# Copyright CNRS/Inria/UNS # Contributor(s): Eric Debreuve (since 2019), Morgane Nadal (2020) # # eric.debreuve@cnrs.fr # # This software is governed by the CeCILL license under French law and # abiding by the rules of distribution of free software. You can use, # modify and/ or redistribute the software under the terms of the CeCILL # license as circulated by CEA, CNRS and INRIA at the following URL # "http://www.cecill.info". # # As a counterpart to the access to the source code and rights to copy, # modify and redistribute granted by the license, users are provided only # with a limited warranty and the software's author, the holder of the # economic rights, and the successive licensors have only limited # liability. # # In this respect, the user's attention is drawn to the risks associated # with loading, using, modifying and/or developing or reproducing the # software by the user in light of its specific status of free software, # that may mean that it is complicated to manipulate, and that also # therefore means that it is reserved for developers and experienced # professionals having in-depth computer knowledge. Users are therefore # encouraged to load and test the software's suitability as regards their # requirements in conditions enabling the security of their systems and/or # data to be ensured and, more generally, to use and operate it in the # same conditions as regards security. # # The fact that you are presently reading this means that you have had # knowledge of the CeCILL license and that you accept its terms. ; -------- 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 # D:\\MorganeNadal\\IBA1-Microglies\\DIO_1H_16_1.58_2.1\DIO_1H_16_1.58_2.1_3.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 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). crop_image # TODO save_images : D:\\MorganeNadal\\Results\\Images ; if None, no saving. Otherwise, path where to save images (MIP & graphs) condition ; TODO CHO, DIO, ... duration ; TODO 1H, 3H, 1W, 3W, ... statistical_analysis : True [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 diff_mode : indirect 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