# 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 : ./data/DIO_6H_6_1.70bis_2.2_3.tif #/home/eric/Pictures/carole-rovere/clara-test/TO5_2_12W_pos1.tif #/home/eric/Pictures/carole-rovere/clara-test/ST8_1.tif #/home/eric/Pictures/carole-rovere/CHO_1H_D_1.70_3.3_8.tif #.\\data\\DIO_6H_6_1.70bis_2.2_3.tif ; direct data path to the image channel : G ; Can take the values R, G or B. ; Can also be set to None (cf. README above). size_voxel_in_micron ; size_voxel_in_micron -> [X,Y,Z] ; Can also be set to None (cf. README above). save_images : /home/eric/Code/project/mno/nutrimorph/2-morgane/result/image ; if None, no saving. Otherwise, path where to save images (MIP & graphs) save_csv : /home/eric/Code/project/mno/nutrimorph/2-morgane/result/features ; where to save the csv. if None, by default it is in the .tif directory save_features_analysis : /home/eric/Code/project/mno/nutrimorph/2-morgane/result/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 : indirect bright_on_dark : True method : python [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