cellects 0.1.3__py3-none-any.whl → 0.2.7__py3-none-any.whl

cellects/core/program_organizer.py

@@ -1,1316 +1,1687 @@
-#!/usr/bin/env python3
-"""This file contains the class constituting the link between the graphical interface and the computations
- First, Cellects analyze one image in order to get a color space combination maximizing the contrast between the specimens
- and the background.
- Second, Cellects automatically delineate each arena.
- Third, Cellects write one video for each arena.
- Fourth, Cellects segments the video and apply post-processing algorithms to improve the segmentation.
- Fifth, Cellects extract variables and store them in .csv files.
-"""
-
-import logging
-import os
-import pickle
-import sys
-from copy import deepcopy
-import cv2
-from numba.typed import Dict as TDict
-import pandas as pd
-import numpy as np
-from psutil import virtual_memory
-from pathlib import Path
-import natsort
-from cellects.image_analysis.image_segmentation import generate_color_space_combination
-from cellects.utils.load_display_save import extract_time  # named exif
-from cellects.image_analysis.one_image_analysis_threads import ProcessFirstImage
-from cellects.core.one_image_analysis import OneImageAnalysis
-from cellects.utils.load_display_save import PickleRick, read_and_rotate, readim, is_raw_image, read_h5_array, get_h5_keys
-from cellects.utils.utilitarian import insensitive_glob, vectorized_len
-from cellects.image_analysis.morphological_operations import Ellipse, cross_33
-from cellects.core.cellects_paths import CELLECTS_DIR, ALL_VARS_PKL_FILE
-from cellects.core.motion_analysis import MotionAnalysis
-from cellects.core.one_video_per_blob import OneVideoPerBlob
-from cellects.config.all_vars_dict import DefaultDicts
-from cellects.image_analysis.shape_descriptors import from_shape_descriptors_class
-
-
-class ProgramOrganizer:
-    def __init__(self):
-        """
-            This class stores all variables required for analysis as well as
-            methods to process it.
-            Global variables (i.e. that does not concern the MotionAnalysis)
-            are directly stored in self.
-            Variables used in the MotionAnalysis class are stored in a dict
-            called self.vars
-        """
-        if os.path.isfile('PickleRick.pkl'):
-            os.remove('PickleRick.pkl')
-        if os.path.isfile('PickleRick0.pkl'):
-            os.remove('PickleRick0.pkl')
-        if os.path.isfile(Path(CELLECTS_DIR.parent / 'PickleRick.pkl')):
-            os.remove(Path(CELLECTS_DIR.parent / 'PickleRick.pkl'))
-        if os.path.isfile(Path(CELLECTS_DIR.parent / 'PickleRick0.pkl')):
-            os.remove(Path(CELLECTS_DIR.parent / 'PickleRick0.pkl'))
-        # self.delineation_number = 0
-        self.one_arena_done: bool = False
-        self.reduce_image_dim: bool = False
-        self.first_exp_ready_to_run: bool = False
-        self.data_to_save = {'first_image': False, 'coordinates': False, 'exif': False, 'vars': False}
-        self.videos = None
-        self.motion = None
-        self.analysis_instance = None
-        self.computed_video_options = np.zeros(5, bool)
-        self.vars = {}
-        self.all = {}
-        self.all['folder_list'] = []
-        self.all['first_detection_frame'] = 1
-        self.first_im = None
-        self.last_im = None
-        self.vars['background_list'] = []
-        self.starting_blob_hsize_in_pixels = None
-        self.vars['first_move_threshold'] = None
-        self.vars['convert_for_origin'] = None
-        self.vars['convert_for_motion'] = None
-        self.current_combination_id = 0
-        self.data_list = []
-        self.one_row_per_arena = None
-        self.one_row_per_frame = None
-        self.one_row_per_oscillating_cluster = None
-        # self.fractal_box_sizes = None
-
-    def save_variable_dict(self):
-        logging.info("Save the parameters dictionaries in the Cellects folder")
-        self.all['vars'] = self.vars
-        all_vars = deepcopy(self.all)
-        if not self.all['keep_cell_and_back_for_all_folders']:
-            all_vars['bio_mask'] = None
-            all_vars['back_mask'] = None
-        pickle_rick = PickleRick(0)
-        pickle_rick.write_file(all_vars, ALL_VARS_PKL_FILE)
-
-    def load_variable_dict(self):
-        # loading_succeed: bool = False
-        # if os.path.isfile('Data to run Cellects quickly.pkl'):
-        #     try:
-        #         with open('Data to run Cellects quickly.pkl', 'rb') as fileopen:
-        #             data_to_run_cellects_quickly = pickle.load(fileopen)
-        #         if 'vars' in data_to_run_cellects_quickly:
-        #             self.vars = data_to_run_cellects_quickly['vars']
-        #             loading_succeed = True
-        #             logging.info("Success to load vars from the data folder")
-        #     except EOFError:
-        #         logging.error("Pickle error: will try to load vars from the Cellects folder")
-
-        if os.path.isfile(ALL_VARS_PKL_FILE):
-            logging.info("Load the parameters from all_vars.pkl in the config of the Cellects folder")
-            try:  # NEW
-                with open(ALL_VARS_PKL_FILE, 'rb') as fileopen:  # NEW
-                    self.all = pickle.load(fileopen)  # NEW
-                self.vars = self.all['vars']
-                self.update_data()
-                logging.info("Success to load the parameters dictionaries from the Cellects folder")
-                logging.info(os.getcwd())
-            except Exception as exc:  # NEW
-                logging.error(f"Initialize default parameters because error: {exc}")  # NEW
-                default_dicts = DefaultDicts()  # NEW
-                self.all = default_dicts.all  # NEW
-                self.vars = default_dicts.vars  # NEW
-        else:
-            logging.info("Initialize default parameters")
-            default_dicts = DefaultDicts()
-            self.all = default_dicts.all
-            self.vars = default_dicts.vars
-        if self.all['cores'] == 1:
-            self.all['cores'] = os.cpu_count() - 1
-
-    def analyze_without_gui(self):
-        # Eventually load "all" dir before calling this function
-        # self = po
-        # if len(self.all['folder_list']) == 0:
-        #     folder_list = "/"
-        # else:
-        #     folder_list = self.all['folder_list']
-        # for exp_i, folder_name in enumerate(folder_list):
-        #     # exp_i = 0 ; folder_name = folder_list
-
-        self=ProgramOrganizer()
-        self.load_variable_dict()
-        # dd = DefaultDicts()
-        # self.all = dd.all
-        # self.vars = dd.vars
-        self.all['global_pathway'] = "/Users/Directory/Data/dossier1"
-        self.all['first_folder_sample_number'] = 6
-        # self.all['global_pathway'] = "D:\Directory\Data\Audrey\dosier1"
-        # self.all['first_folder_sample_number'] = 6
-        # self.all['radical'] = "IMG"
-        # self.all['extension'] = ".jpg"
-        # self.all['im_or_vid'] = 0
-        self.look_for_data()
-        self.load_data_to_run_cellects_quickly()
-        if not self.first_exp_ready_to_run:
-            self.get_first_image()
-            self.fast_image_segmentation(True)
-            # self.first_image.find_first_im_csc(sample_number=self.sample_number,
-            #                                    several_blob_per_arena=None,
-            #                                    spot_shape=None, spot_size=None,
-            #                                    kmeans_clust_nb=2,
-            #                                    biomask=None, backmask=None,
-            #                                    color_space_dictionaries=None,
-            #                                    carefully=True)
-            self.cropping(is_first_image=True)
-            self.get_average_pixel_size()
-            self.delineate_each_arena()
-            self.get_background_to_subtract()
-            self.get_origins_and_backgrounds_lists()
-            self.get_last_image()
-            self.fast_image_segmentation(is_first_image=False)
-            self.find_if_lighter_background()
-            self.extract_exif()
-        self.update_output_list()
-        look_for_existing_videos = insensitive_glob('ind_' + '*' + '.npy')
-        there_already_are_videos = len(look_for_existing_videos) == len(self.vars['analyzed_individuals'])
-        logging.info(
-            f"{len(look_for_existing_videos)} .npy video files found for {len(self.vars['analyzed_individuals'])} arenas to analyze")
-        do_write_videos = not there_already_are_videos or (
-                there_already_are_videos and self.all['overwrite_unaltered_videos'])
-        if do_write_videos:
-            self.videos = OneVideoPerBlob(self.first_image, self.starting_blob_hsize_in_pixels, self.all['raw_images'])
-            self.videos.left = self.left
-            self.videos.right = self.right
-            self.videos.top = self.top
-            self.videos.bot = self.bot
-            self.videos.first_image.shape_number = self.sample_number
-            self.videos.write_videos_as_np_arrays(
-                self.data_list, self.vars['min_ram_free'], not self.vars['already_greyscale'], self.reduce_image_dim)
-        self.instantiate_tables()
-
-        i=1
-        show_seg=True
-
-        if os.path.isfile(f"coord_specimen{i + 1}_t720_y1475_x1477.npy"):
-            binary_coord = np.load(f"coord_specimen{i + 1}_t720_y1475_x1477.npy")
-            l = [i, i + 1, self.vars, False, False, show_seg, None]
-            sav = self
-            self = MotionAnalysis(l)
-            self.binary = np.zeros((720, 1475, 1477), dtype=np.uint8)
-            self.binary[binary_coord[0, :], binary_coord[1, :], binary_coord[2, :]] = 1
-        else:
-            l = [i, i + 1, self.vars, True, False, show_seg, None]
-            sav = self
-            self = MotionAnalysis(l)
-        self.get_descriptors_from_binary()
-        self.detect_growth_transitions()
-        # self.networks_detection(show_seg)
-        self.study_cytoscillations(show_seg)
-
-        # for i, arena in enumerate(self.vars['analyzed_individuals']):
-        #     l = [i, i + 1, self.vars, True, False, False, None]
-        #     analysis_i = MotionAnalysis(l)
-        #     self.add_analysis_visualization_to_first_and_last_images(i, analysis_i.efficiency_test_1,
-        #                                                              analysis_i.efficiency_test_2)
-        # self.save_tables()
-        #
-        # self = MotionAnalysis(l)
-        # l = [5, 6, self.vars, True, False, False, None]
-        # sav=self
-        # self.get_descriptors_from_binary()
-        # self.detect_growth_transitions()
-
-    def look_for_data(self):
-        # global_pathway = 'I:\Directory\Tracking_data\generalization_and_potentiation\drop_nak1'
-        os.chdir(Path(self.all['global_pathway']))
-        logging.info(f"Dir: {self.all['global_pathway']}")
-        self.data_list = insensitive_glob(
-            self.all['radical'] + '*' + self.all['extension'])  # Provides a list ordered by last modification date
-        self.data_list = insensitive_glob(self.all['radical'] + '*' + self.all['extension'])  # Provides a list ordered by last modification date
-        self.all['folder_list'] = []
-        self.all['folder_number'] = 1
-        if len(self.data_list) > 0:
-            lengths = vectorized_len(self.data_list)
-            if np.max(np.diff(lengths)) > np.log10(len(self.data_list)):
-                logging.error(f"File names present strong variations and cannot be correctly sorted.")
-            self.data_list = natsort.natsorted(self.data_list)
-            self.sample_number = self.all['first_folder_sample_number']
-        else:
-            content = os.listdir()
-            for obj in content:
-                if not os.path.isfile(obj):
-                    data_list = insensitive_glob(obj + "/" + self.all['radical'] + '*' + self.all['extension'])
-                    if len(data_list) > 0:
-                        self.all['folder_list'].append(obj)
-                        self.all['folder_number'] += 1
-            self.all['folder_list'] = np.sort(self.all['folder_list'])
-
-            if isinstance(self.all['sample_number_per_folder'], int) or len(self.all['sample_number_per_folder']) == 1:
-                self.all['sample_number_per_folder'] = np.repeat(self.all['sample_number_per_folder'],
-                                                              self.all['folder_number'])
-
-    def update_folder_id(self, sample_number, folder_name=""):
-        os.chdir(Path(self.all['global_pathway']) / folder_name)
-        self.data_list = insensitive_glob(
-            self.all['radical'] + '*' + self.all['extension'])  # Provides a list ordered by last modification date
-        # Sorting is necessary when some modifications (like rotation) modified the last modification date
-        lengths = vectorized_len(self.data_list)
-        if np.max(np.diff(lengths)) > np.log10(len(self.data_list)):
-            logging.error(f"File names present strong variations and cannot be correctly sorted.")
-        self.data_list = natsort.natsorted(self.data_list)
-        if self.all['im_or_vid'] == 1:
-            self.sample_number = len(self.data_list)
-        else:
-            self.vars['img_number'] = len(self.data_list)
-            self.sample_number = sample_number
-        if len(self.vars['analyzed_individuals']) != sample_number:
-            self.vars['analyzed_individuals'] = np.arange(sample_number) + 1
-
-    def load_data_to_run_cellects_quickly(self):
-        current_global_pathway = self.all['global_pathway']
-        folder_number = self.all['folder_number']
-        if folder_number > 1:
-            folder_list = deepcopy(self.all['folder_list'])
-            sample_number_per_folder = deepcopy(self.all['sample_number_per_folder'])
-
-        if os.path.isfile('Data to run Cellects quickly.pkl'):
-            pickle_rick = PickleRick()
-            data_to_run_cellects_quickly = pickle_rick.read_file('Data to run Cellects quickly.pkl')
-            if data_to_run_cellects_quickly is None:
-                data_to_run_cellects_quickly = {}
-
-            # try:
-            #     with open('Data to run Cellects quickly.pkl', 'rb') as fileopen:
-            #         data_to_run_cellects_quickly = pickle.load(fileopen)
-            # except pickle.UnpicklingError:
-            #     logging.error("Pickle error")
-            #     data_to_run_cellects_quickly = {}
-            if ('validated_shapes' in data_to_run_cellects_quickly) and ('coordinates' in data_to_run_cellects_quickly) and ('all' in data_to_run_cellects_quickly):
-                logging.info("Success to load Data to run Cellects quickly.pkl from the user chosen directory")
-                self.all = data_to_run_cellects_quickly['all']
-                # If you want to add a new variable, first run an updated version of all_vars_dict,
-                # then put a breakpoint here and run the following + self.save_data_to_run_cellects_quickly() :
-                # self.all['vars']['lose_accuracy_to_save_memory'] = False
-                self.vars = self.all['vars']
-                self.update_data()
-                print(self.vars['convert_for_motion'])
-                folder_changed = False
-                if current_global_pathway != self.all['global_pathway']:
-                    folder_changed = True
-                    logging.info(
-                        "Although the folder is ready, it is not at the same place as it was during creation, updating")
-                    self.all['global_pathway'] = current_global_pathway
-                if folder_number > 1:
-                    self.all['global_pathway'] = current_global_pathway
-                    self.all['folder_list'] = folder_list
-                    self.all['folder_number'] = folder_number
-                    self.all['sample_number_per_folder'] = sample_number_per_folder
-
-                if len(self.data_list) == 0:
-                    self.look_for_data()
-                    if folder_changed and folder_number > 1 and len(self.all['folder_list']) > 0:
-                        self.update_folder_id(self.all['sample_number_per_folder'][0], self.all['folder_list'][0])
-                self.get_first_image()
-                self.get_last_image()
-                (ccy1, ccy2, ccx1, ccx2, self.left, self.right, self.top, self.bot) = data_to_run_cellects_quickly[
-                    'coordinates']
-                if self.all['automatically_crop']:
-                    self.first_image.crop_coord = [ccy1, ccy2, ccx1, ccx2]
-                    logging.info("Crop first image")
-                    self.first_image.automatically_crop(self.first_image.crop_coord)
-                    logging.info("Crop last image")
-                    self.last_image.automatically_crop(self.first_image.crop_coord)
-                else:
-                    self.first_image.crop_coord = None
-                # self.cropping(True)
-                # self.cropping(False)
-                self.first_image.validated_shapes = data_to_run_cellects_quickly['validated_shapes']
-                self.first_image.im_combinations = []
-                self.current_combination_id = 0
-                self.first_image.im_combinations.append({})
-                self.first_image.im_combinations[self.current_combination_id]['csc'] = self.vars['convert_for_origin']
-                self.first_image.im_combinations[self.current_combination_id]['binary_image'] = self.first_image.validated_shapes
-                self.first_image.im_combinations[self.current_combination_id]['shape_number'] = data_to_run_cellects_quickly['shape_number']
-                
-                self.first_exp_ready_to_run = True
-                print(f"Overwrite is {self.all['overwrite_unaltered_videos']}")
-                if self.vars['subtract_background'] and len(self.vars['background_list']) == 0:
-                    self.first_exp_ready_to_run = False
-            else:
-                self.first_exp_ready_to_run = False
-        else:
-            self.first_exp_ready_to_run = False
-        if self.first_exp_ready_to_run:
-            logging.info("The current (or the first) folder is ready to run")
-        else:
-            logging.info("The current (or the first) folder is not ready to run")
-
-    def update_data(self):
-        dd = DefaultDicts()
-        all = len(dd.all) != len(self.all)
-        vars = len(dd.vars) != len(self.vars)
-        all_desc = len(dd.all['descriptors']) != len(self.all['descriptors'])
-        vars_desc = len(dd.vars['descriptors']) != len(self.vars['descriptors'])
-        if all:
-            for key, val in dd.all.items():
-                if not key in self.all:
-                    self.all[key] = val
-        if vars:
-            for key, val in dd.vars.items():
-                if not key in self.vars:
-                    self.vars[key] = val
-        if all_desc:
-            for key, val in dd.all['descriptors'].items():
-                if not key in self.all['descriptors']:
-                    self.all['descriptors'][key] = val
-        if vars_desc:
-            for key, val in dd.vars['descriptors'].items():
-                if not key in self.vars['descriptors']:
-                    self.vars['descriptors'][key] = val
-
-    def save_data_to_run_cellects_quickly(self, new_one_if_does_not_exist=True):
-        data_to_run_cellects_quickly = None
-        if os.path.isfile('Data to run Cellects quickly.pkl'):
-            logging.info("Update -Data to run Cellects quickly.pkl- in the user chosen directory")
-            pickle_rick = PickleRick()
-            data_to_run_cellects_quickly = pickle_rick.read_file('Data to run Cellects quickly.pkl')
-            if data_to_run_cellects_quickly is None:
-                logging.error("Failed to load Data to run Cellects quickly.pkl before update. Abort saving.")
-
-            # try:
-            #     with open('Data to run Cellects quickly.pkl', 'rb') as fileopen:
-            #         data_to_run_cellects_quickly = pickle.load(fileopen)
-            # except pickle.UnpicklingError:
-            #     logging.error("Pickle error")
-            #     data_to_run_cellects_quickly = {}
-        else:
-            if new_one_if_does_not_exist:
-                logging.info("Create Data to run Cellects quickly.pkl in the user chosen directory")
-                data_to_run_cellects_quickly = {}
-        if data_to_run_cellects_quickly is not None:
-            if self.data_to_save['first_image']:
-                data_to_run_cellects_quickly['validated_shapes'] = self.first_image.im_combinations[self.current_combination_id]['binary_image']
-                data_to_run_cellects_quickly['shape_number'] = self.first_image.im_combinations[self.current_combination_id]['shape_number']
-                    # data_to_run_cellects_quickly['converted_image'] = self.first_image.im_combinations[self.current_combination_id]['converted_image']
-            if self.data_to_save['coordinates']:
-                data_to_run_cellects_quickly['coordinates'] = self.list_coordinates()
-                logging.info("When they exist, do overwrite unaltered video")
-                self.all['overwrite_unaltered_videos'] = True
-            if self.data_to_save['exif']:
-                self.vars['exif'] = self.extract_exif()
-                # data_to_run_cellects_quickly['exif'] = self.extract_exif()
-            # if self.data_to_save['background_and_origin_list']:
-            #     logging.info(f"Origin shape is {self.vars['origin_list'][0].shape}")
-            #     data_to_run_cellects_quickly['background_and_origin_list'] = [self.vars['origin_list'], self.vars['background_list'], self.vars['background_list2']]
-            self.all['vars'] = self.vars
-            print(self.vars['convert_for_motion'])
-            data_to_run_cellects_quickly['all'] = self.all
-            # data_to_run_cellects_quickly['all']['vars']['origin_state'] = "fluctuating"
-            pickle_rick = PickleRick()
-            pickle_rick.write_file(data_to_run_cellects_quickly, 'Data to run Cellects quickly.pkl')
-
-    def list_coordinates(self):
-        if self.first_image.crop_coord is None:
-            self.first_image.crop_coord = [0, self.first_image.image.shape[0], 0,
-                                                       self.first_image.image.shape[1]]
-        videos_coordinates = self.first_image.crop_coord + [self.left, self.right, self.top, self.bot]
-        return videos_coordinates
-
-    def extract_exif(self):
-        if self.all['im_or_vid'] == 1:
-            timings = np.arange(self.vars['dims'][0])
-        else:
-            if sys.platform.startswith('win'):
-                pathway = os.getcwd() + '\\'
-            else:
-                pathway = os.getcwd() + '/'
-            arbitrary_time_step: bool = True
-            if self.all['extract_time_interval']:
-                self.vars['time_step'] = 1
-                try:
-                    timings = extract_time(self.data_list, pathway, self.all['raw_images'])
-                    timings = timings - timings[0]
-                    timings = timings / 60
-                    time_step = np.mean(np.diff(timings))
-                    digit_nb = 0
-                    for i in str(time_step):
-                        if i in {'.'}:
-                            pass
-                        elif i in {'0'}:
-                            digit_nb += 1
-                        else:
-                            break
-                    self.vars['time_step'] = np.round(time_step, digit_nb + 1)
-                    arbitrary_time_step = False
-                except:
-                    pass
-            if arbitrary_time_step:
-                timings = np.arange(0, self.vars['dims'][0] * self.vars['time_step'], self.vars['time_step'])
-                timings = timings - timings[0]
-                timings = timings / 60
-        return timings
-
-        #
-        # if not os.path.isfile("timings.csv") or self.all['overwrite_cellects_data']:
-        #     if self.vars['time_step'] == 0:
-        #         if self.all['im_or_vid'] == 1:
-        #             savetxt("timings.csv", np.arange(self.vars['dims'][0]), fmt='%10d', delimiter=',')
-        #         else:
-        #             if sys.platform.startswith('win'):
-        #                 pathway = os.getcwd() + '\\'
-        #             else:
-        #                 pathway = os.getcwd() + '/'
-        #             timings = extract_time(self.data_list, pathway, self.all['raw_images'])
-        #             timings = timings - timings[0]
-        #             timings = timings / 60
-        #     else:
-        #         timings = np.arange(0, self.vars['dims'][0] * self.vars['time_step'], self.vars['time_step'])
-        #     savetxt("timings.csv", timings, fmt='%1.2f', delimiter=',')
-
-    def get_first_image(self):
-        logging.info("Load first image")
-        just_read_image = self.first_im is not None
-        self.reduce_image_dim = False
-        # just_read_image = self.analysis_instance is not None
-        if self.all['im_or_vid'] == 1:
-            cap = cv2.VideoCapture(self.data_list[0])
-            counter = 0
-            if not just_read_image:
-                self.sample_number = len(self.data_list)
-                self.vars['img_number'] = int(cap.get(cv2.CAP_PROP_FRAME_COUNT))
-                self.analysis_instance = np.zeros(
-                    [int(cap.get(cv2.CAP_PROP_FRAME_COUNT)), int(cap.get(cv2.CAP_PROP_FRAME_HEIGHT)),
-                     int(cap.get(cv2.CAP_PROP_FRAME_WIDTH)), 3])
-                while cap.isOpened() and counter < 1:
-                    ret, frame = cap.read()
-                    if counter == 0:
-                        self.first_im = frame
-                        self.analysis_instance[0, ...] = self.first_im
-                        break
-                cap.release()
-            elif np.sum(self.analysis_instance[self.all['first_detection_frame'] - 1, ...] == 0):
-                cap = cv2.VideoCapture(self.data_list[0])
-                counter = 0
-                while cap.isOpened() and (counter < self.all['first_detection_frame']):
-                    ret, frame = cap.read()
-                    # if self.reduce_image_dim:
-                    #     frame = frame[:, :, 0]
-                    self.analysis_instance[counter, ...] = frame
-                    counter += 1
-
-                cap.release()
-                self.first_im = self.analysis_instance[
-                    self.all['first_detection_frame'] - 1, ...]
-            self.vars['dims'] = self.analysis_instance.shape[:3]
-
-        else:
-            self.vars['img_number'] = len(self.data_list)
-            self.all['raw_images'] = is_raw_image(self.data_list[0])
-            self.first_im = readim(self.data_list[self.all['first_detection_frame'] - 1], self.all['raw_images'])
-            # if self.reduce_image_dim:
-            #     self.first_im = self.first_im[:, :, 0]
-            self.vars['dims'] = [self.vars['img_number'], self.first_im.shape[0], self.first_im.shape[1]]
-            # self.first_im = readim(self.data_list[0], self.all['raw_images'])
-        if len(self.first_im.shape) == 3:
-            if np.all(np.equal(self.first_im[:, :, 0], self.first_im[:, :, 1])) and np.all(
-                    np.equal(self.first_im[:, :, 1], self.first_im[:, :, 2])):
-                self.reduce_image_dim = True
-            if self.reduce_image_dim:
-                self.first_im = self.first_im[:, :, 0]
-                if self.all['im_or_vid'] == 1:
-                    self.analysis_instance = self.analysis_instance[:, :, :, 0]
-        self.first_image = OneImageAnalysis(self.first_im)
-        self.vars['already_greyscale'] = self.first_image.already_greyscale
-        if self.vars['already_greyscale']:
-            self.vars["convert_for_origin"] = {"bgr": np.array((1, 1, 1), dtype=np.uint8), "logical": "None"}
-            self.vars["convert_for_motion"] = {"bgr": np.array((1, 1, 1), dtype=np.uint8), "logical": "None"}
-        if np.mean((np.mean(self.first_image.image[2, :, ...]), np.mean(self.first_image.image[-3, :, ...]), np.mean(self.first_image.image[:, 2, ...]), np.mean(self.first_image.image[:, -3, ...]))) > 127:
-            self.vars['contour_color']: np.uint8 = 0
-        else:
-            self.vars['contour_color']: np.uint8 = 255
-        if self.all['first_detection_frame'] > 1:
-            self.vars['origin_state'] = 'invisible'
-
-    def get_last_image(self):
-        logging.info("Load last image")
-        if self.all['im_or_vid'] == 1:
-            cap = cv2.VideoCapture(self.data_list[0])
-            counter = 0
-            while cap.isOpened() and counter < self.vars['img_number']:
-                ret, frame = cap.read()
-                if self.reduce_image_dim:
-                    frame = frame[:, :, 0]
-                self.analysis_instance[-1, ...] = frame
-                # if counter == self.vars['img_number'] - 1:
-                #     if self.reduce_image_dim:
-                #         frame = frame[:, :, 0]
-                #     break
-                counter += 1
-            self.last_im = frame
-            cap.release()
-        else:
-            # self.last_im = readim(self.data_list[-1], self.all['raw_images'])
-            is_landscape = self.first_image.image.shape[0] < self.first_image.image.shape[1]
-            self.last_im = read_and_rotate(self.data_list[-1], self.first_im, self.all['raw_images'], is_landscape)
-            if self.reduce_image_dim:
-                self.last_im = self.last_im[:, :, 0]
-        self.last_image = OneImageAnalysis(self.last_im)
-
-    # self.message_when_thread_finished.emit("")
-    def fast_image_segmentation(self, is_first_image, biomask=None, backmask=None, spot_size=None):
-        if is_first_image:
-            self.first_image.convert_and_segment(self.vars['convert_for_origin'], self.vars["color_number"],
-                                                 self.all["bio_mask"], self.all["back_mask"], subtract_background=None,
-                                                 subtract_background2=None, grid_segmentation=False,
-                                                 filter_spec=self.vars["filter_spec"])
-            if not self.first_image.drift_correction_already_adjusted:
-                self.vars['drift_already_corrected'] = self.first_image.check_if_image_border_attest_drift_correction()
-                if self.vars['drift_already_corrected']:
-                    logging.info("Cellects detected that the images have already been corrected for drift")
-                    self.first_image.adjust_to_drift_correction(self.vars['convert_for_origin']['logical'])
-            if self.vars["grid_segmentation"]:
-                self.first_image.convert_and_segment(self.vars['convert_for_origin'], self.vars["color_number"],
-                                                     self.all["bio_mask"], self.all["back_mask"],
-                                                     subtract_background=None, subtract_background2=None,
-                                                     grid_segmentation=True,
-                                                     filter_spec=self.vars["filter_spec"])
-
-            self.first_image.set_spot_shapes_and_size_confint(self.all['starting_blob_shape'])
-            logging.info(self.sample_number)
-            process_i = ProcessFirstImage(
-                [self.first_image, False, False, None, self.vars['several_blob_per_arena'],
-                 self.sample_number, spot_size, self.vars["color_number"], self.all["bio_mask"], self.all["back_mask"], None])
-            process_i.binary_image = self.first_image.binary_image
-            process_i.process_binary_image(use_bio_and_back_masks=True)
-
-            if self.all["back_mask"] is not None:
-                if np.any(process_i.shapes[self.all["back_mask"]]):
-                    process_i.shapes[np.isin(process_i.shapes, np.unique(process_i.shapes[self.all["back_mask"]]))] = 0
-                    process_i.validated_shapes = (process_i.shapes > 0).astype(np.uint8)
-            if self.all["bio_mask"] is not None:
-                process_i.validated_shapes[self.all["bio_mask"]] = 1
-            if self.all["back_mask"] is not None or self.all["bio_mask"] is not None:
-                process_i.shape_number, process_i.shapes = cv2.connectedComponents(process_i.validated_shapes, connectivity=8)
-                process_i.shape_number -= 1
-
-            self.first_image.validated_shapes = process_i.validated_shapes
-            self.first_image.shape_number = process_i.shape_number
-            if self.first_image.im_combinations is None:
-                self.first_image.im_combinations = []
-                self.first_image.im_combinations.append({})
-            self.first_image.im_combinations[self.current_combination_id]['csc'] = self.vars['convert_for_origin']
-            self.first_image.im_combinations[self.current_combination_id]['binary_image'] = self.first_image.validated_shapes
-            self.first_image.im_combinations[self.current_combination_id]['converted_image'] = np.round(self.first_image.image).astype(np.uint8)
-            self.first_image.im_combinations[self.current_combination_id]['shape_number'] = process_i.shape_number
-            # self.first_image.generate_color_space_combination(self.vars['convert_for_origin'], subtract_background)
-        else:
-            # self.last_image.segmentation(self.vars['convert_for_motion']['logical'], self.vars['color_number'])
-            # if self.vars['drift_already_corrected']:
-            #     drift_correction, drift_correction2 = self.last_image.adjust_to_drift_correction()
-            #     self.last_image.segmentation(self.vars['convert_for_motion']['logical'], self.vars['color_number'])
-            self.cropping(is_first_image=False)
-            print(self.vars["filter_spec"])
-            self.last_image.convert_and_segment(self.vars['convert_for_motion'], self.vars["color_number"],
-                                                biomask, backmask, self.first_image.subtract_background,
-                                                self.first_image.subtract_background2,
-                                                grid_segmentation=self.vars["grid_segmentation"],
-                                                filter_spec=self.vars["filter_spec"])
-            if self.vars['drift_already_corrected'] and not self.last_image.drift_correction_already_adjusted and not self.vars["grid_segmentation"]:
-                self.last_image.adjust_to_drift_correction(self.vars['convert_for_motion']['logical'])
-            
-            if self.last_image.im_combinations is None:
-                self.last_image.im_combinations = []
-                self.last_image.im_combinations.append({})
-            self.last_image.im_combinations[self.current_combination_id]['csc'] = self.vars['convert_for_motion']
-            self.last_image.im_combinations[self.current_combination_id]['binary_image'] = self.last_image.binary_image
-            self.last_image.im_combinations[self.current_combination_id]['converted_image'] = np.round(self.last_image.image).astype(np.uint8)
-
-            # self.last_image.generate_color_space_combination(self.vars['convert_for_motion'], subtract_background)
-            # if self.all["more_than_two_colors"]:
-            #    self.last_image.kmeans(self.vars["color_number"])
-            # else:
-            # self.last_image.thresholding()
-            # if self.all['are_gravity_centers_moving'] != 1:
-            #     self.delineate_each_arena()
-
-    def cropping(self, is_first_image):
-        if not self.vars['drift_already_corrected']:
-            if is_first_image:
-                if not self.first_image.cropped:
-                    if (not self.all['overwrite_unaltered_videos'] and os.path.isfile('Data to run Cellects quickly.pkl')):
-                        pickle_rick = PickleRick()
-                        data_to_run_cellects_quickly = pickle_rick.read_file('Data to run Cellects quickly.pkl')
-                        if data_to_run_cellects_quickly is not None:
-                            if 'coordinates' in data_to_run_cellects_quickly:
-                                logging.info("Get crop coordinates from Data to run Cellects quickly.pkl")
-                                (ccy1, ccy2, ccx1, ccx2, self.left, self.right, self.top, self.bot) = \
-                                    data_to_run_cellects_quickly['coordinates']
-                                self.first_image.crop_coord = [ccy1, ccy2, ccx1, ccx2]
-                            else:
-                                self.first_image.get_crop_coordinates()
-                        else:
-                            self.first_image.get_crop_coordinates()
-
-
-                        # try:
-                        #     with open('Data to run Cellects quickly.pkl', 'rb') as fileopen:
-                        #         data_to_run_cellects_quickly = pickle.load(fileopen)
-                        #         if 'coordinates' in data_to_run_cellects_quickly:
-                        #             logging.info("Get crop coordinates from Data to run Cellects quickly.pkl")
-                        #             (ccy1, ccy2, ccx1, ccx2, self.left, self.right, self.top, self.bot) = \
-                        #                 data_to_run_cellects_quickly['coordinates']
-                        #             self.first_image.crop_coord = [ccy1, ccy2, ccx1, ccx2]
-                        #         else:
-                        #             self.first_image.get_crop_coordinates()
-                        # except pickle.UnpicklingError:
-                        #     logging.error("Pickle error")
-                        #     self.first_image.get_crop_coordinates()
-
-
-                    # if (not self.all['overwrite_unaltered_videos'] and os.path.isfile('coordinates.pkl')):
-                    #     with open('coordinates.pkl', 'rb') as fileopen:
-                    #         (ccy1, ccy2, ccx1, ccx2, self.videos.left, self.videos.right, self.videos.top,
-                    #          self.videos.bot) = pickle.load(fileopen)
-                    else:
-                        self.first_image.get_crop_coordinates()
-                    if self.all['automatically_crop']:
-                        self.first_image.automatically_crop(self.first_image.crop_coord)
-                    else:
-                        self.first_image.crop_coord = None
-            else:
-                if not self.last_image.cropped and self.all['automatically_crop']:
-                    self.last_image.automatically_crop(self.first_image.crop_coord)
-        # if self.all['automatically_crop'] and not self.vars['drift_already_corrected']:
-        #     if is_first_image:
-        #         self.first_image.get_crop_coordinates()
-        #         self.first_image.automatically_crop(self.first_image.crop_coord)
-        #     else:
-        #         self.last_image.automatically_crop(self.first_image.crop_coord)
-
-    def get_average_pixel_size(self):
-        logging.info("Get average pixel size")
-        (self.first_image.shape_number,
-            self.first_image.shapes,
-            self.first_image.stats,
-            centroids) = cv2.connectedComponentsWithStats(
-                self.first_image.validated_shapes,
-                connectivity=8)
-        self.first_image.shape_number -= 1
-        if self.all['scale_with_image_or_cells'] == 0:
-            self.vars['average_pixel_size'] = np.square(
-                self.all['image_horizontal_size_in_mm'] /
-                self.first_im.shape[1])
-        else:
-            self.vars['average_pixel_size'] = np.square(
-                self.all['starting_blob_hsize_in_mm'] /
-                np.mean(self.first_image.stats[1:, 2]))
-        if self.all['set_spot_size']:
-            self.starting_blob_hsize_in_pixels = (
-                self.all['starting_blob_hsize_in_mm'] /
-                np.sqrt(self.vars['average_pixel_size']))
-        else:
-            self.starting_blob_hsize_in_pixels = None
-
-        if self.all['automatic_size_thresholding']:
-            self.vars['first_move_threshold'] = 10
-        else:
-            # if self.vars['origin_state'] != "invisible":
-            self.vars['first_move_threshold'] = np.round(
-                self.all['first_move_threshold_in_mm²'] /
-                self.vars['average_pixel_size']).astype(np.uint8)
-        logging.info(f"The average pixel size is: {self.vars['average_pixel_size']} mm²")
-
-    def delineate_each_arena(self):
-        self.videos = OneVideoPerBlob(
-            self.first_image,
-            self.starting_blob_hsize_in_pixels,
-            self.all['raw_images'])
-        # self.delineation_number += 1
-        # if self.delineation_number > 1:
-        #     print('stophere')
-        analysis_status = {"continue": True, "message": ""}
-        if (self.sample_number > 1 and not self.vars['several_blob_per_arena']):
-            compute_get_bb: bool = True
-            if (not self.all['overwrite_unaltered_videos'] and os.path.isfile('Data to run Cellects quickly.pkl')):
-
-                pickle_rick = PickleRick()
-                data_to_run_cellects_quickly = pickle_rick.read_file('Data to run Cellects quickly.pkl')
-                if data_to_run_cellects_quickly is not None:
-                    if 'coordinates' in data_to_run_cellects_quickly:
-                        (ccy1, ccy2, ccx1, ccx2, self.left, self.right, self.top, self.bot) = \
-                            data_to_run_cellects_quickly['coordinates']
-                        self.videos.left, self.videos.right, self.videos.top, self.videos.bot = self.left, self.right, self.top, self.bot
-                        self.first_image.crop_coord = [ccy1, ccy2, ccx1, ccx2]
-                        if (self.first_image.image.shape[0] == (ccy2 - ccy1)) and (
-                                self.first_image.image.shape[1] == (ccx2 - ccx1)):  # maybe useless now
-                            logging.info("Get the coordinates of all arenas from Data to run Cellects quickly.pkl")
-                            compute_get_bb = False
-
-
-                # try:
-                #     with open('Data to run Cellects quickly.pkl', 'rb') as fileopen:
-                #         data_to_run_cellects_quickly = pickle.load(fileopen)
-                # except pickle.UnpicklingError:
-                #     logging.error("Pickle error")
-                #     data_to_run_cellects_quickly = {}
-                # if 'coordinates' in data_to_run_cellects_quickly:
-                #     (ccy1, ccy2, ccx1, ccx2, self.left, self.right, self.top, self.bot) = \
-                #         data_to_run_cellects_quickly['coordinates']
-                #     self.first_image.crop_coord = [ccy1, ccy2, ccx1, ccx2]
-                #     if (self.first_image.image.shape[0] == (ccy2 - ccy1)) and (
-                #             self.first_image.image.shape[1] == (ccx2 - ccx1)):  # maybe useless now
-                #         logging.info("Get the coordinates of all arenas from Data to run Cellects quickly.pkl")
-                #         compute_get_bb = False
-
-            # if (not self.all['overwrite_unaltered_videos'] and os.path.isfile('coordinates.pkl')):
-            #     with open('coordinates.pkl', 'rb') as fileopen:
-            #         (ccy1, ccy2, ccx1, ccx2, self.videos.left, self.videos.right, self.videos.top, self.videos.bot) = pickle.load(fileopen)
-
-            # if (not self.all['overwrite_unaltered_videos'] and
-            #         os.path.isfile('coordinates.pkl')):
-            #     with open('coordinates.pkl', 'rb') as fileopen:
-            #         (vertical_shape, horizontal_shape, self.videos.left, self.videos.right, self.videos.top,
-            #             self.videos.bot) = pickle.load(fileopen)
-
-            if compute_get_bb:
-                if self.all['im_or_vid'] == 1:
-                    self.videos.get_bounding_boxes(
-                        are_gravity_centers_moving=self.all['are_gravity_centers_moving'] == 1,
-                        img_list=self.analysis_instance,
-                        color_space_combination=self.vars['convert_for_origin'],#self.vars['convert_for_motion']
-                        color_number=self.vars["color_number"],
-                        sample_size=5,
-                        all_specimens_have_same_direction=self.all['all_specimens_have_same_direction'],
-                        filter_spec=self.vars['filter_spec'])
-                else:
-                    self.videos.get_bounding_boxes(
-                        are_gravity_centers_moving=self.all['are_gravity_centers_moving'] == 1,
-                        img_list=self.data_list,
-                        color_space_combination=self.vars['convert_for_origin'],
-                        color_number=self.vars["color_number"],
-                        sample_size=5,
-                        all_specimens_have_same_direction=self.all['all_specimens_have_same_direction'],
-                        filter_type=self.vars['filter_spec'])
-                if np.any(self.videos.ordered_stats[:, 4] > 100 * np.median(self.videos.ordered_stats[:, 4])):
-                    analysis_status['message'] = "A specimen is at least 100 times larger: (re)do the first image analysis."
-                    analysis_status['continue'] = False
-                if np.any(self.videos.ordered_stats[:, 4] < 0.01 * np.median(self.videos.ordered_stats[:, 4])):
-                    analysis_status['message'] = "A specimen is at least 100 times smaller: (re)do the first image analysis."
-                    analysis_status['continue'] = False
-                logging.info(
-                    str(self.videos.not_analyzed_individuals) + " individuals are out of picture scope and cannot be analyzed")
-            self.left, self.right, self.top, self.bot = self.videos.left, self.videos.right, self.videos.top, self.videos.bot
-
-        else:
-            self.left, self.right, self.top, self.bot = np.array([1]), np.array([self.first_image.image.shape[1] - 2]), np.array([1]), np.array([self.first_image.image.shape[0] - 2])
-            self.videos.left, self.videos.right, self.videos.top, self.videos.bot = np.array([1]), np.array([self.first_image.image.shape[1] - 2]), np.array([1]), np.array([self.first_image.image.shape[0] - 2])
-
-        self.vars['analyzed_individuals'] = np.arange(self.sample_number) + 1
-        if self.videos.not_analyzed_individuals is not None:
-            self.vars['analyzed_individuals'] = np.delete(self.vars['analyzed_individuals'],
-                                                       self.videos.not_analyzed_individuals - 1)
-        # logging.info(self.top)
-        return analysis_status
-
-    def get_background_to_subtract(self):
-        """
-            Repenser le moment où ça arrive et trouver pourquoi ça marche pas
-        """
-        # self.vars['subtract_background'] = False
-        if self.vars['subtract_background']:
-            self.first_image.generate_subtract_background(self.vars['convert_for_motion'])
-
-    def get_origins_and_backgrounds_lists(self):
-        logging.info("Create origins and background lists")
-        if self.top is None:
-            # self.top = [1]
-            # self.bot = [self.first_im.shape[0] - 2]
-            # self.left = [1]
-            # self.right = [self.first_im.shape[1] - 2]
-            self.top = np.array([1])
-            self.bot = np.array([self.first_im.shape[0] - 2])
-            self.left = np.array([1])
-            self.right = np.array([self.first_im.shape[1] - 2])
-
-        add_to_c = 1
-        first_im = self.first_image.validated_shapes
-        self.vars['origin_list'] = []
-        self.vars['background_list'] = []
-        self.vars['background_list2'] = []
-        for rep in np.arange(len(self.vars['analyzed_individuals'])):
-            self.vars['origin_list'].append(first_im[self.top[rep]:(self.bot[rep] + add_to_c),
-                                             self.left[rep]:(self.right[rep] + add_to_c)])
-            if self.vars['subtract_background']:
-                self.vars['background_list'].append(
-                    self.first_image.subtract_background[self.top[rep]:(self.bot[rep] + add_to_c),
-                    self.left[rep]:(self.right[rep] + add_to_c)])
-                if self.vars['convert_for_motion']['logical'] != 'None':
-                    self.vars['background_list2'].append(
-                        self.first_image.subtract_background2[self.top[rep]:(self.bot[rep] + add_to_c),
-                        self.left[rep]:(self.right[rep] + add_to_c)])
-
-    def get_origins_and_backgrounds_one_by_one(self):
-        add_to_c = 1
-        self.vars['origin_list'] = []
-        self.vars['background_list'] = []
-        self.vars['background_list2'] = []
-
-        for arena in np.arange(len(self.vars['analyzed_individuals'])):
-            bgr_image = self.first_image.bgr[self.top[arena]:(self.bot[arena] + add_to_c),
-                                             self.left[arena]:(self.right[arena] + add_to_c), ...]
-            image = OneImageAnalysis(bgr_image)
-            if self.vars['subtract_background']:
-                image.generate_subtract_background(self.vars['convert_for_motion'])
-                self.vars['background_list'].append(image.image)
-                if self.vars['convert_for_motion']['logical'] != 'None':
-                    self.vars['background_list2'].append(image.image2)
-
-            # self.vars['origins_list'].append(self.first_image.validated_shapes[self.top[arena]:(self.bot[arena]),
-            #                                  self.left[arena]:(self.right[arena])])
-            #
-            if self.vars['several_blob_per_arena']:
-                image.validated_shapes = image.binary_image
-            else:
-                image.get_largest_shape()
-
-            self.vars['origin_list'].append(image.validated_shapes)
-
-    def choose_color_space_combination(self):
-        # self = po
-        # 2) Represent the segmentation using a particular color space combination
-        if self.all['are_gravity_centers_moving'] != 1:
-            analysis_status = self.delineate_each_arena()
-        # self.fi.automatically_crop(self.first_image.crop_coord)
-        self.last_image = OneImageAnalysis(self.last_im)
-        self.last_image.automatically_crop(self.videos.first_image.crop_coord)
-        # csc = ColorSpaceCombination(self.last_image.image)
-
-        concomp_nb = [self.sample_number, self.sample_number * 50]
-        if self.all['are_zigzag'] == "columns":
-            inter_dist = np.mean(np.diff(np.nonzero(self.videos.first_image.y_boundaries)))
-        elif self.all['are_zigzag'] == "rows":
-            inter_dist = np.mean(np.diff(np.nonzero(self.videos.first_image.x_boundaries)))
-        else:
-            dist1 = np.mean(np.diff(np.nonzero(self.videos.first_image.y_boundaries)))
-            dist2 = np.mean(np.diff(np.nonzero(self.videos.first_image.x_boundaries)))
-            inter_dist = np.max(dist1, dist2)
-        if self.all['starting_blob_shape'] == "circle":
-            max_shape_size = np.pi * np.square(inter_dist)
-        else:
-            max_shape_size = np.square(2 * inter_dist)
-        total_surfarea = max_shape_size * self.sample_number
-        if self.all['are_gravity_centers_moving'] != 1:
-            out_of_arenas = np.ones_like(self.videos.first_image.validated_shapes)
-            for blob_i in np.arange(len(self.vars['analyzed_individuals'])):
-                out_of_arenas[self.top[blob_i]: (self.bot[blob_i] + 1),
-                self.left[blob_i]: (self.right[blob_i] + 1)] = 0
-        else:
-            out_of_arenas = None
-        ref_image = self.videos.first_image.validated_shapes
-        self.last_image.find_potential_channels(concomp_nb, total_surfarea, max_shape_size, out_of_arenas, ref_image)
-        # csc.find_potential_channels(concomp_nb, total_surfarea, max_shape_size, out_of_arenas, ref_image)
-        # csc.find_potential_channels(concomp_nb, total_surfarea, max_shape_size, out_of_arenas, ref_image, self.first_image.subtract_background)
-        self.vars['convert_for_motion'] = self.last_image.channel_combination
-
-        self.fast_image_segmentation(False)
-        # if self.vars['subtract_background']:
-        #     csc = ColorSpaceCombination(self.last_image.image)
-        #     csc.generate(self.vars['convert_for_motion'], self.first_image.subtract_background)
-        # if self.all["more_than_two_colors"]:
-        #     csc.kmeans(self.vars["color_number"])
-        # else:
-        #     csc.thresholding()
-        # self.last_image.image = csc.image
-        # self.last_image.binary_image = csc.binary_image
-
-    def untype_csc_dict(self):
-        new_convert_for_origin = {}
-        for k, v in self.vars['convert_for_origin'].items():
-            new_convert_for_origin[k] = v
-        if self.vars['logical_between_csc_for_origin'] is not None:
-            new_convert_for_origin['logical'] = self.vars['logical_between_csc_for_origin']
-            for k, v in self.vars['convert_for_origin2'].items():
-                new_convert_for_origin[k] = v
-        self.vars['convert_for_origin'] = new_convert_for_origin
-        self.vars['convert_for_origin2'] = {}
-
-        new_convert_for_motion = {}
-        for k, v in self.vars['convert_for_motion'].items():
-            new_convert_for_motion[k] = v
-        if self.vars['convert_for_motion']['logical']  != 'None':
-            new_convert_for_motion['logical'] = self.vars['convert_for_motion']['logical']
-            for k, v in self.vars['convert_for_motion2'].items():
-                new_convert_for_motion[k] = v
-        self.vars['convert_for_motion'] = new_convert_for_motion
-        self.vars['convert_for_motion2'] = {}
-
-    def type_csc_dict(self):
-        # self.vars['convert_for_motion']['logical'] = 'And'
-        # self.vars['convert_for_motion']['hsv'] = np.array((0, 0, 1))
-        # self.vars['convert_for_motion']['logical'] = 'And'
-        # self.vars['convert_for_motion']['lab2'] = np.array((0, 0, 1))
-
-        new_convert_for_origin = TDict()
-        self.vars['convert_for_origin2'] = TDict()
-        self.vars['logical_between_csc_for_origin'] = None
-        for k, v in self.vars['convert_for_origin'].items():
-             if k != 'logical' and v.sum() > 0:
-                 if k[-1] != '2':
-                     new_convert_for_origin[k] = v
-                 else:
-                     self.vars['convert_for_origin2'][k[:-1]] = v
-             else:
-                 self.vars['logical_between_csc_for_origin'] = v
-        self.vars['convert_for_origin'] = new_convert_for_origin
-
-        new_convert_for_motion = TDict()
-        self.vars['convert_for_motion2'] = TDict()
-        self.vars['convert_for_motion']['logical'] = None
-        for k, v in self.vars['convert_for_motion'].items():
-            if k != 'logical' and v.sum() > 0:
-                if k[-1] != '2':
-                    new_convert_for_motion[k] = v
-                else:
-                    self.vars['convert_for_motion2'][k[:-1]] = v
-            else:
-                self.vars['convert_for_motion']['logical'] = v
-        self.vars['convert_for_motion'] = new_convert_for_motion
-
-        if self.vars['color_number'] > 2:
-            self.vars['bio_label'] = None#self.first_image.bio_label
-            if self.vars['convert_for_motion']['logical']  != 'None':
-                self.vars['bio_label2'] = None
-
-    def find_if_lighter_background(self):
-        logging.info("Find if the background is lighter or darker than the cells")
-        self.vars['lighter_background']: bool = True
-        self.vars['contour_color']: np.uint8 = 0
-        are_dicts_equal: bool = True
-        for key in self.vars['convert_for_origin'].keys():
-            are_dicts_equal = are_dicts_equal and np.all(key in self.vars['convert_for_motion'] and self.vars['convert_for_origin'][key] == self.vars['convert_for_motion'][key])
-        for key in self.vars['convert_for_motion'].keys():
-            are_dicts_equal = are_dicts_equal and np.all(key in self.vars['convert_for_origin'] and self.vars['convert_for_motion'][key] == self.vars['convert_for_origin'][key])
-
-        if are_dicts_equal:
-
-            if self.first_im is None:
-                self.get_first_image()
-                self.fast_image_segmentation(True)
-                self.cropping(is_first_image=True)
-            among = np.nonzero(self.first_image.validated_shapes)
-            not_among = np.nonzero(1 - self.first_image.validated_shapes)
-            # Use the converted image to tell if the background is lighter, for analysis purposes
-            if self.first_image.image[among[0], among[1]].mean() > self.first_image.image[not_among[0], not_among[1]].mean():
-                self.vars['lighter_background'] = False
-            # Use the original image to tell if the background is lighter, for display purposes
-            if self.first_image.bgr[among[0], among[1], ...].mean() > self.first_image.bgr[not_among[0], not_among[1], ...].mean():
-                self.vars['contour_color'] = 255
-        else:
-            if self.last_im is None:
-                self.get_last_image()
-                # self.cropping(is_first_image=False)
-                self.fast_image_segmentation(is_first_image=False)
-            if self.last_image.binary_image.sum() == 0:
-                self.fast_image_segmentation(is_first_image=False)
-            among = np.nonzero(self.last_image.binary_image)
-            not_among = np.nonzero(1 - self.last_image.binary_image)
-            # Use the converted image to tell if the background is lighter, for analysis purposes
-            if self.last_image.image[among[0], among[1]].mean() > self.last_image.image[not_among[0], not_among[1]].mean():
-                self.vars['lighter_background'] = False
-            # Use the original image to tell if the background is lighter, for display purposes
-            if self.last_image.bgr[among[0], among[1], ...].mean() > self.last_image.bgr[not_among[0], not_among[1], ...].mean():
-                self.vars['contour_color'] = 255
-        if self.vars['origin_state'] == "invisible":
-            binary_image = deepcopy(self.first_image.binary_image)
-            self.first_image.convert_and_segment(self.vars['convert_for_motion'], self.vars["color_number"],
-                                                 None, None, subtract_background=None,
-                                                 subtract_background2=None,
-                                                 grid_segmentation=self.vars["grid_segmentation"],
-                                                 filter_spec=self.vars["filter_spec"])
-            covered_values = self.first_image.image[np.nonzero(binary_image)]
-            if self.vars['lighter_background']:
-                if np.max(covered_values) < 255:
-                    self.vars['luminosity_threshold'] = np.max(covered_values) + 1
-                else:
-                    self.vars['luminosity_threshold'] = 127
-            else:
-                if np.min(covered_values) > 0:
-                    self.vars['luminosity_threshold'] = np.min(covered_values) - 1
-                else:
-                    self.vars['luminosity_threshold'] = 127
-
-    def load_one_arena(self, arena):
-        #self.delineate_each_arena()
-        #self.choose_color_space_combination()
-        add_to_c = 1
-        self.one_arena_done = True
-        i = np.nonzero(self.vars['analyzed_individuals'] == arena)[0][0]
-        self.converted_video = np.zeros(
-            (len(self.data_list), self.bot[i] - self.top[i] + add_to_c, self.right[i] - self.left[i] + add_to_c),
-            dtype=float)
-        if not self.vars['already_greyscale']:
-            self.visu = np.zeros((len(self.data_list), self.bot[i] - self.top[i] + add_to_c, self.right[i] - self.left[i] + add_to_c, 3), dtype=np.uint8)
-            if self.vars['convert_for_motion']['logical'] != 'None':
-                self.converted_video2 = np.zeros((len(self.data_list), self.bot[i] - self.top[i] + add_to_c, self.right[i] - self.left[i] + add_to_c), dtype=float)
-            first_dict = TDict()
-            second_dict = TDict()
-            c_spaces = []
-            for k, v in self.vars['convert_for_motion'].items():
-                if k != 'logical' and v.sum() > 0:
-                    if k[-1] != '2':
-                        first_dict[k] = v
-                        c_spaces.append(k)
-                    else:
-                        second_dict[k[:-1]] = v
-                        c_spaces.append(k[:-1])
-        prev_img = None
-        background = None
-        background2 = None
-        is_landscape = self.first_image.image.shape[0] < self.first_image.image.shape[1]
-        for image_i, image_name in enumerate(self.data_list):
-            img = read_and_rotate(image_name, prev_img, self.all['raw_images'], is_landscape, self.first_image.crop_coord)
-            prev_img = deepcopy(img)
-            # if self.videos.first_image.crop_coord is not None:
-            #     img = img[self.videos.first_image.crop_coord[0]:self.videos.first_image.crop_coord[1],
-            #               self.videos.first_image.crop_coord[2]:self.videos.first_image.crop_coord[3], :]
-            img = img[self.top[arena - 1]: (self.bot[arena - 1] + add_to_c),
-                                                    self.left[arena - 1]: (self.right[arena - 1] + add_to_c), :]
-
-            if self.vars['already_greyscale']:
-                if self.reduce_image_dim:
-                    self.converted_video[image_i, ...] = img[:, :, 0]
-                else:
-                    self.converted_video[image_i, ...] = img
-            else:
-                self.visu[image_i, ...] = img
-                if self.vars['subtract_background']:
-                    background = self.vars['background_list'][i]
-                    if self.vars['convert_for_motion']['logical'] != 'None':
-                        background2 = self.vars['background_list2'][i]
-                greyscale_image, greyscale_image2 = generate_color_space_combination(img, c_spaces, first_dict,
-                                                                                     second_dict, background, background2,
-                                                                                     self.vars[
-                                                                                         'lose_accuracy_to_save_memory'])
-                self.converted_video[image_i, ...] = greyscale_image
-                if self.vars['convert_for_motion']['logical'] != 'None':
-                    self.converted_video2[image_i, ...] = greyscale_image2
-                # csc = OneImageAnalysis(img)
-                # else:
-                #     csc.generate_color_space_combination(c_spaces, first_dict, second_dict, None, None)
-                # # self.converted_video[image_i, ...] = csc.image
-                # self.converted_video[image_i, ...] = csc.image
-                # if self.vars['convert_for_motion']['logical'] != 'None':
-                #     self.converted_video2[image_i, ...] = csc.image2
-
-        # write_video(self.visu, f"ind_{arena}{self.vars['videos_extension']}", is_color=True, fps=1)
-
-    def update_output_list(self):
-        self.vars['descriptors'] = {}
-        # self.vars['descriptors']['final_area'] = True  # [False, True, False]
-        # if self.vars['first_move_threshold'] is not None:
-        #     self.vars['descriptors']['first_move'] = True  # [False, True, False]
-
-        # if self.vars['iso_digi_analysis']:
-        #     self.vars['descriptors']['is_growth_isotropic'] = True  # [False, True, False]
-        #     self.vars['descriptors']['iso_digi_transi'] = True  # [False, True, False]
-
-        # if self.vars['oscilacyto_analysis']:
-        # self.vars['descriptors']['max_magnitude'] = True#[False, True, False]
-        # self.vars['descriptors']['frequency_of_max_magnitude'] = True#[False, True, False]
-        for descriptor in self.all['descriptors'].keys():
-            if descriptor == 'standard_deviation_xy':
-                self.vars['descriptors']['standard_deviation_x'] = self.all['descriptors'][descriptor]
-                self.vars['descriptors']['standard_deviation_y'] = self.all['descriptors'][descriptor]
-            elif descriptor == 'skewness_xy':
-                self.vars['descriptors']['skewness_x'] = self.all['descriptors'][descriptor]
-                self.vars['descriptors']['skewness_y'] = self.all['descriptors'][descriptor]
-            elif descriptor == 'kurtosis_xy':
-                self.vars['descriptors']['kurtosis_x'] = self.all['descriptors'][descriptor]
-                self.vars['descriptors']['kurtosis_y'] = self.all['descriptors'][descriptor]
-            elif descriptor == 'major_axes_len_and_angle':
-                self.vars['descriptors']['major_axis_len'] = self.all['descriptors'][descriptor]
-                self.vars['descriptors']['minor_axis_len'] = self.all['descriptors'][descriptor]
-                self.vars['descriptors']['axes_orientation'] = self.all['descriptors'][descriptor]
-            else:
-                if np.isin(descriptor, list(from_shape_descriptors_class.keys())):
-                
-                    self.vars['descriptors'][descriptor] = self.all['descriptors'][descriptor]
-        self.vars['descriptors']['cluster_number'] = self.vars['oscilacyto_analysis']
-        self.vars['descriptors']['mean_cluster_area'] = self.vars['oscilacyto_analysis']
-        self.vars['descriptors']['vertices_number'] = self.vars['network_analysis']
-        self.vars['descriptors']['edges_number'] = self.vars['network_analysis']
-        self.vars['descriptors']['newly_explored_area'] = self.vars['do_fading']
-        """                             if self.vars['descriptors_means']:
-                    self.vars['output_list'] += [f'{descriptor}_mean']
-                    self.vars['output_list'] += [f'{descriptor}_std']
-                if self.vars['descriptors_regressions']:
-                    self.vars['output_list'] += [f"{descriptor}_reg_start"]
-                    self.vars['output_list'] += [f"{descriptor}_reg_end"]
-                    self.vars['output_list'] += [f'{descriptor}_slope']
-                    self.vars['output_list'] += [f'{descriptor}_intercept']
-        """
-
-    def update_available_core_nb(self, image_bit_number=256, video_bit_number=140):# video_bit_number=176
-        if self.vars['lose_accuracy_to_save_memory']:
-            video_bit_number -= 56
-        if self.vars['convert_for_motion']['logical'] != 'None':
-            video_bit_number += 64
-            if self.vars['lose_accuracy_to_save_memory']:
-                video_bit_number -= 56
-        if self.vars['already_greyscale']:
-            video_bit_number -= 64
-        if self.vars['save_coord_thickening_slimming'] or self.vars['oscilacyto_analysis']:
-            video_bit_number += 16
-            image_bit_number += 128
-        if self.vars['save_coord_network'] or self.vars['network_analysis']:
-            video_bit_number += 8
-            image_bit_number += 64
-
-        if isinstance(self.bot, list):
-            one_image_memory = np.multiply((self.bot[0] - self.top[0] + 1),
-                                        (self.right[0] - self.left[0] + 1)).max().astype(np.uint64)
-        else:
-            one_image_memory = np.multiply((self.bot - self.top + 1).astype(np.uint64),
-                                        (self.right - self.left + 1).astype(np.uint64)).max()
-        one_video_memory = self.vars['img_number'] * one_image_memory
-        necessary_memory = (one_image_memory * image_bit_number + one_video_memory * video_bit_number) * 1.16415e-10
-        available_memory = (virtual_memory().available >> 30) - self.vars['min_ram_free']
-        max_repeat_in_memory = (available_memory // necessary_memory).astype(np.uint16)
-        if max_repeat_in_memory > 1:
-            max_repeat_in_memory = np.max(((available_memory // (2 * necessary_memory)).astype(np.uint16), 1))
-        # if sys.platform.startswith('win'):
-        #     available_memory = (virtual_memory().available >> 30) - self.vars['min_ram_free']
-        # else:
-
-        self.cores = np.min((self.all['cores'], max_repeat_in_memory))
-        if self.cores > self.sample_number:
-            self.cores = self.sample_number
-        return np.round(np.absolute(available_memory - necessary_memory), 3)
-
-
-    def update_one_row_per_arena(self, i, table_to_add):
-        if not self.vars['several_blob_per_arena']:
-            if self.one_row_per_arena is None:
-                self.one_row_per_arena = pd.DataFrame(np.zeros((len(self.vars['analyzed_individuals']), len(table_to_add)), dtype=float),
-                                            columns=table_to_add.keys())
-            self.one_row_per_arena.iloc[i, :] = table_to_add.values()
-
-
-    def update_one_row_per_frame(self, i, j, table_to_add):
-        if not self.vars['several_blob_per_arena']:
-            if self.one_row_per_frame is None:
-                self.one_row_per_frame = pd.DataFrame(index=range(len(self.vars['analyzed_individuals']) *
-                                                        self.vars['img_number']),
-                                            columns=table_to_add.keys())
-
-            self.one_row_per_frame.iloc[i:j, :] = table_to_add
-
-
-    def instantiate_tables(self):
-        self.update_output_list()
-        logging.info("Instantiate results tables and validation images")
-        self.one_row_per_oscillating_cluster = None
-        self.fractal_box_sizes = None
-        # if self.vars['oscilacyto_analysis']:
-        #     self.one_row_per_oscillating_cluster = pd.DataFrame(columns=['arena', 'mean_pixel_period', 'phase', 'cluster_size',
-        #                                                        'edge_distance'])
-        # if self.vars['fractal_analysis']:
-        #     self.fractal_box_sizes = pd.DataFrame(columns=['arena', 'time', 'fractal_box_lengths', 'fractal_box_widths'])
-
-        if self.vars['already_greyscale']:
-            if len(self.first_image.bgr.shape) == 2:
-                self.first_image.bgr = np.stack((self.first_image.bgr, self.first_image.bgr, self.first_image.bgr), axis=2).astype(np.uint8)
-            if len(self.last_image.bgr.shape) == 2:
-                self.last_image.bgr = np.stack((self.last_image.bgr, self.last_image.bgr, self.last_image.bgr), axis=2).astype(np.uint8)
-            self.vars["convert_for_motion"] = {"bgr": np.array((1, 1, 1), dtype=np.uint8), "logical": "None"}
-
-    def add_analysis_visualization_to_first_and_last_images(self, i, first_visualization, last_visualization):
-        cr = ((self.top[i], self.bot[i] + 1),
-              (self.left[i], self.right[i] + 1))
-        if self.vars['arena_shape'] == 'circle':
-            ellipse = Ellipse((cr[0][1] - cr[0][0], cr[1][1] - cr[1][0])).create()
-            ellipse = np.stack((ellipse, ellipse, ellipse), axis=2).astype(np.uint8)
-            first_visualization *= ellipse
-            self.first_image.bgr[cr[0][0]:cr[0][1], cr[1][0]:cr[1][1], ...] *= (1 - ellipse)
-            self.first_image.bgr[cr[0][0]:cr[0][1], cr[1][0]:cr[1][1], ...] += first_visualization
-            last_visualization *= ellipse
-            self.last_image.bgr[cr[0][0]:cr[0][1], cr[1][0]:cr[1][1], ...] *= (1 - ellipse)
-            self.last_image.bgr[cr[0][0]:cr[0][1], cr[1][0]:cr[1][1], ...] += last_visualization
-        else:
-            self.first_image.bgr[cr[0][0]:cr[0][1], cr[1][0]:cr[1][1], ...] = first_visualization
-            self.last_image.bgr[cr[0][0]:cr[0][1], cr[1][0]:cr[1][1], ...] = last_visualization
-
-
-    def save_tables(self):
-        logging.info("Save results tables and validation images")
-        if not self.vars['several_blob_per_arena']:
-            try:
-                self.one_row_per_arena.to_csv("one_row_per_arena.csv", sep=";", index=False, lineterminator='\n')
-                del self.one_row_per_arena
-            except PermissionError:
-                logging.error("Never let one_row_per_arena.csv open when Cellects runs")
-                self.message_from_thread.emit(f"Never let one_row_per_arena.csv open when Cellects runs")
-            try:
-                self.one_row_per_frame.to_csv("one_row_per_frame.csv", sep=";", index=False, lineterminator='\n')
-                del self.one_row_per_frame
-            except PermissionError:
-                logging.error("Never let one_row_per_frame.csv open when Cellects runs")
-                self.message_from_thread.emit(f"Never let one_row_per_frame.csv open when Cellects runs")
-        if self.vars['oscilacyto_analysis']:
-            try:
-                if self.one_row_per_oscillating_cluster is None:
-                    self.one_row_per_oscillating_cluster = pd.DataFrame(columns=['arena', 'mean_pixel_period', 'phase', 'cluster_size',
-                                                                       'edge_distance'])
-                self.one_row_per_oscillating_cluster.to_csv("one_row_per_oscillating_cluster.csv", sep=";", index=False,
-                                                            lineterminator='\n')
-                del self.one_row_per_oscillating_cluster
-            except PermissionError:
-                logging.error("Never let one_row_per_oscillating_cluster.csv open when Cellects runs")
-                self.message_from_thread.emit(f"Never let one_row_per_oscillating_cluster.csv open when Cellects runs")
-
-            if self.vars['fractal_analysis']:
-                if os.path.isfile(f"oscillating_clusters_temporal_dynamics.h5"):
-                    array_names = get_h5_keys(f"oscillating_clusters_temporal_dynamics.h5")
-                    arena_fractal_dynamics = read_h5_array(f"oscillating_clusters_temporal_dynamics.h5", key=array_names[0])
-                    arena_fractal_dynamics = np.hstack((np.repeat(np.uint32(array_names[0][-1]), arena_fractal_dynamics.shape[0]), arena_fractal_dynamics))
-                    for array_name in array_names[1:]:
-                        fractal_dynamics = read_h5_array(f"oscillating_clusters_temporal_dynamics.h5", key=array_name)
-                        fractal_dynamics = np.hstack((np.repeat(np.uint32(array_name[-1]), fractal_dynamics.shape[0]), fractal_dynamics))
-                        arena_fractal_dynamics = np.vstack((arena_fractal_dynamics, fractal_dynamics))
-                    arena_fractal_dynamics = pd.DataFrame(arena_fractal_dynamics, columns=["arena", "time", "cluster_id", "flow", "centroid_y", "centroid_x", "area", "inner_network_area", "box_count_dim", "inner_network_box_count_dim"])
-                    arena_fractal_dynamics.to_csv(f"oscillating_clusters_temporal_dynamics.csv", sep=";", index=False,
-                                                                lineterminator='\n')
-                    del arena_fractal_dynamics
-                    os.remove(f"oscillating_clusters_temporal_dynamics.h5")
-        if self.all['extension'] == '.JPG':
-            extension = '.PNG'
-        else:
-            extension = '.JPG'
-        cv2.imwrite(f"Analysis efficiency, last image{extension}", self.last_image.bgr)
-        cv2.imwrite(
-            f"Analysis efficiency, {np.ceil(self.vars['img_number'] / 10).astype(np.uint64)}th image{extension}",
-            self.first_image.bgr)
-        # self.save_analysis_parameters.to_csv("analysis_parameters.csv", sep=";")
-
-        software_settings = deepcopy(self.vars)
-        for key in ['descriptors', 'analyzed_individuals', 'exif', 'dims', 'origin_list', 'background_list', 'background_list2', 'descriptors', 'folder_list', 'sample_number_per_folder']:
-            software_settings.pop(key, None)
-        global_settings = deepcopy(self.all)
-        for key in ['analyzed_individuals', 'night_mode', 'expert_mode', 'is_auto', 'arena', 'video_option', 'compute_all_options', 'vars', 'dims', 'origin_list', 'background_list', 'background_list2', 'descriptors', 'folder_list', 'sample_number_per_folder']:
-            global_settings.pop(key, None)
-        software_settings.update(global_settings)
-        software_settings = pd.DataFrame.from_dict(software_settings, columns=["Setting"], orient='index')
-        try:
-            software_settings.to_csv("software_settings.csv", sep=";")
-        except PermissionError:
-            logging.error("Never let software_settings.csv open when Cellects runs")
-            self.message_from_thread.emit(f"Never let software_settings.csv open when Cellects runs")
-
-
-
-# if __name__ == "__main__":
-#     po = ProgramOrganizer()
-#     os.chdir(Path("D:\Directory\Data\Example\Example\Example"))
-#     # po.all['global_pathway'] = Path("C:/Users/APELab/Documents/Aurèle/Cellects/install/Installer_and_example/Example")
-#     po.load_variable_dict()
-#     po.all['global_pathway']
-#     po.load_data_to_run_cellects_quickly()
-#     po.all['global_pathway']
-#     po.save_data_to_run_cellects_quickly()
+#!/usr/bin/env python3
+"""This file contains the class constituting the link between the graphical interface and the computations.
+ First, Cellects analyze one image in order to get a color space combination maximizing the contrast between the specimens
+ and the background.
+ Second, Cellects automatically delineate each arena.
+ Third, Cellects write one video for each arena.
+ Fourth, Cellects segments the video and apply post-processing algorithms to improve the segmentation.
+ Fifth, Cellects extract variables and store them in .csv files.
+"""
+
+import pickle
+import sys
+import os
+import logging
+from copy import deepcopy
+import psutil
+import cv2
+from numba.typed import Dict as TDict
+import pandas as pd
+import numpy as np
+from numpy.typing import NDArray
+from psutil import virtual_memory
+from pathlib import Path
+import natsort
+from cellects.utils.formulas import bracket_to_uint8_image_contrast
+from cellects.utils.load_display_save import extract_time
+from cellects.image_analysis.network_functions import detect_network_dynamics, extract_graph_dynamics
+from cellects.utils.load_display_save import PickleRick, readim, is_raw_image, read_h5_array, get_h5_keys
+from cellects.utils.utilitarian import insensitive_glob, vectorized_len
+from cellects.core.cellects_paths import CELLECTS_DIR, ALL_VARS_PKL_FILE
+from cellects.config.all_vars_dict import DefaultDicts
+from cellects.image_analysis.shape_descriptors import from_shape_descriptors_class, compute_one_descriptor_per_frame, compute_one_descriptor_per_colony
+from cellects.image_analysis.morphological_operations import create_ellipse, rank_from_top_to_bottom_from_left_to_right, \
+    get_quick_bounding_boxes, get_bb_with_moving_centers, get_contours, keep_one_connected_component, box_counting_dimension, prepare_box_counting
+from cellects.image_analysis.progressively_add_distant_shapes import ProgressivelyAddDistantShapes
+from cellects.core.one_image_analysis import OneImageAnalysis
+from cellects.utils.load_display_save import read_and_rotate, video2numpy
+from cellects.image_analysis.morphological_operations import shape_selection, draw_img_with_mask
+
+
+class ProgramOrganizer:
+    """
+    Organizes and manages variables, configuration settings, and processing workflows for motion analysis in a Cellects project.
+
+    This class maintains global state and analysis-specific data structures, handles file operations,
+    processes image/video inputs, and generates output tables. It provides methods to load/save configurations,
+    segment images, track objects across frames, and export results with metadata.
+
+    Attributes
+    ----------
+    one_arena_done : bool
+        Flag indicating whether a single arena has been processed.
+    reduce_image_dim : bool
+        Whether image dimensions should be reduced (e.g., from color to grayscale).
+    first_exp_ready_to_run : bool
+        Indicates if the initial experiment setup is complete and ready for execution.
+    data_to_save : dict of {str: bool}
+        Specifies which data types (first image, coordinates, EXIF) require saving.
+    videos : OneVideoPerBlob or None
+        Video processing container instance.
+    motion : MotionAnalysis or None
+        Motion tracking and analysis module.
+    all : dict
+        Global configuration parameters for the entire workflow.
+    vars : dict
+        Analysis-specific variables used by `MotionAnalysis`.
+    first_im, last_im : np.ndarray or None
+        First and last images of the dataset for preprocessing.
+    data_list : list of str
+        List of video/image file paths in the working directory.
+    computed_video_options : np.ndarray of bool
+        Flags indicating which video processing options have been applied.
+    one_row_per_arena, one_row_per_frame : pd.DataFrame or None
+        Result tables for different levels of analysis (per arena, per frame, and oscillating clusters).
+
+    Methods:
+    --------
+    save_variable_dict() : Save configuration dictionaries to file.
+    load_variable_dict() : Load saved configuration or initialize defaults.
+    look_for_data() : Discover video/image files in the working directory.
+    update_folder_id(...) : Update folder-specific metadata based on file structure.
+    ...
+
+    """
+    def __init__(self):
+        """
+            This class stores all variables required for analysis as well as
+            methods to process it.
+            Global variables (i.e. that does not concern the MotionAnalysis)
+            are directly stored in self.
+            Variables used in the MotionAnalysis class are stored in a dict
+            called self.vars
+        """
+        if os.path.isfile('PickleRick.pkl'):
+            os.remove('PickleRick.pkl')
+        if os.path.isfile('PickleRick0.pkl'):
+            os.remove('PickleRick0.pkl')
+        self.one_arena_done: bool = False
+        self.reduce_image_dim: bool = False
+        self.first_exp_ready_to_run: bool = False
+        self.data_to_save = {'first_image': False, 'coordinates': False, 'exif': False, 'vars': False}
+        self.sample_number = None
+        self.top = None
+        self.motion = None
+        self.analysis_instance = None
+        self.computed_video_options = np.zeros(5, bool)
+        self.vars = {}
+        self.all = {}
+        self.all['folder_list'] = []
+        self.vars['first_detection_frame'] = 0
+        self.first_im = None
+        self.last_im = None
+        self.vars['background_list'] = []
+        self.starting_blob_hsize_in_pixels = None
+        self.vars['first_move_threshold'] = None
+        self.vars['convert_for_origin'] = None
+        self.vars['convert_for_motion'] = None
+        self.current_combination_id = 0
+        self.data_list = []
+        self.one_row_per_arena = None
+        self.one_row_per_frame = None
+        self.not_analyzed_individuals = None
+        self.visualize: bool = True
+
+    def update_variable_dict(self):
+        """
+
+        Update the `all` and `vars` dictionaries with new data from `DefaultDicts`.
+
+        This method updates the `all` and `vars` dictionaries of the current object with
+        data from a new instance of `DefaultDicts`. It checks if any keys or descriptors
+        are missing and adds them accordingly.
+
+        Examples
+        --------
+        >>> organizer = ProgramOrganizer()
+        >>> organizer.update_variable_dict()
+        """
+        dd = DefaultDicts()
+        all = len(dd.all) != len(self.all)
+        vars = len(dd.vars) != len(self.vars)
+        all_desc = not 'descriptors' in self.all or len(dd.all['descriptors']) != len(self.all['descriptors'])
+        vars_desc = not 'descriptors' in self.vars or len(dd.vars['descriptors']) != len(self.vars['descriptors'])
+        if all:
+            for key, val in dd.all.items():
+                if not key in self.all:
+                    self.all[key] = val
+        if vars:
+            for key, val in dd.vars.items():
+                if not key in self.vars:
+                    self.vars[key] = val
+        if all_desc:
+            for key, val in dd.all['descriptors'].items():
+                if not key in self.all['descriptors']:
+                    self.all['descriptors'][key] = val
+        if vars_desc:
+            for key, val in dd.vars['descriptors'].items():
+                if not key in self.vars['descriptors']:
+                    self.vars['descriptors'][key] = val
+        self._set_analyzed_individuals()
+
+    def save_variable_dict(self):
+        """
+        Saves the configuration dictionaries (`self.all` and `self.vars`) to a pickle file.
+
+        If bio_mask or back_mask are not required for all folders, they are excluded from the saved data.
+
+        Notes
+        -----
+        This method is used to preserve state between Cellects sessions or restart scenarios.
+        """
+        logging.info("Save the parameters dictionaries in the Cellects folder")
+        self.all['vars'] = self.vars
+        all_vars = deepcopy(self.all)
+        if not self.all['keep_cell_and_back_for_all_folders']:
+            all_vars['bio_mask'] = None
+            all_vars['back_mask'] = None
+        pickle_rick = PickleRick(0)
+        pickle_rick.write_file(all_vars, ALL_VARS_PKL_FILE)
+
+    def load_variable_dict(self):
+        """
+        Loads configuration dictionaries from a pickle file if available, otherwise initializes defaults.
+
+        Tries to load saved parameters. If the file doesn't exist or loading fails due to corruption,
+        default values are used instead (logging relevant warnings).
+
+        Raises
+        ------
+        FileNotFoundError
+            If no valid configuration file is found and default initialization fails.
+
+        Notes
+        -----
+        This method ensures robust operation by handling missing or corrupted configuration files gracefully.
+        """
+        if os.path.isfile(ALL_VARS_PKL_FILE):
+            logging.info("Load the parameters from all_vars.pkl in the config of the Cellects folder")
+            try:
+                with open(ALL_VARS_PKL_FILE, 'rb') as fileopen:
+                    self.all = pickle.load(fileopen)
+                self.vars = self.all['vars']
+                self.update_variable_dict()
+                logging.info("Success to load the parameters dictionaries from the Cellects folder")
+            except Exception as exc:
+                logging.error(f"Initialize default parameters because error: {exc}")
+                default_dicts = DefaultDicts()
+                self.all = default_dicts.all
+                self.vars = default_dicts.vars
+        else:
+            logging.info("Initialize default parameters")
+            default_dicts = DefaultDicts()
+            self.all = default_dicts.all
+            self.vars = default_dicts.vars
+        if self.all['cores'] == 1:
+            self.all['cores'] = os.cpu_count() - 1
+
+    def look_for_data(self):
+        """
+        Discovers all relevant video/image data in the working directory.
+
+        Uses natural sorting to handle filenames with numeric suffixes. Validates file consistency and logs warnings
+        if filename patterns are inconsistent across folders.
+
+        Raises
+        ------
+        ValueError
+            If no files match the specified naming convention.
+
+        Notes
+        -----
+        This method assumes all data files follow a predictable pattern with numeric extensions. Use caution in
+        unpredictable directory structures where this may fail silently or produce incorrect results.
+
+        Examples
+        --------
+        >>> organizer.look_for_data()
+        >>> print(organizer.data_list)
+        ['/path/to/video1.avi', '/path/to/video2.avi']
+        """
+        os.chdir(Path(self.all['global_pathway']))
+        logging.info(f"Dir: {self.all['global_pathway']}")
+        self.data_list = insensitive_glob(self.all['radical'] + '*' + self.all['extension'])  # Provides a list ordered by last modification date
+        self.all['folder_list'] = []
+        self.all['folder_number'] = 1
+        if len(self.data_list) > 0:
+            self._sort_data_list()
+            self.sample_number = self.all['first_folder_sample_number']
+        else:
+            content = os.listdir()
+            for obj in content:
+                if not os.path.isfile(obj):
+                    data_list = insensitive_glob(obj + "/" + self.all['radical'] + '*' + self.all['extension'])
+                    if len(data_list) > 0:
+                        self.all['folder_list'].append(obj)
+                        self.all['folder_number'] += 1
+            self.all['folder_list'] = np.sort(self.all['folder_list'])
+
+            if isinstance(self.all['sample_number_per_folder'], int) or len(self.all['sample_number_per_folder']) == 1:
+                self.all['sample_number_per_folder'] = np.repeat(self.all['sample_number_per_folder'],
+                                                              self.all['folder_number'])
+
+    def _sort_data_list(self):
+        """
+        Sorts the data list using natural sorting.
+
+        Extended Description
+        --------------------
+        This function sorts the `data_list` attribute of an instance using the natsort library,
+        which is useful when filenames have a mixture of numbers and letters.
+        """
+        if len(self.data_list) > 0:
+            lengths = vectorized_len(self.data_list)
+            if len(lengths) > 1 and np.max(np.diff(lengths)) > np.log10(len(self.data_list)):
+                logging.error(f"File names present strong variations and cannot be correctly sorted.")
+            wrong_images = np.nonzero(np.char.startswith(self.data_list, "Analysis efficiency, ", ))[0]
+            for w_im in wrong_images[::-1]:
+                self.data_list.pop(w_im)
+            self.data_list = natsort.natsorted(self.data_list)
+        if self.all['im_or_vid'] == 1:
+            self.vars['video_list'] = self.data_list
+        else:
+            self.vars['video_list'] = None
+
+    def update_folder_id(self, sample_number: int, folder_name: str=""):
+        """
+        Update the current working directory and data list based on the given sample number
+        and optional folder name.
+
+        Parameters
+        ----------
+        sample_number : int
+            The number of samples to analyze.
+        folder_name : str, optional
+            The name of the folder to change to. Default is an empty string.
+
+        Notes
+        -----
+        This function changes the current working directory to the specified folder name
+        and updates the data list based on the file names in that directory. It also performs
+        sorting of the data list and checks for strong variations in file names.
+
+        """
+        os.chdir(Path(self.all['global_pathway']) / folder_name)
+        self.data_list = insensitive_glob(
+            self.all['radical'] + '*' + self.all['extension'])  # Provides a list ordered by last modification date
+        # Sorting is necessary when some modifications (like rotation) modified the last modification date
+        self._sort_data_list()
+        if self.all['im_or_vid'] == 1:
+            self.sample_number = sample_number
+        else:
+            self.vars['img_number'] = len(self.data_list)
+            self.sample_number = sample_number
+        if not 'analyzed_individuals' in self.vars:
+            self._set_analyzed_individuals()
+
+    def _set_analyzed_individuals(self):
+        """
+        Set the analyzed individuals variable in the dataset.
+        """
+        if self.sample_number is not None:
+            self.vars['analyzed_individuals'] = np.arange(self.sample_number) + 1
+        if self.not_analyzed_individuals is not None:
+            self.vars['analyzed_individuals'] = np.delete(self.vars['analyzed_individuals'],
+                                                       self.not_analyzed_individuals - 1)
+
+    def load_data_to_run_cellects_quickly(self):
+        """
+        Load data from a pickle file and update the current state of the object.
+
+        Summarizes, loads, and validates data needed to run Cellects,
+        updating the object's state accordingly. If the necessary data
+        are not present or valid, it ensures the experiment is marked as
+        not ready to run.
+
+        Parameters
+        ----------
+        self : CellectsObject
+            The instance of the class (assumed to be a subclass of
+            CellectsObject) that this method belongs to.
+
+        Returns
+        -------
+        None
+
+        Notes
+        -----
+        This function relies on the presence of a pickle file 'Data to run Cellects quickly.pkl'.
+        It updates the state of various attributes based on the loaded data
+        and logs appropriate messages.
+        """
+        self.first_im = None
+        current_global_pathway = self.all['global_pathway']
+        folder_number = self.all['folder_number']
+        if folder_number > 1:
+            folder_list = deepcopy(self.all['folder_list'])
+            sample_number_per_folder = deepcopy(self.all['sample_number_per_folder'])
+
+        if os.path.isfile('Data to run Cellects quickly.pkl'):
+            pickle_rick = PickleRick()
+            data_to_run_cellects_quickly = pickle_rick.read_file('Data to run Cellects quickly.pkl')
+            if data_to_run_cellects_quickly is None:
+                data_to_run_cellects_quickly = {}
+
+            if ('validated_shapes' in data_to_run_cellects_quickly) and ('coordinates' in data_to_run_cellects_quickly) and ('all' in data_to_run_cellects_quickly):
+                logging.info("Success to load Data to run Cellects quickly.pkl from the user chosen directory")
+                self.all = data_to_run_cellects_quickly['all']
+                # If you want to add a new variable, first run an updated version of all_vars_dict,
+                # then put a breakpoint here and run the following + self.save_data_to_run_cellects_quickly() :
+                self.vars = self.all['vars']
+                self.update_variable_dict()
+                folder_changed = False
+                if current_global_pathway != self.all['global_pathway']:
+                    folder_changed = True
+                    logging.info(
+                        "Although the folder is ready, it is not at the same place as it was during creation, updating")
+                    self.all['global_pathway'] = current_global_pathway
+                if folder_number > 1:
+                    self.all['global_pathway'] = current_global_pathway
+                    self.all['folder_list'] = folder_list
+                    self.all['folder_number'] = folder_number
+                    self.all['sample_number_per_folder'] = sample_number_per_folder
+
+                if len(self.data_list) == 0:
+                    self.look_for_data()
+                    if folder_changed and folder_number > 1 and len(self.all['folder_list']) > 0:
+                        self.update_folder_id(self.all['sample_number_per_folder'][0], self.all['folder_list'][0])
+                self.get_first_image()
+                self.get_last_image()
+                (ccy1, ccy2, ccx1, ccx2, self.left, self.right, self.top, self.bot) = data_to_run_cellects_quickly[
+                    'coordinates']
+                if self.all['automatically_crop']:
+                    self.first_image.crop_coord = [ccy1, ccy2, ccx1, ccx2]
+                    logging.info("Crop first image")
+                    self.first_image.automatically_crop(self.first_image.crop_coord)
+                    logging.info("Crop last image")
+                    self.last_image.automatically_crop(self.first_image.crop_coord)
+                else:
+                    self.first_image.crop_coord = None
+                self.first_image.validated_shapes = data_to_run_cellects_quickly['validated_shapes']
+                self.first_image.im_combinations = []
+                self.current_combination_id = 0
+                self.first_image.im_combinations.append({})
+                self.first_image.im_combinations[self.current_combination_id]['csc'] = self.vars['convert_for_origin']
+                self.first_image.im_combinations[self.current_combination_id]['binary_image'] = self.first_image.validated_shapes
+                self.first_image.im_combinations[self.current_combination_id]['shape_number'] = data_to_run_cellects_quickly['shape_number']
+                
+                self.first_exp_ready_to_run = True
+                if self.vars['subtract_background'] and len(self.vars['background_list']) == 0:
+                    self.first_exp_ready_to_run = False
+            else:
+                self.first_exp_ready_to_run = False
+        else:
+            self.first_exp_ready_to_run = False
+        if self.first_exp_ready_to_run:
+            logging.info("The current (or the first) folder is ready to run")
+        else:
+            logging.info("The current (or the first) folder is not ready to run")
+
+    def save_data_to_run_cellects_quickly(self, new_one_if_does_not_exist: bool=True):
+        """
+        Save data to a pickled file if it does not exist or update existing data.
+
+        Parameters
+        ----------
+        new_one_if_does_not_exist : bool, optional
+            Whether to create a new data file if it does not already exist.
+            Default is True.
+
+        Notes
+        -----
+        This method logs various information about its operations and handles the writing of data to a pickled file.
+        """
+        data_to_run_cellects_quickly = None
+        if os.path.isfile('Data to run Cellects quickly.pkl'):
+            logging.info("Update -Data to run Cellects quickly.pkl- in the user chosen directory")
+            pickle_rick = PickleRick()
+            data_to_run_cellects_quickly = pickle_rick.read_file('Data to run Cellects quickly.pkl')
+            if data_to_run_cellects_quickly is None:
+                os.remove('Data to run Cellects quickly.pkl')
+                logging.error("Failed to load Data to run Cellects quickly.pkl before update. Remove pre existing.")
+        else:
+            if new_one_if_does_not_exist:
+                logging.info("Create Data to run Cellects quickly.pkl in the user chosen directory")
+                data_to_run_cellects_quickly = {}
+        if data_to_run_cellects_quickly is not None:
+            if self.data_to_save['first_image']:
+                data_to_run_cellects_quickly['validated_shapes'] = self.first_image.im_combinations[self.current_combination_id]['binary_image']
+                data_to_run_cellects_quickly['shape_number'] = self.first_image.im_combinations[self.current_combination_id]['shape_number']
+                    # data_to_run_cellects_quickly['converted_image'] = self.first_image.im_combinations[self.current_combination_id]['converted_image']
+            if self.data_to_save['coordinates']:
+                data_to_run_cellects_quickly['coordinates'] = self._list_coordinates()
+                logging.info("When they exist, do overwrite unaltered video")
+                self.all['overwrite_unaltered_videos'] = True
+            if self.data_to_save['exif']:
+                self.vars['exif'] = self.extract_exif()
+            self.all['vars'] = self.vars
+            data_to_run_cellects_quickly['all'] = self.all
+            pickle_rick = PickleRick()
+            pickle_rick.write_file(data_to_run_cellects_quickly, 'Data to run Cellects quickly.pkl')
+
+    def _list_coordinates(self):
+        """
+        Summarize the coordinates of images and video.
+
+        Combine the crop coordinates from the first image with additional
+        coordinates for left, right, top, and bottom boundaries to form a list of
+        video coordinates. If the crop coordinates are not already set, initialize
+        them to cover the entire image.
+
+        Returns
+        -------
+        list of int
+            A list containing the coordinates [left, right, top, bottom] for video.
+
+        """
+        if self.first_image.crop_coord is None:
+            self.first_image.crop_coord = [0, self.first_image.image.shape[0], 0,
+                                                       self.first_image.image.shape[1]]
+        videos_coordinates = self.first_image.crop_coord + [self.left, self.right, self.top, self.bot]
+        return videos_coordinates
+
+    def get_first_image(self, first_im: NDArray=None, sample_number: int=None):
+        """
+        Load and process the first image or frame from a video.
+
+        This method handles loading the first image or the first frame of a video
+        depending on whether the data is an image or a video. It performs necessary
+        preprocessing and initializes relevant attributes for subsequent analysis.
+        """
+        self.reduce_image_dim = False
+        if first_im is not None:
+            self.first_im = first_im
+            if sample_number is not None:
+                self.sample_number = sample_number
+        else:
+            logging.info("Load first image")
+            just_read_image = self.first_im is not None
+            # just_read_image = self.analysis_instance is not None
+            if self.all['im_or_vid'] == 1:
+                if not just_read_image:
+                    self.analysis_instance = video2numpy(self.data_list[0])
+                    self.sample_number = len(self.data_list)
+                    self.vars['img_number'] = self.analysis_instance.shape[0]
+                    self.first_im = self.analysis_instance[0, ...]
+                else:
+                    self.first_im = self.analysis_instance[self.vars['first_detection_frame'], ...]
+                self.vars['dims'] = self.analysis_instance.shape[:3]
+
+            else:
+                self.vars['img_number'] = len(self.data_list)
+                self.all['raw_images'] = is_raw_image(self.data_list[0])
+                self.first_im = readim(self.data_list[self.vars['first_detection_frame']], self.all['raw_images'])
+                self.vars['dims'] = [self.vars['img_number'], self.first_im.shape[0], self.first_im.shape[1]]
+
+                if len(self.first_im.shape) == 3:
+                    if np.all(np.equal(self.first_im[:, :, 0], self.first_im[:, :, 1])) and np.all(
+                            np.equal(self.first_im[:, :, 1], self.first_im[:, :, 2])):
+                        self.reduce_image_dim = True
+                    if self.reduce_image_dim:
+                        self.first_im = self.first_im[:, :, 0]
+        self.first_image = OneImageAnalysis(self.first_im)
+        self.vars['already_greyscale'] = self.first_image.already_greyscale
+        if self.vars['already_greyscale']:
+            self.vars["convert_for_origin"] = {"bgr": np.array((1, 1, 1), dtype=np.uint8), "logical": "None"}
+            self.vars["convert_for_motion"] = {"bgr": np.array((1, 1, 1), dtype=np.uint8), "logical": "None"}
+        if np.mean((np.mean(self.first_image.image[2, :, ...]), np.mean(self.first_image.image[-3, :, ...]), np.mean(self.first_image.image[:, 2, ...]), np.mean(self.first_image.image[:, -3, ...]))) > 127:
+            self.vars['contour_color']: np.uint8 = 0
+        else:
+            self.vars['contour_color']: np.uint8 = 255
+        if self.vars['first_detection_frame'] > 0:
+            self.vars['origin_state'] = 'invisible'
+
+    def get_last_image(self, last_im: NDArray=None):
+        """
+
+        Load the last image from a video or image list and process it based on given parameters.
+
+        Parameters
+        ----------
+        last_im : NDArray, optional
+            The last image to be loaded. If not provided, the last image will be loaded from the data list.
+        """
+        logging.info("Load last image")
+        if last_im is not None:
+            self.last_im = last_im
+        else:
+            if self.all['im_or_vid'] == 1:
+                cap = cv2.VideoCapture(self.data_list[0])
+                counter = 0
+                while cap.isOpened() and counter < self.vars['img_number']:
+                    ret, frame = cap.read()
+                    if self.reduce_image_dim:
+                        frame = frame[:, :, 0]
+                    self.analysis_instance[-1, ...] = frame
+                    counter += 1
+                self.last_im = frame
+                cap.release()
+            else:
+                is_landscape = self.first_image.image.shape[0] < self.first_image.image.shape[1]
+                self.last_im = read_and_rotate(self.data_list[-1], self.first_im, self.all['raw_images'], is_landscape)
+                if self.reduce_image_dim:
+                    self.last_im = self.last_im[:, :, 0]
+        self.last_image = OneImageAnalysis(self.last_im)
+
+    def extract_exif(self):
+        """
+        Extract EXIF data from image or video files.
+
+        Notes
+        -----
+        If `extract_time_interval` is True and unsuccessful, arbitrary time steps will be used.
+        Timings are normalized to minutes for consistency across different files.
+        """
+        self.vars['time_step_is_arbitrary'] = True
+        if self.all['im_or_vid'] == 1:
+            self.vars['dims'] = self.analysis_instance.shape
+            timings = np.arange(self.vars['dims'][0])
+        else:
+            timings = np.arange(len(self.data_list))
+            if sys.platform.startswith('win'):
+                pathway = os.getcwd() + '\\'
+            else:
+                pathway = os.getcwd() + '/'
+            if not 'extract_time_interval' in self.all:
+                self.all['extract_time_interval'] = True
+            if self.all['extract_time_interval']:
+                self.vars['time_step'] = 1
+                try:
+                    timings = extract_time(self.data_list, pathway, self.all['raw_images'])
+                    timings = timings - timings[0]
+                    timings = timings / 60
+                    time_step = np.diff(timings)
+                    if len(time_step) > 0:
+                        time_step = np.mean(time_step)
+                        digit_nb = 0
+                        for i in str(time_step):
+                            if i in {'.'}:
+                                pass
+                            elif i in {'0'}:
+                                digit_nb += 1
+                            else:
+                                break
+                        self.vars['time_step'] = np.round(time_step, digit_nb + 1)
+                        self.vars['time_step_is_arbitrary'] = False
+                except:
+                    pass
+            else:
+                timings = np.arange(0, len(self.data_list) * self.vars['time_step'], self.vars['time_step'])
+                self.vars['time_step_is_arbitrary'] = False
+        return timings
+
+    def fast_first_image_segmentation(self):
+        """
+        Segment the first or subsequent image in a series for biological and background masks.
+
+        Notes
+        -----
+        This function processes the first or subsequent image in a sequence, applying biological and background masks,
+        segmenting the image, and updating internal data structures accordingly. The function is specific to handling
+        image sequences for biological analysis
+
+        """
+        if not "color_number" in self.vars:
+            self.update_variable_dict()
+        if self.vars['convert_for_origin'] is None:
+            self.vars['convert_for_origin'] = {"logical": 'None', "PCA": np.ones(3, dtype=np.uint8)}
+        self.first_image.convert_and_segment(self.vars['convert_for_origin'], self.vars["color_number"],
+                                             self.all["bio_mask"], self.all["back_mask"], subtract_background=None,
+                                             subtract_background2=None,
+                                             rolling_window_segmentation=self.vars["rolling_window_segmentation"],
+                                             filter_spec=self.vars["filter_spec"])
+        if not self.first_image.drift_correction_already_adjusted:
+            self.vars['drift_already_corrected'] = self.first_image.check_if_image_border_attest_drift_correction()
+            if self.vars['drift_already_corrected']:
+                logging.info("Cellects detected that the images have already been corrected for drift")
+                self.first_image.convert_and_segment(self.vars['convert_for_origin'], self.vars["color_number"],
+                                                     self.all["bio_mask"], self.all["back_mask"],
+                                                     subtract_background=None, subtract_background2=None,
+                                                     rolling_window_segmentation=self.vars["rolling_window_segmentation"],
+                                                     filter_spec=self.vars["filter_spec"],
+                                                     allowed_window=self.first_image.drift_mask_coord)
+
+        shapes_features = shape_selection(self.first_image.binary_image, true_shape_number=self.sample_number,
+                                          horizontal_size=self.starting_blob_hsize_in_pixels,
+                                          spot_shape=self.all['starting_blob_shape'],
+                                          several_blob_per_arena=self.vars['several_blob_per_arena'],
+                                          bio_mask=self.all["bio_mask"], back_mask=self.all["back_mask"])
+        self.first_image.validated_shapes, shape_number, stats, centroids = shapes_features
+        self.first_image.shape_number = shape_number
+        if self.first_image.im_combinations is None:
+            self.first_image.im_combinations = []
+        if len(self.first_image.im_combinations) == 0:
+            self.first_image.im_combinations.append({})
+        self.current_combination_id = np.min((self.current_combination_id, len(self.first_image.im_combinations) - 1))
+        self.first_image.im_combinations[self.current_combination_id]['csc'] = self.vars['convert_for_origin']
+        self.first_image.im_combinations[self.current_combination_id]['binary_image'] = self.first_image.validated_shapes
+        if self.first_image.greyscale is not None:
+            greyscale = self.first_image.greyscale
+        else:
+            greyscale = self.first_image.image
+        self.first_image.im_combinations[self.current_combination_id]['converted_image'] = bracket_to_uint8_image_contrast(greyscale)
+        self.first_image.im_combinations[self.current_combination_id]['shape_number'] = shape_number
+
+    def fast_last_image_segmentation(self, biomask: NDArray[np.uint8] = None, backmask: NDArray[np.uint8] = None):
+        """
+        Segment the first or subsequent image in a series for biological and background masks.
+
+        Parameters
+        ----------
+        biomask : NDArray[np.uint8], optional
+            The biological mask to be applied to the image.
+        backmask : NDArray[np.uint8], optional
+            The background mask to be applied to the image.
+
+        Returns
+        -------
+        None
+
+        Notes
+        -----
+        This function processes the first or subsequent image in a sequence, applying biological and background masks,
+        segmenting the image, and updating internal data structures accordingly. The function is specific to handling
+        image sequences for biological analysis
+
+        """
+        if self.vars['convert_for_motion'] is None:
+            self.vars['convert_for_motion'] = {"logical": 'None', "PCA": np.ones(3, dtype=np.uint8)}
+        self.cropping(is_first_image=False)
+        self.last_image.convert_and_segment(self.vars['convert_for_motion'], self.vars["color_number"],
+                                            biomask, backmask, self.first_image.subtract_background,
+                                            self.first_image.subtract_background2,
+                                            rolling_window_segmentation=self.vars["rolling_window_segmentation"],
+                                            filter_spec=self.vars["filter_spec"])
+        if self.vars['drift_already_corrected'] and not self.last_image.drift_correction_already_adjusted and not self.vars["rolling_window_segmentation"]['do']:
+            self.last_image.check_if_image_border_attest_drift_correction()
+            self.last_image.convert_and_segment(self.vars['convert_for_motion'], self.vars["color_number"],
+                                                biomask, backmask, self.first_image.subtract_background,
+                                                self.first_image.subtract_background2,
+                                                allowed_window=self.last_image.drift_mask_coord,
+                                                filter_spec=self.vars["filter_spec"])
+        
+        if self.last_image.im_combinations is None:
+            self.last_image.im_combinations = []
+        if len(self.last_image.im_combinations) == 0:
+            self.last_image.im_combinations.append({})
+        self.current_combination_id = np.min((self.current_combination_id, len(self.last_image.im_combinations) - 1))
+        self.last_image.im_combinations[self.current_combination_id]['csc'] = self.vars['convert_for_motion']
+        self.last_image.im_combinations[self.current_combination_id]['binary_image'] = self.last_image.binary_image
+        if self.last_image.greyscale is not None:
+            greyscale = self.last_image.greyscale
+        else:
+            greyscale = self.last_image.image
+        self.last_image.im_combinations[self.current_combination_id]['converted_image'] = bracket_to_uint8_image_contrast(greyscale)
+
+    def cropping(self, is_first_image: bool):
+        """
+        Crops the image based on specified conditions and settings.
+
+        This method checks if drift correction has already been applied.
+        If the image is the first one and hasn't been cropped yet, it will attempt
+        to use pre-stored coordinates or compute new crop coordinates. If automatic
+        cropping is enabled, it will apply the cropping process.
+
+        Parameters
+        ----------
+        is_first_image : bool
+            Indicates whether the image being processed is the first one in the sequence.
+        """
+        if not self.vars['drift_already_corrected']:
+            if is_first_image:
+                if not self.first_image.cropped:
+                    if (not self.all['overwrite_unaltered_videos'] and os.path.isfile('Data to run Cellects quickly.pkl')):
+                        pickle_rick = PickleRick()
+                        data_to_run_cellects_quickly = pickle_rick.read_file('Data to run Cellects quickly.pkl')
+                        if data_to_run_cellects_quickly is not None:
+                            if 'coordinates' in data_to_run_cellects_quickly:
+                                logging.info("Get crop coordinates from Data to run Cellects quickly.pkl")
+                                (ccy1, ccy2, ccx1, ccx2, self.left, self.right, self.top, self.bot) = \
+                                    data_to_run_cellects_quickly['coordinates']
+                                self.first_image.crop_coord = [ccy1, ccy2, ccx1, ccx2]
+                            else:
+                                self.first_image.get_crop_coordinates()
+                        else:
+                            self.first_image.get_crop_coordinates()
+
+                    else:
+                        self.first_image.get_crop_coordinates()
+                    if self.all['automatically_crop']:
+                        self.first_image.automatically_crop(self.first_image.crop_coord)
+                    else:
+                        self.first_image.crop_coord = None
+            else:
+                if not self.last_image.cropped and self.all['automatically_crop']:
+                    self.last_image.automatically_crop(self.first_image.crop_coord)
+
+    def get_average_pixel_size(self):
+        """
+        Calculate the average pixel size and related variables.
+
+        Logs information about calculation steps, computes the average
+        pixel size based on image or cell scaling settings,
+        and sets initial thresholds for object detection.
+
+        Notes
+        -----
+        - The average pixel size is determined by either image dimensions or blob sizes.
+        - Thresholds for automatic detection are set based on configuration settings.
+
+        """
+        logging.info("Getting average pixel size")
+        (self.first_image.shape_number,
+            self.first_image.shapes,
+            self.first_image.stats,
+            centroids) = cv2.connectedComponentsWithStats(
+                self.first_image.validated_shapes,
+                connectivity=8)
+        self.first_image.shape_number -= 1
+        if self.all['scale_with_image_or_cells'] == 0:
+            self.vars['average_pixel_size'] = np.square(
+                self.all['image_horizontal_size_in_mm'] /
+                self.first_im.shape[1])
+        else:
+            self.vars['average_pixel_size'] = np.square(
+                self.all['starting_blob_hsize_in_mm'] /
+                np.mean(self.first_image.stats[1:, 2]))
+        if self.all['set_spot_size']:
+            self.starting_blob_hsize_in_pixels = (
+                self.all['starting_blob_hsize_in_mm'] /
+                np.sqrt(self.vars['average_pixel_size']))
+        else:
+            self.starting_blob_hsize_in_pixels = None
+
+        if self.all['automatic_size_thresholding']:
+            self.vars['first_move_threshold'] = 10
+        else:
+            self.vars['first_move_threshold'] = np.round(
+                self.all['first_move_threshold_in_mm²'] /
+                self.vars['average_pixel_size']).astype(np.uint8)
+        logging.info(f"The average pixel size is: {self.vars['average_pixel_size']} mm²")
+
+    def get_background_to_subtract(self):
+        """
+        Determine if background subtraction should be applied to the image.
+
+        Extended Description
+        --------------------
+        This function checks whether background subtraction should be applied.
+        It utilizes the 'subtract_background' flag and potentially converts
+        the image for motion estimation.
+
+        Parameters
+        ----------
+        self : object
+            The instance of the class containing this method.
+            Must have attributes `vars` and `first_image`.
+        """
+        if self.vars['subtract_background']:
+            self.first_image.generate_subtract_background(self.vars['convert_for_motion'], self.vars['drift_already_corrected'])
+
+    def find_if_lighter_background(self):
+        """
+        Determines whether the background is lighter or darker than the cells.
+
+        This function analyzes images to determine if their backgrounds are lighter
+        or darker relative to the cells, updating attributes accordingly for analysis and display purposes.
+
+
+        Notes
+        -----
+        This function modifies instance variables and does not return any value.
+        The analysis involves comparing mean pixel values in specific areas of the image.
+        """
+        logging.info("Find if the background is lighter or darker than the cells")
+        self.vars['lighter_background']: bool = True
+        self.vars['contour_color']: np.uint8 = 0
+        are_dicts_equal: bool = True
+        if self.vars['convert_for_origin'] is not None and self.vars['convert_for_origin'] is not None:
+            for key in self.vars['convert_for_origin'].keys():
+                are_dicts_equal = are_dicts_equal and np.all(key in self.vars['convert_for_motion'] and self.vars['convert_for_origin'][key] == self.vars['convert_for_motion'][key])
+
+            for key in self.vars['convert_for_motion'].keys():
+                are_dicts_equal = are_dicts_equal and np.all(key in self.vars['convert_for_origin'] and self.vars['convert_for_motion'][key] == self.vars['convert_for_origin'][key])
+        else:
+            self.vars['convert_for_origin'] = {"logical": 'None', "PCA": np.ones(3, dtype=np.uint8)}
+            are_dicts_equal = True
+        if are_dicts_equal:
+            if self.first_im is None:
+                self.get_first_image()
+                self.fast_first_image_segmentation()
+                self.cropping(is_first_image=True)
+            among = np.nonzero(self.first_image.validated_shapes)
+            not_among = np.nonzero(1 - self.first_image.validated_shapes)
+            # Use the converted image to tell if the background is lighter, for analysis purposes
+            if self.first_image.image[among[0], among[1]].mean() > self.first_image.image[not_among[0], not_among[1]].mean():
+                self.vars['lighter_background'] = False
+            # Use the original image to tell if the background is lighter, for display purposes
+            if self.first_image.bgr[among[0], among[1], ...].mean() > self.first_image.bgr[not_among[0], not_among[1], ...].mean():
+                self.vars['contour_color'] = 255
+        else:
+            if self.last_im is None:
+                self.get_last_image()
+                # self.cropping(is_first_image=False)
+                self.fast_last_image_segmentation()
+            if self.last_image.binary_image.sum() == 0:
+                self.fast_last_image_segmentation()
+            among = np.nonzero(self.last_image.binary_image)
+            not_among = np.nonzero(1 - self.last_image.binary_image)
+            # Use the converted image to tell if the background is lighter, for analysis purposes
+            if self.last_image.image[among[0], among[1]].mean() > self.last_image.image[not_among[0], not_among[1]].mean():
+                self.vars['lighter_background'] = False
+            # Use the original image to tell if the background is lighter, for display purposes
+            if self.last_image.bgr[among[0], among[1], ...].mean() > self.last_image.bgr[not_among[0], not_among[1], ...].mean():
+                self.vars['contour_color'] = 255
+        if self.vars['origin_state'] == "invisible":
+            binary_image = deepcopy(self.first_image.binary_image)
+            self.first_image.convert_and_segment(self.vars['convert_for_motion'], self.vars["color_number"],
+                                                 None, None, subtract_background=None,
+                                                 subtract_background2=None,
+                                                 rolling_window_segmentation=self.vars['rolling_window_segmentation'],
+                                                 filter_spec=self.vars["filter_spec"])
+            covered_values = self.first_image.image[np.nonzero(binary_image)]
+            self.vars['luminosity_threshold'] = 127
+            if len(covered_values) > 0:
+                if self.vars['lighter_background']:
+                    if np.max(covered_values) < 255:
+                        self.vars['luminosity_threshold'] = np.max(covered_values) + 1
+                else:
+                    if np.min(covered_values) > 0:
+                        self.vars['luminosity_threshold'] = np.min(covered_values) - 1
+
+    def delineate_each_arena(self):
+        """
+        Determine the coordinates of each arena for video analysis.
+
+        The function processes video frames to identify bounding boxes around
+        specimens and determines valid arenas for analysis. In case of existing data,
+        it uses previously computed coordinates if available and valid.
+
+        Returns
+        -------
+        analysis_status : dict
+            A dictionary containing flags and messages indicating the status of
+            the analysis.
+            - 'continue' (bool): Whether to continue processing.
+            - 'message' (str): Informational or error message.
+
+        Raises
+        ------
+        None
+
+        Notes
+        -----
+        This function relies on the existence of certain attributes and variables
+        defined in the class instance.
+
+        Examples
+        --------
+        >>> self.delineate_each_arena()
+        {'continue': True, 'message': ''}
+        """
+        analysis_status = {"continue": True, "message": ""}
+        if not self.vars['several_blob_per_arena'] and (self.sample_number > 1):
+            compute_get_bb: bool = True
+            if (not self.all['overwrite_unaltered_videos'] and os.path.isfile('Data to run Cellects quickly.pkl')):
+
+                pickle_rick = PickleRick()
+                data_to_run_cellects_quickly = pickle_rick.read_file('Data to run Cellects quickly.pkl')
+                if data_to_run_cellects_quickly is not None:
+                    if 'coordinates' in data_to_run_cellects_quickly:
+                        (ccy1, ccy2, ccx1, ccx2, self.left, self.right, self.top, self.bot) = \
+                            data_to_run_cellects_quickly['coordinates']
+                        self.first_image.crop_coord = [ccy1, ccy2, ccx1, ccx2]
+                        if (self.first_image.image.shape[0] == (ccy2 - ccy1)) and (
+                                self.first_image.image.shape[1] == (ccx2 - ccx1)):  # maybe useless now
+                            logging.info("Get the coordinates of all arenas from Data to run Cellects quickly.pkl")
+                            compute_get_bb = False
+
+            if compute_get_bb:
+                motion_list = None
+                if self.all['are_gravity_centers_moving']:
+                    motion_list = self._segment_blob_motion(sample_size=5)
+                # if self.all['im_or_vid'] == 1:
+                self.get_bounding_boxes(are_gravity_centers_moving=self.all['are_gravity_centers_moving'] == 1,
+                    motion_list=motion_list, all_specimens_have_same_direction=self.all['all_specimens_have_same_direction'])
+
+                if np.any(self.ordered_stats[:, 4] > 100 * np.median(self.ordered_stats[:, 4])):
+                    analysis_status['message'] = "A specimen is at least 100 times larger: click previous and retry by specifying 'back' areas."
+                    analysis_status['continue'] = False
+                if np.any(self.ordered_stats[:, 4] < 0.01 * np.median(self.ordered_stats[:, 4])):
+                    analysis_status['message'] = "A specimen is at least 100 times smaller: click previous and retry by specifying 'back' areas."
+                    analysis_status['continue'] = False
+                del self.ordered_stats
+                logging.info(
+                    str(self.not_analyzed_individuals) + " individuals are out of picture scope and cannot be analyzed")
+
+        else:
+            self._whole_image_bounding_boxes()
+            self.sample_number = 1
+        self._set_analyzed_individuals()
+        return analysis_status
+
+    def _segment_blob_motion(self, sample_size: int) -> list:
+        """
+        Segment blob motion from the data list at specified sample sizes.
+
+        Parameters
+        ----------
+        sample_size : int
+            Number of samples to take from the data list.
+
+        Returns
+        -------
+        list
+            List containing segmented binary images at sampled frames.
+
+        Notes
+        -----
+        This function uses numpy for handling array operations and assumes the presence of certain attributes in the object, namely `data_list`, `first_image`, and `vars`.
+
+        Examples
+        --------
+        >>> motion_samples = _segment_blob_motion(10)
+        >>> print(len(motion_samples))  # Expected output: 10
+        """
+        motion_list = list()
+        if isinstance(self.data_list, list):
+            frame_number = len(self.data_list)
+        else:
+            frame_number = self.data_list.shape[0]
+        sample_numbers = np.floor(np.linspace(0, frame_number, sample_size)).astype(int)
+        if not 'lighter_background' in self.vars.keys():
+            self.find_if_lighter_background()
+        for frame_idx in np.arange(sample_size):
+            if frame_idx == 0:
+                motion_list.insert(frame_idx, self.first_image.validated_shapes)
+            else:
+                if isinstance(self.data_list[0], str):
+                    image = self.data_list[sample_numbers[frame_idx] - 1]
+                else:
+                    image = self.data_list[sample_numbers[frame_idx] - 1]
+                if isinstance(image, str):
+                    is_landscape = self.first_image.image.shape[0] < self.first_image.image.shape[1]
+                    image = read_and_rotate(image, self.first_image.bgr, self.all['raw_images'],
+                                            is_landscape, self.first_image.crop_coord)
+                    # image = readim(image)
+                In = OneImageAnalysis(image)
+                if self.vars['drift_already_corrected']:
+                    In.check_if_image_border_attest_drift_correction()
+                    # In.adjust_to_drift_correction(self.vars['convert_for_motion']['logical'])
+                In.convert_and_segment(self.vars['convert_for_motion'], self.vars['color_number'], None, None,
+                                       self.first_image.subtract_background, self.first_image.subtract_background2,
+                                       self.vars['rolling_window_segmentation'], self.vars['lighter_background'],
+                                       allowed_window=In.drift_mask_coord, filter_spec=self.vars['filter_spec'])
+                motion_list.insert(frame_idx, In.binary_image)
+        return motion_list
+
+
+    def get_bounding_boxes(self, are_gravity_centers_moving: bool, motion_list: list=(), all_specimens_have_same_direction: bool=True, original_shape_hsize: int=None):
+        """Get the coordinates of arenas using bounding boxes.
+
+        Parameters
+        ----------
+        are_gravity_centers_moving : bool
+            Flag indicating whether gravity centers are moving or not.
+        motion_list : list
+            List of motion information for the specimens.
+        all_specimens_have_same_direction : bool, optional
+            Flag indicating whether all specimens have the same direction,
+            by default True.
+        Notes
+        -----
+        This method uses various internal methods and variables to determine the bounding boxes.
+        """
+        # 7) Create required empty arrays: especially the bounding box coordinates of each video
+        self.ordered_first_image = None
+        self.shapes_to_remove = None
+        if self.first_image.crop_coord is None:
+            self.first_image.get_crop_coordinates()
+
+        logging.info("Get the coordinates of all arenas using the get_bounding_boxes method of the VideoMaker class")
+        if self.first_image.validated_shapes.any() and self.first_image.shape_number > 0:
+            self.ordered_stats, ordered_centroids, self.ordered_first_image = rank_from_top_to_bottom_from_left_to_right(
+                self.first_image.validated_shapes, self.first_image.y_boundaries, get_ordered_image=True)
+            self.unchanged_ordered_fimg = deepcopy(self.ordered_first_image)
+            self.modif_validated_shapes = deepcopy(self.first_image.validated_shapes)
+            self.standard = - 1
+            counter = 0
+            while np.any(np.less(self.standard, 0)) and counter < 20:
+                counter += 1
+                self.left = np.zeros(self.first_image.shape_number, dtype=np.int64)
+                self.right = np.repeat(self.modif_validated_shapes.shape[1], self.first_image.shape_number)
+                self.top = np.zeros(self.first_image.shape_number, dtype=np.int64)
+                self.bot = np.repeat(self.modif_validated_shapes.shape[0], self.first_image.shape_number)
+                if are_gravity_centers_moving:
+                    self.top, self.bot, self.left, self.right, self.ordered_first_image = get_bb_with_moving_centers(motion_list, all_specimens_have_same_direction,
+                                                     original_shape_hsize, self.first_image.validated_shapes,
+                                                     self.first_image.y_boundaries)
+                    new_ordered_first_image = np.zeros(self.ordered_first_image.shape, dtype=np.uint8)
+
+                    for i in np.arange(1, self.first_image.shape_number + 1):
+                        previous_shape = np.zeros(self.ordered_first_image.shape, dtype=np.uint8)
+                        previous_shape[np.nonzero(self.unchanged_ordered_fimg == i)] = 1
+                        new_potentials = np.zeros(self.ordered_first_image.shape, dtype=np.uint8)
+                        new_potentials[np.nonzero(self.ordered_first_image == i)] = 1
+                        new_potentials[np.nonzero(self.unchanged_ordered_fimg == i)] = 0
+
+                        pads = ProgressivelyAddDistantShapes(new_potentials, previous_shape, max_distance=2)
+                        pads.consider_shapes_sizes(min_shape_size=10)
+                        pads.connect_shapes(only_keep_connected_shapes=True, rank_connecting_pixels=False)
+                        new_ordered_first_image[np.nonzero(pads.expanded_shape)] = i
+                    self.ordered_first_image = new_ordered_first_image
+                    self.modif_validated_shapes = np.zeros(self.ordered_first_image.shape, dtype=np.uint8)
+                    self.modif_validated_shapes[np.nonzero(self.ordered_first_image)] = 1
+                    self.ordered_stats, ordered_centroids, self.ordered_first_image = rank_from_top_to_bottom_from_left_to_right(
+                        self.modif_validated_shapes, self.first_image.y_boundaries, get_ordered_image=True)
+                    self.top, self.bot, self.left, self.right = get_quick_bounding_boxes(self.modif_validated_shapes, self.ordered_first_image, self.ordered_stats)
+                else:
+                    self.top, self.bot, self.left, self.right = get_quick_bounding_boxes(self.modif_validated_shapes, self.ordered_first_image, self.ordered_stats)
+                self._standardize_video_sizes()
+            if counter == 20:
+                self.top[self.top < 0] = 1
+                self.bot[self.bot >= self.ordered_first_image.shape[0] - 1] = self.ordered_first_image.shape[0] - 2
+                self.left[self.left < 0] = 1
+                self.right[self.right >= self.ordered_first_image.shape[1] - 1] = self.ordered_first_image.shape[1] - 2
+            del self.ordered_first_image
+            del self.unchanged_ordered_fimg
+            del self.modif_validated_shapes
+            del self.standard
+            del self.shapes_to_remove
+            self.bot += 1
+            self.right += 1
+        else:
+            self._whole_image_bounding_boxes()
+
+    def _whole_image_bounding_boxes(self):
+        self.top, self.bot, self.left, self.right = np.array([0]), np.array([self.first_image.image.shape[0]]), np.array([0]), np.array([self.first_image.image.shape[1]])
+
+    def _standardize_video_sizes(self):
+        """
+        Standardize video sizes by adjusting bounding boxes.
+
+        Extended Description
+        --------------------
+        This function adjusts the bounding boxes of detected shapes in a video frame.
+        It ensures that all bounding boxes are within the frame's boundaries and
+        standardizes their sizes to avoid issues with odd dimensions during video writing.
+
+        Returns
+        -------
+        None
+            The function modifies the following attributes of the class instance:
+
+        Attributes Modified
+        ------------------
+        standard : numpy.ndarray
+            Standardized bounding boxes.
+        shapes_to_remove : numpy.ndarray
+            Indices of shapes to be removed from the image.
+        modif_validated_shapes : numpy.ndarray
+            Modified validated shapes after removing out-of-picture areas.
+        ordered_stats : list of float
+            Updated order statistics for the shapes.
+        ordered_centroids : numpy.ndarray
+            Centroids of the ordered shapes.
+        ordered_first_image : numpy.ndarray
+            First image with updated order statistics and centroids.
+        first_image.shape_number : int
+            Updated number of shapes in the first image.
+        not_analyzed_individuals : numpy.ndarray
+            Indices of individuals not analyzed after modifications.
+
+        """
+        distance_threshold_to_consider_an_arena_out_of_the_picture = None# in pixels, worked nicely with - 50
+
+        # The modifications allowing to not make videos of setups out of view, do not work for moving centers
+        y_diffs = self.bot - self.top
+        x_diffs = self.right - self.left
+        add_to_y = ((np.max(y_diffs) - y_diffs) / 2)
+        add_to_x = ((np.max(x_diffs) - x_diffs) / 2)
+        self.standard = np.zeros((len(self.top), 4), dtype=np.int64)
+        self.standard[:, 0] = self.top - np.uint8(np.floor(add_to_y))
+        self.standard[:, 1] = self.bot + np.uint8(np.ceil(add_to_y))
+        self.standard[:, 2] = self.left - np.uint8(np.floor(add_to_x))
+        self.standard[:, 3] = self.right + np.uint8(np.ceil(add_to_x))
+
+        # Monitor if one bounding box gets out of picture shape
+        out_of_pic = deepcopy(self.standard)
+        out_of_pic[:, 1] = self.ordered_first_image.shape[0] - out_of_pic[:, 1] - 1
+        out_of_pic[:, 3] = self.ordered_first_image.shape[1] - out_of_pic[:, 3] - 1
+
+        if distance_threshold_to_consider_an_arena_out_of_the_picture is None:
+            distance_threshold_to_consider_an_arena_out_of_the_picture = np.min(out_of_pic) - 1
+
+        # If it occurs at least one time, apply a correction, otherwise, continue and write videos
+        # If the overflow is strong, remove the corresponding individuals and remake bounding_box finding
+        if np.any(np.less(out_of_pic, distance_threshold_to_consider_an_arena_out_of_the_picture)):
+            # Remove shapes
+            self.standard = - 1
+            self.shapes_to_remove = np.nonzero(np.less(out_of_pic, - 20))[0]
+            for shape_i in self.shapes_to_remove:
+                self.ordered_first_image[self.ordered_first_image == (shape_i + 1)] = 0
+            self.modif_validated_shapes = np.zeros(self.ordered_first_image.shape, dtype=np.uint8)
+            self.modif_validated_shapes[np.nonzero(self.ordered_first_image)] = 1
+            self.ordered_stats, ordered_centroids, self.ordered_first_image = rank_from_top_to_bottom_from_left_to_right(
+                self.modif_validated_shapes, self.first_image.y_boundaries, get_ordered_image=True)
+
+            self.first_image.shape_number = self.first_image.shape_number - len(self.shapes_to_remove)
+            self.not_analyzed_individuals = np.unique(self.unchanged_ordered_fimg -
+                                                      (self.unchanged_ordered_fimg * self.modif_validated_shapes))[1:]
+
+        else:
+            # Reduce all box sizes if necessary and proceed
+            if np.any(np.less(out_of_pic, 0)):
+                # When the overflow is weak, remake standardization with lower "add_to_y" and "add_to_x"
+                overflow = np.nonzero(np.logical_and(np.less(out_of_pic, 0), np.greater_equal(out_of_pic, distance_threshold_to_consider_an_arena_out_of_the_picture)))[0]
+                # Look if overflow occurs on the y axis
+                if np.any(np.less(out_of_pic[overflow, :2], 0)):
+                    add_to_top_and_bot = np.min(out_of_pic[overflow, :2])
+                    self.standard[:, 0] = self.standard[:, 0] - add_to_top_and_bot
+                    self.standard[:, 1] = self.standard[:, 1] + add_to_top_and_bot
+                # Look if overflow occurs on the x axis
+                if np.any(np.less(out_of_pic[overflow, 2:], 0)):
+                    add_to_left_and_right = np.min(out_of_pic[overflow, 2:])
+                    self.standard[:, 2] = self.standard[:, 2] - add_to_left_and_right
+                    self.standard[:, 3] = self.standard[:, 3] + add_to_left_and_right
+            # If x or y sizes are odd, make them even :
+            # Don't know why, but opencv remove 1 to odd shapes when writing videos
+            if (self.standard[0, 1] - self.standard[0, 0]) % 2 != 0:
+                self.standard[:, 1] -= 1
+            if (self.standard[0, 3] - self.standard[0, 2]) % 2 != 0:
+                self.standard[:, 3] -= 1
+            self.top = self.standard[:, 0]
+            self.bot = self.standard[:, 1]
+            self.left = self.standard[:, 2]
+            self.right = self.standard[:, 3]
+
+    def get_origins_and_backgrounds_lists(self):
+        """
+        Create origins and background lists for image processing.
+
+        Extended Description
+        --------------------
+        This method generates the origin and background lists by slicing the first image
+        and its background subtraction based on predefined boundaries. It handles cases where
+        the top, bottom, left, and right boundaries are not yet initialized.
+
+        Notes
+        -----
+        This method directly modifies the input image data. The `self.vars` dictionary is populated
+        with lists of sliced arrays from the first image and its background.
+
+        Attributes
+        ----------
+        self.vars : dict
+            Dictionary to store processed data.
+        self.first_image : ImageObject
+            The first image object containing validated shapes and background subtraction arrays.
+        """
+        logging.info("Create origins and background lists")
+        if self.top is None:
+            self._whole_image_bounding_boxes()
+        first_im = self.first_image.validated_shapes
+        self.vars['origin_list'] = []
+        self.vars['background_list'] = []
+        self.vars['background_list2'] = []
+        for rep in np.arange(len(self.vars['analyzed_individuals'])):
+            self.vars['origin_list'].append(first_im[self.top[rep]:self.bot[rep], self.left[rep]:self.right[rep]])
+        if self.vars['subtract_background']:
+            for rep in np.arange(len(self.vars['analyzed_individuals'])):
+                self.vars['background_list'].append(
+                    self.first_image.subtract_background[self.top[rep]:self.bot[rep], self.left[rep]:self.right[rep]])
+                if self.vars['convert_for_motion']['logical'] != 'None':
+                    self.vars['background_list2'].append(self.first_image.subtract_background2[self.top[rep]:
+                                                         self.bot[rep], self.left[rep]:self.right[rep]])
+
+    def complete_image_analysis(self):
+        if not self.visualize and len(self.last_image.im_combinations) > 0:
+            self.last_image.binary_image = self.last_image.im_combinations[self.current_combination_id]['binary_image']
+            self.last_image.image = self.last_image.im_combinations[self.current_combination_id]['converted_image']
+        self.instantiate_tables()
+        if len(self.vars['exif']) > 1:
+            self.vars['exif'] = self.vars['exif'][0]
+        if len(self.last_image.all_c_spaces) == 0:
+            self.last_image.all_c_spaces['bgr'] = self.last_image.bgr.copy()
+        if self.all['bio_mask'] is not None:
+            self.last_image.binary_image[self.all['bio_mask']] = 1
+        if self.all['back_mask'] is not None:
+            self.last_image.binary_image[self.all['back_mask']] = 0
+        for i, arena in enumerate(self.vars['analyzed_individuals']):
+            binary = self.last_image.binary_image[self.top[i]:self.bot[i], self.left[i]:self.right[i]]
+            efficiency_test = self.last_image.all_c_spaces['bgr'][self.top[i]:self.bot[i], self.left[i]:self.right[i], :]
+            if not self.vars['several_blob_per_arena']:
+                binary = keep_one_connected_component(binary)
+                one_row_per_frame = compute_one_descriptor_per_frame(binary[None, :, :],
+                                                                     arena,
+                                                                     self.vars['exif'],
+                                                                     self.vars['descriptors'],
+                                                                     self.vars['output_in_mm'],
+                                                                     self.vars['average_pixel_size'],
+                                                                     self.vars['do_fading'],
+                                                                     self.vars['save_coord_specimen'])
+                coord_network = None
+                coord_pseudopods = None
+                if self.vars['save_graph']:
+                    if coord_network is None:
+                        coord_network = np.array(np.nonzero(binary))
+                    extract_graph_dynamics(self.last_image.image[None, :, :], coord_network, arena,
+                                           0, None, coord_pseudopods)
+
+            else:
+                one_row_per_frame = compute_one_descriptor_per_colony(binary[None, :, :],
+                                                                      arena,
+                                                                      self.vars['exif'],
+                                                                      self.vars['descriptors'],
+                                                                      self.vars['output_in_mm'],
+                                                                      self.vars['average_pixel_size'],
+                                                                      self.vars['do_fading'],
+                                                                      self.vars['first_move_threshold'],
+                                                                      self.vars['save_coord_specimen'])
+            if self.vars['fractal_analysis']:
+                zoomed_binary, side_lengths = prepare_box_counting(binary,
+                                                                   min_mesh_side=self.vars[
+                                                                       'fractal_box_side_threshold'],
+                                                                   zoom_step=self.vars['fractal_zoom_step'],
+                                                                   contours=True)
+                box_counting_dimensions = box_counting_dimension(zoomed_binary, side_lengths)
+                one_row_per_frame["fractal_dimension"] = box_counting_dimensions[0]
+                one_row_per_frame["fractal_box_nb"] = box_counting_dimensions[1]
+                one_row_per_frame["fractal_r_value"] = box_counting_dimensions[2]
+
+            one_descriptor_per_arena = {}
+            one_descriptor_per_arena["arena"] = arena
+            one_descriptor_per_arena["first_move"] = pd.NA
+            one_descriptor_per_arena["final_area"] = binary.sum()
+            one_descriptor_per_arena["iso_digi_transi"] = pd.NA
+            one_descriptor_per_arena["is_growth_isotropic"] = pd.NA
+            self.update_one_row_per_arena(i, one_descriptor_per_arena)
+            self.update_one_row_per_frame(i * 1, (i + 1) * 1, one_row_per_frame)
+            contours = np.nonzero(get_contours(binary))
+            efficiency_test[contours[0], contours[1], :] = np.array((94, 0, 213), dtype=np.uint8)
+            self.add_analysis_visualization_to_first_and_last_images(i, efficiency_test, None)
+        self.save_tables(with_last_image=False)
+
+    def prepare_video_writing(self, img_list: list, min_ram_free: float, in_colors: bool=False, pathway: str=""):
+        """
+
+        Prepare the raw video (.npy) writing process for Cellects.
+
+        Parameters
+        ----------
+        img_list : list
+            List of images to be processed.
+        min_ram_free : float
+            Minimum amount of RAM in GB that should remain free.
+        in_colors : bool, optional
+            Whether the images are in color. Default is False.
+        pathway : str, optional
+            Path to save the video files. Default is an empty string.
+
+        Returns
+        -------
+        tuple
+            A tuple containing:
+            - bunch_nb: int, number of bunches needed for video writing.
+            - video_nb_per_bunch: int, number of videos per bunch.
+            - sizes: ndarray, dimensions of each video.
+            - video_bunch: list or ndarray, initialized video arrays.
+            - vid_names: list, names of the video files.
+            - rom_memory_required: None or float, required ROM memory.
+            - analysis_status: dict, status and message of the analysis process.
+            - remaining: int, remainder videos that do not fit in a complete bunch.
+
+        Notes
+        -----
+        - The function calculates necessary memory and ensures 10% extra to avoid issues.
+        - It checks for available RAM and adjusts the number of bunches accordingly.
+        - If using color images, memory requirements are tripled.
+
+        expected output depends on the provided images and RAM availability
+        """
+        # 1) Create a list of video names
+        if self.not_analyzed_individuals is not None:
+            number_to_add = len(self.not_analyzed_individuals)
+        else:
+            number_to_add = 0
+        vid_names = list()
+        ind_i = 0
+        counter = 0
+        while ind_i < (self.first_image.shape_number + number_to_add):
+            ind_i += 1
+            while np.any(np.isin(self.not_analyzed_individuals, ind_i)):
+                ind_i += 1
+            vid_names.append(pathway + "ind_" + str(ind_i) + ".npy")
+            counter += 1
+        img_nb = len(img_list)
+
+        # 2) Create a table of the dimensions of each video
+        # Add 10% to the necessary memory to avoid problems
+        necessary_memory = img_nb * np.multiply((self.bot - self.top).astype(np.uint64), (self.right - self.left).astype(np.uint64)).sum() * 8 * 1.16415e-10
+        if in_colors:
+            sizes = np.column_stack(
+                (np.repeat(img_nb, self.first_image.shape_number), self.bot - self.top, self.right - self.left,
+                 np.repeat(3, self.first_image.shape_number)))
+            necessary_memory *= 3
+        else:
+            sizes = np.column_stack(
+                (np.repeat(img_nb, self.first_image.shape_number), self.bot - self.top, self.right - self.left))
+        use_list_of_vid = True
+        if np.all(sizes[0, :] == sizes):
+            use_list_of_vid = False
+        available_memory = (psutil.virtual_memory().available >> 30) - min_ram_free
+        if available_memory == 0:
+            analysis_status = {"continue": False, "message": "There are not enough RAM available"}
+            bunch_nb = 1
+        else:
+            bunch_nb = int(np.ceil(necessary_memory / available_memory))
+            if bunch_nb > 1:
+                # The program will need twice the memory to create the second bunch.
+                bunch_nb = int(np.ceil(2 * necessary_memory / available_memory))
+
+        video_nb_per_bunch = np.floor(self.first_image.shape_number / bunch_nb).astype(np.uint8)
+        analysis_status = {"continue": True, "message": ""}
+        video_bunch = None
+        try:
+            if use_list_of_vid:
+                video_bunch = [np.zeros(sizes[i, :], dtype=np.uint8) for i in range(video_nb_per_bunch)]
+            else:
+                video_bunch = np.zeros(np.append(sizes[0, :], video_nb_per_bunch), dtype=np.uint8)
+        except ValueError as v_err:
+            analysis_status = {"continue": False, "message": "Probably failed to detect the right cell(s) number, do the first image analysis manually."}
+            logging.error(f"{analysis_status['message']} error is: {v_err}")
+        # Check for available ROM memory
+        if (psutil.disk_usage('/')[2] >> 30) < (necessary_memory + 2):
+            rom_memory_required = necessary_memory + 2
+        else:
+            rom_memory_required = None
+        remaining = self.first_image.shape_number % bunch_nb
+        if remaining > 0:
+            bunch_nb += 1
+        is_landscape = self.first_image.image.shape[0] < self.first_image.image.shape[1]
+        logging.info(f"Cellects will start writing {self.first_image.shape_number} videos. Given available memory, it will do it in {bunch_nb} time(s)")
+        return bunch_nb, video_nb_per_bunch, sizes, video_bunch, vid_names, rom_memory_required, analysis_status, remaining, use_list_of_vid, is_landscape
+
+
+
+    def update_output_list(self):
+        """
+        Update the output list with various descriptors from the analysis results.
+
+        This method processes different types of descriptors and assigns them to
+        the `self.vars['descriptors']` dictionary. It handles special cases for
+        descriptors related to 'xy' dimensions and ensures that all relevant metrics
+        are stored in the output list.
+        """
+        self.vars['descriptors'] = {}
+        for descriptor in self.all['descriptors'].keys():
+            if descriptor == 'standard_deviation_xy':
+                self.vars['descriptors']['standard_deviation_x'] = self.all['descriptors'][descriptor]
+                self.vars['descriptors']['standard_deviation_y'] = self.all['descriptors'][descriptor]
+            elif descriptor == 'skewness_xy':
+                self.vars['descriptors']['skewness_x'] = self.all['descriptors'][descriptor]
+                self.vars['descriptors']['skewness_y'] = self.all['descriptors'][descriptor]
+            elif descriptor == 'kurtosis_xy':
+                self.vars['descriptors']['kurtosis_x'] = self.all['descriptors'][descriptor]
+                self.vars['descriptors']['kurtosis_y'] = self.all['descriptors'][descriptor]
+            elif descriptor == 'major_axes_len_and_angle':
+                self.vars['descriptors']['major_axis_len'] = self.all['descriptors'][descriptor]
+                self.vars['descriptors']['minor_axis_len'] = self.all['descriptors'][descriptor]
+                self.vars['descriptors']['axes_orientation'] = self.all['descriptors'][descriptor]
+            else:
+                if np.isin(descriptor, list(from_shape_descriptors_class.keys())):
+                
+                    self.vars['descriptors'][descriptor] = self.all['descriptors'][descriptor]
+        self.vars['descriptors']['newly_explored_area'] = self.vars['do_fading']
+
+    def update_available_core_nb(self, image_bit_number=256, video_bit_number=140):# video_bit_number=176
+        """
+        Update available computation resources based on memory and processing constraints.
+
+        Parameters
+        ----------
+        image_bit_number : int, optional
+            Number of bits per image pixel (default is 256).
+        video_bit_number : int, optional
+            Number of bits per video frame pixel (default is 140).
+
+        Other Parameters
+        ----------------
+        lose_accuracy_to_save_memory : bool
+            Flag to reduce accuracy for memory savings.
+        convert_for_motion : dict
+            Conversion settings for motion analysis.
+        already_greyscale : bool
+            Flag indicating if the image is already greyscale.
+        save_coord_thickening_slimming : bool
+            Flag to save coordinates for thickening and slimming.
+        oscilacyto_analysis : bool
+            Flag indicating if oscilacyto analysis is enabled.
+        save_coord_network : bool
+            Flag to save coordinates for network analysis.
+
+        Returns
+        -------
+        float
+            Rounded absolute difference between available memory and necessary memory in GB.
+
+        Notes
+        -----
+        Performance considerations and limitations should be noted here if applicable.
+
+        """
+        if self.vars['lose_accuracy_to_save_memory']:
+            video_bit_number -= 56
+        if self.vars['convert_for_motion']['logical'] != 'None':
+            video_bit_number += 64
+            if self.vars['lose_accuracy_to_save_memory']:
+                video_bit_number -= 56
+        if self.vars['already_greyscale']:
+            video_bit_number -= 64
+        if self.vars['save_coord_thickening_slimming'] or self.vars['oscilacyto_analysis']:
+            video_bit_number += 16
+            image_bit_number += 128
+        if self.vars['save_coord_network']:
+            video_bit_number += 8
+            image_bit_number += 64
+
+        if isinstance(self.bot, list):
+            one_image_memory = np.multiply((self.bot[0] - self.top[0]),
+                                        (self.right[0] - self.left[0])).max().astype(np.uint64)
+        else:
+            one_image_memory = np.multiply((self.bot - self.top).astype(np.uint64),
+                                        (self.right - self.left).astype(np.uint64)).max()
+        one_video_memory = self.vars['img_number'] * one_image_memory
+        necessary_memory = (one_image_memory * image_bit_number + one_video_memory * video_bit_number) * 1.16415e-10
+        available_memory = (virtual_memory().available >> 30) - self.vars['min_ram_free']
+        max_repeat_in_memory = (available_memory // necessary_memory).astype(np.uint16)
+        if max_repeat_in_memory > 1:
+            max_repeat_in_memory = np.max(((available_memory // (2 * necessary_memory)).astype(np.uint16), 1))
+
+
+        self.cores = np.min((self.all['cores'], max_repeat_in_memory))
+        if self.cores > self.sample_number:
+            self.cores = self.sample_number
+        return np.round(np.absolute(available_memory - necessary_memory), 3)
+
+
+    def update_one_row_per_arena(self, i: int, table_to_add):
+        """
+        Update one row of the dataframe per arena.
+
+        Add a row to a DataFrame for each arena, based on the provided table_to_add. If no previous rows exist,
+        initialize a new DataFrame with zeros.
+
+        Parameters
+        ----------
+        i : int
+            Index of the arena to update.
+        table_to_add : dict
+            Dictionary containing values to add. Keys are column names, values are the data.
+
+        """
+        if not self.vars['several_blob_per_arena']:
+            if self.one_row_per_arena is None:
+                self.one_row_per_arena = pd.DataFrame(np.zeros((len(self.vars['analyzed_individuals']), len(table_to_add)), dtype=float),
+                                            columns=table_to_add.keys())
+            self.one_row_per_arena.iloc[i, :] = table_to_add.values()
+
+
+    def update_one_row_per_frame(self, i: int, j: int, table_to_add):
+        """
+        Update a range of rows in `self.one_row_per_frame` DataFrame with values from
+        `table_to_add`.
+
+        Parameters
+        ----------
+        i : int
+            The starting row index to update in `self.one_row_per_frame`.
+        j : int
+            The ending row index (exclusive) to update in `self.one_row_per_frame`.
+        table_to_add : dict
+            A dictionary where keys are column labels and values are lists or arrays of
+            data to insert into `self.one_row_per_frame`.
+        Notes
+        -----
+        Ensures that one row per arena is being updated. If `self.one_row_per_frame` is
+        None, it initializes a DataFrame to hold the data.
+        """
+        if not self.vars['several_blob_per_arena']:
+            if self.one_row_per_frame is None:
+                self.one_row_per_frame = pd.DataFrame(index=range(len(self.vars['analyzed_individuals']) *
+                                                        self.vars['img_number']),
+                                            columns=table_to_add.keys())
+
+            self.one_row_per_frame.iloc[i:j, :] = table_to_add
+
+
+    def instantiate_tables(self):
+        """
+        Update output list and prepare results tables and validation images.
+
+        Extended Description
+        --------------------
+        This method performs necessary preparations for processing image sequences,
+        including updating the output list and initializing key attributes required
+        for subsequent operations.
+
+        """
+        self.update_output_list()
+        logging.info("Instantiate results tables and validation images")
+        self.fractal_box_sizes = None
+        self.one_row_per_arena = None
+        self.one_row_per_frame = None
+        if self.vars['already_greyscale']:
+            if len(self.first_image.bgr.shape) == 2:
+                self.first_image.bgr = np.stack((self.first_image.bgr, self.first_image.bgr, self.first_image.bgr), axis=2).astype(np.uint8)
+            if len(self.last_image.bgr.shape) == 2:
+                self.last_image.bgr = np.stack((self.last_image.bgr, self.last_image.bgr, self.last_image.bgr), axis=2).astype(np.uint8)
+            self.vars["convert_for_motion"] = {"bgr": np.array((1, 1, 1), dtype=np.uint8), "logical": "None"}
+
+    def add_analysis_visualization_to_first_and_last_images(self, i: int, first_visualization: NDArray, last_visualization: NDArray=None):
+        """
+        Adds analysis visualizations to the first and last images of a sequence.
+
+        Parameters
+        ----------
+        i : int
+            Index of the image in the sequence.
+        first_visualization : NDArray[np.uint8]
+            The visualization to add to the first image.
+        last_visualization : NDArray[np.uint8]
+            The visualization to add to the last image.
+
+        Other Parameters
+        ----------------
+        vars : dict
+            Dictionary containing various parameters.
+        arena_shape : str, optional
+            The shape of the arena. Either 'circle' or other shapes.
+
+        Notes
+        -----
+        If `arena_shape` is 'circle', the visualization will be masked by an ellipse.
+
+        """
+        minmax = (self.top[i], self.bot[i], self.left[i], self.right[i])
+        self.first_image.bgr = draw_img_with_mask(self.first_image.bgr, self.first_image.bgr.shape[:2], minmax,
+                                                  self.vars['arena_shape'], first_visualization)
+        if last_visualization is not None:
+            self.last_image.bgr = draw_img_with_mask(self.last_image.bgr, self.last_image.bgr.shape[:2], minmax,
+                                                      self.vars['arena_shape'], last_visualization)
+
+        # cr = ((self.top[i], self.bot[i]),
+        #       (self.left[i], self.right[i]))
+        # if self.vars['arena_shape'] == 'circle':
+        #     ellipse = create_ellipse(cr[0][1] - cr[0][0], cr[1][1] - cr[1][0])
+        #     ellipse = np.stack((ellipse, ellipse, ellipse), axis=2).astype(np.uint8)
+        #     first_visualization *= ellipse
+        #     self.first_image.bgr[cr[0][0]:cr[0][1], cr[1][0]:cr[1][1], ...] *= (1 - ellipse)
+        #     self.first_image.bgr[cr[0][0]:cr[0][1], cr[1][0]:cr[1][1], ...] += first_visualization
+        #     if last_visualization is not None:
+        #         last_visualization *= ellipse
+        #         self.last_image.bgr[cr[0][0]:cr[0][1], cr[1][0]:cr[1][1], ...] *= (1 - ellipse)
+        #         self.last_image.bgr[cr[0][0]:cr[0][1], cr[1][0]:cr[1][1], ...] += last_visualization
+        # else:
+        #     self.first_image.bgr[cr[0][0]:cr[0][1], cr[1][0]:cr[1][1], ...] = first_visualization
+        #     if last_visualization is not None:
+        #         self.last_image.bgr[cr[0][0]:cr[0][1], cr[1][0]:cr[1][1], ...] = last_visualization
+
+
+    def save_tables(self, with_last_image: bool=True):
+        """
+        Exports analysis results to CSV files and saves visualization outputs.
+
+        Generates the following output:
+        - one_row_per_arena.csv, one_row_per_frame.csv : Tracking data per arena/frame.
+        - software_settings.csv : Full configuration settings for reproducibility.
+
+        Raises
+        ------
+        PermissionError
+            If any output file is already open in an external program (logged and re-raised).
+
+        Notes
+        -----
+        Ensure no exported CSV files are open while running this method to avoid permission errors. This
+        function will fail gracefully if the files cannot be overwritten.
+
+        """
+        logging.info("Save results tables and validation images")
+        if not self.vars['several_blob_per_arena']:
+            try:
+                self.one_row_per_arena.to_csv("one_row_per_arena.csv", sep=";", index=False, lineterminator='\n')
+                del self.one_row_per_arena
+            except PermissionError:
+                logging.error("Never let one_row_per_arena.csv open when Cellects runs")
+                self.message_from_thread.emit(f"Never let one_row_per_arena.csv open when Cellects runs")
+            try:
+                self.one_row_per_frame.to_csv("one_row_per_frame.csv", sep=";", index=False, lineterminator='\n')
+                del self.one_row_per_frame
+            except PermissionError:
+                logging.error("Never let one_row_per_frame.csv open when Cellects runs")
+                self.message_from_thread.emit(f"Never let one_row_per_frame.csv open when Cellects runs")
+        if self.all['extension'] == '.JPG':
+            extension = '.PNG'
+        else:
+            extension = '.JPG'
+        if with_last_image:
+            cv2.imwrite(f"Analysis efficiency, last image{extension}", self.last_image.bgr)
+        cv2.imwrite(
+            f"Analysis efficiency, {np.ceil(self.vars['img_number'] / 10).astype(np.uint64)}th image{extension}",
+            self.first_image.bgr)
+        software_settings = deepcopy(self.vars)
+        for key in ['descriptors', 'analyzed_individuals', 'exif', 'dims', 'origin_list', 'background_list', 'background_list2', 'descriptors', 'folder_list', 'sample_number_per_folder']:
+            software_settings.pop(key, None)
+        global_settings = deepcopy(self.all)
+        for key in ['analyzed_individuals', 'night_mode', 'expert_mode', 'is_auto', 'arena', 'video_option', 'compute_all_options', 'vars', 'dims', 'origin_list', 'background_list', 'background_list2', 'descriptors', 'folder_list', 'sample_number_per_folder']:
+            global_settings.pop(key, None)
+        software_settings.update(global_settings)
+        software_settings = pd.DataFrame.from_dict(software_settings, columns=["Setting"], orient='index')
+        try:
+            software_settings.to_csv("software_settings.csv", sep=";")
+        except PermissionError:
+            logging.error("Never let software_settings.csv open when Cellects runs")
+            self.message_from_thread.emit(f"Never let software_settings.csv open when Cellects runs")
+
+