ":").
; See the example below:

[Example]
; RIGHT WAY TO SET YOUR PARAMETER TO None:
parameter

; if you write:
parameter2                  :
; then your parameter has the value empty string: '', and not None
parameter3                  :   None
; then your parameter has the value string: 'None', and not None

[Input]
data_path                   :   D:\\MorganeNadal\\IBA1-Microglies\\CHO_1H_D_1.70_3.3\\CHO_1H_D_1.70_3.3_1.tif
#D:\\MorganeNadal\\IBA1-Microglies\\CHO_1H_D_1.70_3.3\\CHO_1H_D_1.70_3.3_1.tif
#.\data\DIO_6H_6_1.70bis_2.2_3.tif
#D:\MorganeNadal\IBA1-Microglies\standard conditions\020620_ST8_20W_1_2.lif - Position 3.tif
#D:\\MorganeNadal\\IBA1-Microglies\\standard conditions\\ST8_crop2(1024x1024)_vert.tif
; direct data path to the image
file_path
# D:\\MorganeNadal\\IBA1-Microglies
; TODO path to the repository containing the different condition repository
; Set to None if data_path exists
conditions
# ["CHO_1H_D_1.70_3.3", "CHO_3H_H_1.82_3.2", "CHO_6H_LL_1.70_1.3", "DIO_1H_16_1.58_2.1", "DIO_3H_F_1.82_3.1", "DIO_6H_6_1.70bis_2.2"]
; TODO list of the repository containing the different conditions
; Set to None if data_path exists
channel
; Can take the values R, G or B.
; Can also be set to None (cf. README above).
size_voxel_in_micron
#: [0.167,0.167,0.5]
#:   [0.071, 0.071, 0.4997]
; size_voxel_in_micron ->  [X,Y,Z]
; Can also be set to None (cf. README above).
save_images
; # TODO if None, no saving. Otherwise, path where to save images

[Somas]
soma_low_c                 :    0.15
# low = 10 #0.15
; this is a coefficient => not in micron
soma_high_c                :    0.7126
; this is a coefficient => not in micron
# high = 67.4 # 0.7126
soma_selem_micron_c        :    0.481
soma_min_area_c            :    58
soma_max_area_c            :    580

[Extensions]
adapt_hist_equalization    :    False
; for hysteresis
ext_low_c                  :    10
#7.5e-8
#1e-20
# low = 0.02
ext_high_c                 :    0.6
#1e-5
# 0.5e-5
# high = 0.04
; for morphological cleaning
ext_selem_micron_c         :    0.2405
ext_min_area_c             :    5.7840
ext_max_length_c           :    60

[Connexions]
max_straight_sq_dist_c     :    216.45
max_weighted_length_c      :    4.81

[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
## 12.5 if normalized btw 0 and 1
# 60.12506 # 500.0
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
; by default, 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
in_parallel                :    False