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

cellects/core/motion_analysis.py

@@ -1,2010 +1,1664 @@
-#!/usr/bin/env python3
-"""
-This script contains the MotionAnalysis class. This class, called by program_organizer,
- calls all methods used to read, process videos and save results.
-1. load_images_and_videos: It starts by loading a video in .npy (which must have been written before, thanks to the one_video_per_blob file)
- and if it exists, the background used for background subtraction. Then, it uses a particular color space combination
- to convert the rgb video into greyscale.
- At this point, arenas have been delimited and each can be analyzed separately. The following describes what happens during the analysis of one arena. Also, while Cellects can work with either one or several cells in each arena, we will describe the algorithm for a single cell, making clarifications whenever anything changes for multiple cells.
-Cellects starts by reading and converting the video of each arena into grayscale, using the selected color space combination. Then, it processes it through the following steps.
-3. It validates the presence/absence of the specimen(s) in the first image of the video, named origin.
-Cellects finds the frame in which the cell is visible for the first time in each arena. When the seed image is the first image, then all cells are visible from the beginning. Otherwise, it will apply the same segmentation as for the seed image to the first, second, third images, etc. until the cell appears in one of them.
-4. It browses the first frames of the video to find the average covering duration of a pixel.
-It does so using a very conservative method, to make sure that only pixels that really are covered by the specimen(s)
-are used to do compute that covering duration.
-5. It performs the main segmentation algorithm on the whole video.
-This segmentation will consist in transforming the grayscale video resulting from the color space combination conversion
- into a binary video of presence/absence. To do this, Cellects provides several different options to detect specimen
- motion and growth throughout the video. The video segmentation transforms a grayscale video into a binary one.
- In simple datasets with strong contrast between specimens and background, Cellects can simply segment each image by
- thresholding. In more challenging conditions, the algorithm tracks the intensity of each pixel over time,
- using this dynamical information to determine when a pixel has been covered. This is done through an automatically
- determined threshold on the intensity or on its derivative. Additionally, Cellects can apply the logical operators
- AND or OR to these intensity and derivative thresholds. The default option is the dynamical intensity threshold and it
- works in many cases, but the user interface lets the user quickly check the results of different options and choose
- the best one by visual inspection of the segmentation result in different frames.
- For Cellects to be as versatile as possible, the user can select across five segmentation strategies.
-The first option is the simplest: It starts at the frame in which the cell is visible for the first time and segments the video frame by frame, using the same method as when analyzing only one image (as described in sections 1 and 2). The only difference is an optional background subtraction algorithm, which subtracts the first image to all others.
-The second option segments each frame by intensity thresholding. The threshold changes over time to adapt to changes in the background over time. To estimate the optimal threshold for each frame, Cellects proceeds as follows: It first estimates the typical background intensity of each frame as an intensity higher than the first decile of all pixels in the frame. Then, it defines an initial threshold for each frame at a fixed distance above this decile. This fixed distance is initially low, so that the initial segmentation is an overestimation of the actual area covered by the specimen. Then, it performs segmentation of all frames. If any frame presents a growth greater than a user_set threshold (whose default value is 5% of the area), all thresholds are diminished by 10%. Then the segmentation is performed again, and this process continues until no frame presents excessive growth. This description refers to cases in which the background is darker than the specimen. Cellects automatically detects if contrast is reversed, and adapts the method accordingly. Finally, Cellects segments the whole video with these adjusted intensity thresholds.
-The third option uses the change in intensity over time: For each pixel, it considers the evolution in time of its intensity, and considers that the cell covers the pixel when the slope of this intensity over time exceeds a threshold (Fig 3d in the main text).  For each frame, Cellects computes each frame’s threshold with the similar procedure as in the second option, except for the following. As the value of the slope of a derivative is highly sensitive to noise, Cellects first smooths the intensity curves using a moving average with a window length adapted to the typical time it takes for the cell to cover each pixel. Cellects tries to compute this typical time using the dynamics of a subset of pixels whose intensity varies strongly at the beginning of the growth (see the code for further details), and uses a default value of 10 frames when this computation fails. Cellects also uses this subset of pixels to get the reference slope threshold. Finally, it progressively modifies this reference until the video segmentation matches the required growth ratio, as in the second step.
-The two next options are combinations of the two first ones.
-The fourth is a logical OR between the intensity value and the intensity slope segmentations. It provides a very permissive segmentation, which is useful when parts of the cells are very hard to detect.
-The fifth is the logical AND between the intensity value and the intensity slope segmentations. It provides a more restrictive segmentation that can be useful when both the value and the slope segmentations detect areas that are not covered by the cell.
-6. Video post-processing improves the resulting binary video obtained through segmentation.
-The final step consists in improving the segmentation (see section S3.5 of the Supplementary Materials for more information). Cellects will first apply several filters that consistently improve the results, such as checking that each detected pixel was also detected at least twice in the three previous frames, omitting images containing too many detected pixels, and performing morphological opening and closing. Optionally, the user can activate the detection of areas left by the cell (See section S3.5.B of the Supplementary Materials for details).
-
-Additionally, optional algorithms correct particular types of errors. The first algorithm is useful when the substrate on which the cells are at the first image is of a different color than the substrate on which they will grow, expand or move. This color difference may produce holes in the segmentation and we developed an optional algorithm to correct this kind of error around the initial shape. The second algorithm should be used when each arena contains a single specimen, which should generate a single connected component. We can use this information to correct mistakes in models such as P. polycephalum, whose strong heterogeneity produces large variations of opacity. In these cases, segmentation may fail in the most transparent parts of the specimens and identify two disconnected components. The correction algorithm merges these disconnecting components by finding the most likely pixels connecting them and the most likely times at which those pixels were covered during growth.
-6.A Basic post-processing
-This process improves the raw segmentation. It includes algorithms to filter out aberrant frames, remove small artifacts and holes, and to detect when the specimens leave pixels. First, it checks that every pixel was detected at least twice in the three previous frames. Second, it excludes frames containing too many newly detected pixels, according to the maximal growth ratio per frame (as defined in section 3B). For these frames, the previous segmentation is kept, making the analysis robust to events producing a sharp variation in the brightness of a few images in the video (for example, when an enclosed device is temporarily opened or a light is switched on or off). Third, it removes potential small artifacts and holes by performing morphological opening followed by morphological closing.
-
-6.B Cell leaving detection
-This optional algorithm detects when areas are left by the specimens. It is useful when the cells not only grow but also move, so they can leave pixels that were covered before. When a pixel is covered, Cellects saves the intensity it had before being covered, computed as the median of the pixel’s intensity over a time window before it was covered. The length of this time window matches the typical time it takes for the cell to cover each pixel (computed as described in section 4.B, third segmentation strategy). Then, pixels at the border of the cell whose intensity fall below the saved intensity, rescaled by a user-defined multiplier (set by default at 1) are considered to be left by the cell. When there should be only one cell in the arena, Cellects tries to remove each component one by one, accepting this removal only when it does not break the connectivity of all parts of the cell.
-
-6.C Special error correction algorithms
-At the time of writing, Cellects contains two post-processing algorithms adapted to two specific situations. The first one is useful when there should be only one specimen per arena and when Cellects fails to detect its distant parts because their connections are not sufficiently visible. The second one is useful when Cellects fails to detect small areas around the initial shape, for example due to reflections near the edges. The following explains how these optional algorithms work.
-
-6.D Connect distant components:
-This algorithm automatically and progressively adds distant shapes to the main one. This correcting process occurs in three steps. First, it selects which distant component should get connected to the main one. The user can adjust this selection process according to the distance of the distant components with the main shape, and the minimal and maximal size of these components. Second, for each distant component, it computes and creates the shortest connection with the main shape. The width of that connection depends on the size of the distant shape where the connection occurs. Third, it uses an algorithm similar to the one used to correct errors around initial shape to estimate how quickly the gaps should be filled. This algorithm uses distance and timing vectors to create a dynamic connection between these two shapes (Figure 3f-h in the main text).
-
-6.E Correct errors around initial shape:
-This correcting process occurs in two steps. The first one scans the formation of holes around the initial segmentation during the beginning of the growth. The second one finds out when and how these holes are to be filled. To determine how the holes should be covered, Cellects uses the same algorithm as the one used to connect distant components. Computing the speed at which growth occurs from the initial position allows Cellects to fill the holes at the same speed, and therefore to correct these errors.
-
-7. Special algorithms for Physarum polycephalum
-Although done for this organism, these methods can be used with other biological models, such as mycelia.
-7.A. Oscillatory activity detection:
-This algorithm analyzes grayscale video frames to detect whether pixel intensities increase or decrease over time. To prevent artifacts from arena-scale illumination fluctuations, pixel intensities are first standardized by the average intensity of the entire image. A pixel is considered to have increased (or decreased) in intensity if at least four of its eight neighboring pixels have also shown an increase (or decrease). Then, regions with adjacent pixels whose intensity is changing in the same direction are detected, keeping only those larger than a user-selected threshold. Each region is tracked throughout the video, recording its oscillatory period, phase, and coordinates until it dissipates or reaches the video’s end.
-
-7.B. Network detection:
-P. polycephalum cells are composed of two types of compartments: A tubular network that transports cytoplasmic materials, and a thinner compartment that covers the rest of the space. Cellects’ initial segmentation does not distinguish between these two compartments, detecting all pixels that have been covered by any of them. This step distinguishes them, in order to segment the tubular network, whose intensity is further from that of the background.
-Cellects detects such a network using an algorithm that scores the segmentation results after using filters of
-vesselness detection: sato and frangi. On top of testing these filters with around 10 variations of their parameters,
-Cellects tries to segment the images adaptatively: segmenting each part of the image using a 2D rolling window.
-Once the best segmentation strategy is found for the last image of the video, it is used to segment the network in all
-other frames
-
-8. Graph extraction:
-Cellects can extract the graph of the specimen, or if detected, of its internal network.
-To do so, Cellects does the following:
-- Get the skeleton of the binary matrix of presence/absence of the specimen, as well as the specimen/network
- width at avery pixel of the skeleton.
-If the original position from which the specimen started has not the same color as the rest of the arena, apply
-a special algorithm to draw the skeleton at the border of that origin.
-- Smooth the skeleton using an algorithm removing small loops of 3 pixels widths
-- Keep only the largest connected component of the skeleton
-- Use pixel connectivity and their neighborhood connectivity to detect all tips and branching vertices of the graph
-summarizing the skeleton.
-- Find and label all edges connecting tips and remove those that are shorter than the width of the skeleton arm it is connected to
-- Find and label all edges connecting touching vertices
-- Find and label all edges connected to the two previoussly mentioned vertices
-- Find and label all edges forming loops and connected to only one vertex
-- Remove all shapes of 1 or two pixels that are neither detected as vertices nor edges,
-if and only if they do not break the skeleton into more than one connected component.
-- Remove edge duplicates
-- Remove vertices connectiong 2 edges
-- Finally, create and save the tables storing edge and vertex coordinates and properties
-
-9. Save
-Once the image analysis is finished, the software determines the value of each morphological descriptor at each time frame (SI - Table 1). Finally, Cellects saves a new video for each arena with the original video next to the converted video displaying the segmentation result, so that the user can easily validate the result. If an arena shows a poor segmentation result, the user can re-analyze it, tuning all parameters for that specific arena.
-- the final results of the segmentation and its contour (if applicable)
-- descriptors summarizing the whole video
-- validation images (efficiency tests) and videos
-
-10. If this class has been used in the video_analysis_window only on one arena, the method
-change_results_of_one_arena will open (or create if not existing) tables in the focal folder
-and adjust every row corresponding to that particular arena to the current analysis results.
-
-"""
-
-import weakref
-from gc import collect
-from time import sleep
-from numba.typed import Dict as TDict
-from psutil import virtual_memory
-import pandas as pd
-from cellects.core.one_image_analysis import OneImageAnalysis
-from cellects.image_analysis.cell_leaving_detection import cell_leaving_detection
-from cellects.image_analysis.cluster_flux_study import ClusterFluxStudy
-from cellects.image_analysis.image_segmentation import segment_with_lum_value, apply_filter
-from cellects.image_analysis.morphological_operations import (find_major_incline, image_borders, draw_me_a_sun,
-                                                              inverted_distance_transform, dynamically_expand_to_fill_holes,
-                                                              box_counting_dimension, prepare_box_counting,
-                                                              keep_one_connected_component, cc)
-from cellects.image_analysis.network_functions import *
-from cellects.image_analysis.progressively_add_distant_shapes import ProgressivelyAddDistantShapes
-from cellects.image_analysis.shape_descriptors import ShapeDescriptors, from_shape_descriptors_class
-from cellects.utils.utilitarian import PercentAndTimeTracker, smallest_memory_array
-
-
-class MotionAnalysis:
-
-    def __init__(self, l):
-
-        """
-        :param video_name: The name of the video to read
-        :param convert_for_motion: The dict specifying the linear combination
-                                   of color channels (rgb_hsv_lab) to use
-        """
-        self.one_descriptor_per_arena = {}
-        self.one_descriptor_per_arena['arena'] = l[1]
-        vars = l[2]
-        detect_shape = l[3]
-        analyse_shape = l[4]
-        show_seg = l[5]
-        videos_already_in_ram = l[6]
-        self.visu = None
-        self.binary = None
-        self.origin_idx = None
-        self.smoothing_flag: bool = False
-        logging.info(f"Start the motion analysis of the arena n°{self.one_descriptor_per_arena['arena']}")
-
-        self.vars = vars
-        # self.origin = self.vars['first_image'][self.vars['top'][l[0]]:(
-        #    self.vars['bot'][l[0]] + 1),
-        #               self.vars['left'][l[0]]:(self.vars['right'][l[0]] + 1)]
-        self.load_images_and_videos(videos_already_in_ram, l[0])
-
-        self.dims = self.converted_video.shape
-        self.segmentation = np.zeros(self.dims, dtype=np.uint8)
-
-        self.covering_intensity = np.zeros(self.dims[1:], dtype=np.float64)
-        self.mean_intensity_per_frame = np.mean(self.converted_video, (1, 2))
-
-        self.borders = image_borders(self.dims[1:], shape=self.vars['arena_shape'])
-        # if self.vars['arena_shape'] == "circle":
-        #     self.borders = Ellipse(self.dims[1:]).create()
-        #     img_contours = image_borders(self.dims[1:])
-        #     self.borders = self.borders * img_contours
-        # else:
-        #     self.borders = image_borders(self.dims[1:])
-        self.pixel_ring_depth = 9
-        self.step = 10
-        self.lost_frames = 10
-        self.update_ring_width()
-
-        self.start = None
-        if detect_shape:
-            #self=self.motion
-            #self.drift_correction()
-            self.start = None
-            # Here to conditional layers allow to detect if an expansion/exploration occured
-            self.get_origin_shape()
-            # The first, user-defined is the 'first_move_threshold' and the second is the detection of the
-            # substantial image: if any of them is not detected, the program considers there is not exp.
-            if self.dims[0] >= 40:
-                step = self.dims[0] // 20
-            else:
-                step = 1
-            if self.start >= (self.dims[0] - step - 1):
-                self.start = None
-            else:
-                self.get_covering_duration(step)
-                if self.start is not None:
-                    # self.vars['fading'] = -0.5
-                    # self.vars['do_threshold_segmentation']: bool = False
-                    # self.vars['do_slope_segmentation'] = True
-                    # self.vars['true_if_use_light_AND_slope_else_OR']: bool = False
-                    self.detection()
-                    self.initialize_post_processing()
-                    self.t = self.start
-                    while self.t < self.binary.shape[0]:  #200: 
-                        self.update_shape(show_seg)
-                #
-            if self.start is None:
-                self.binary = np.repeat(np.expand_dims(self.origin, 0), self.converted_video.shape[0], axis=0)
-
-            if analyse_shape:
-                self.get_descriptors_from_binary()
-                self.detect_growth_transitions()
-                self.networks_detection(show_seg)
-                self.study_cytoscillations(show_seg)
-                self.fractal_descriptions()
-                self.get_descriptors_summary()
-                if videos_already_in_ram is None:
-                    self.save_results()
-
-    def load_images_and_videos(self, videos_already_in_ram, i):
-        logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Load images and videos")
-        self.origin = self.vars['origin_list'][i]# self.vars['origins_list'][i]
-        if videos_already_in_ram is None:
-            true_frame_width = self.origin.shape[1]
-            vid_name = f"ind_{self.one_descriptor_per_arena['arena']}.npy"
-            if len(self.vars['background_list']) == 0:
-                self.background = None
-            else:
-                self.background = self.vars['background_list'][i]
-            if len(self.vars['background_list2']) == 0:
-                self.background2 = None
-            else:
-                self.background2 = self.vars['background_list2'][i]
-
-            if self.vars['already_greyscale']:
-                self.converted_video = video2numpy(
-                    vid_name, None, self.background, true_frame_width)
-                if len(self.converted_video.shape) == 4:
-                    self.converted_video = self.converted_video[:, :, :, 0]
-            else:
-                self.visu = video2numpy(
-                    vid_name, None, self.background, true_frame_width)
-                self.get_converted_video()
-        else:
-            if self.vars['already_greyscale']:
-                self.converted_video = videos_already_in_ram
-            else:
-                if self.vars['convert_for_motion']['logical'] == 'None':
-                    self.visu, self.converted_video = videos_already_in_ram
-                else:
-                    (self.visu,
-                        self.converted_video,
-                        self.converted_video2) = videos_already_in_ram
-
-    def get_converted_video(self):
-        if not self.vars['already_greyscale']:
-            logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Convert the RGB visu video into a greyscale image using the color space combination: {self.vars['convert_for_motion']}")
-            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])
-            if self.vars['lose_accuracy_to_save_memory']:
-                self.converted_video = np.zeros(self.visu.shape[:3], dtype=np.uint8)
-            else:
-                self.converted_video = np.zeros(self.visu.shape[:3], dtype=np.float64)
-            if self.vars['convert_for_motion']['logical'] != 'None':
-                if self.vars['lose_accuracy_to_save_memory']:
-                    self.converted_video2 = np.zeros(self.visu.shape[:3], dtype=np.uint8)
-                else:
-                    self.converted_video2 = np.zeros(self.visu.shape[:3], dtype=np.float64)
-
-            # Trying to subtract the first image to the first image is a nonsense so,
-            # when doing background subtraction, the first and the second image are equal
-            for counter in np.arange(self.visu.shape[0]):
-                if self.vars['subtract_background'] and counter == 0:
-                    img = self.visu[1, ...]
-                else:
-                    img = self.visu[counter, ...]
-                greyscale_image, greyscale_image2 = generate_color_space_combination(img, c_spaces, first_dict,
-                                                                                     second_dict, self.background,
-                                                                                     self.background2,
-                                                                                     self.vars['lose_accuracy_to_save_memory'])
-                if self.vars['filter_spec'] is not None and self.vars['filter_spec']['filter1_type'] != "":
-                    greyscale_image = apply_filter(greyscale_image, self.vars['filter_spec']['filter1_type'],
-                                                   self.vars['filter_spec']['filter1_param'],
-                                                   self.vars['lose_accuracy_to_save_memory'])
-                    if greyscale_image2 is not None and self.vars['filter_spec']['filter2_type'] != "":
-                        greyscale_image2 = apply_filter(greyscale_image2, self.vars['filter_spec']['filter2_type'],
-                                                        self.vars['filter_spec']['filter2_param'],
-                                                        self.vars['lose_accuracy_to_save_memory'])
-
-                self.converted_video[counter, ...] = greyscale_image
-                if self.vars['convert_for_motion']['logical'] != 'None':
-                    self.converted_video2[counter, ...] = greyscale_image2
-
-    def get_origin_shape(self):
-        logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Make sure of origin shape")
-        if self.vars['origin_state'] == "constant":
-            self.start = 1
-            self.origin_idx = np.nonzero(self.origin)
-            if self.vars['lighter_background']:
-                # Initialize the covering_intensity matrix as a reference for pixel fading
-                self.covering_intensity[self.origin_idx[0], self.origin_idx[1]] = 200
-            self.substantial_growth = 1.2 * self.origin.sum()
-        else:
-            self.start = 0
-            analysisi = OneImageAnalysis(self.converted_video[0, :, :])
-            analysisi.binary_image = 0
-            if self.vars['drift_already_corrected']:
-                mask_coord = np.zeros((self.dims[0], 4), dtype=np.uint32)
-                for frame_i in np.arange(self.dims[0]):  # 100):#
-                    true_pixels = np.nonzero(self.converted_video[frame_i, ...])
-                    mask_coord[frame_i, :] = np.min(true_pixels[0]), np.max(true_pixels[0]), np.min(true_pixels[1]), np.max(
-                        true_pixels[1])
-            else:
-                mask_coord = None
-            while np.logical_and(np.sum(analysisi.binary_image) < self.vars['first_move_threshold'], self.start < self.dims[0]):
-                analysisi = self.frame_by_frame_segmentation(self.start, mask_coord)
-                self.start += 1
-
-                # frame_i = OneImageAnalysis(self.converted_video[self.start, :, :])
-                # frame_i.thresholding(self.vars['luminosity_threshold'], self.vars['lighter_background'])
-                # frame_i.thresholding(self.vars['luminosity_threshold'], self.vars['lighter_background'])
-                # self.start += 1
-
-            # Use connected components to find which shape is the nearest from the image center.
-            if self.vars['several_blob_per_arena']:
-                self.origin = analysisi.binary_image
-            else:
-                nb_components, output, stats, centroids = cv2.connectedComponentsWithStats(analysisi.binary_image,
-                                                                                           connectivity=8)
-                if self.vars['appearance_detection_method'] == 'most_central':
-                    center = np.array((self.dims[2] // 2, self.dims[1] // 2))
-                    stats = np.zeros(nb_components - 1)
-                    for shape_i in np.arange(1, nb_components):
-                        stats[shape_i - 1] = eudist(center, centroids[shape_i, :])
-                    # The shape having the minimal euclidean distance from the center will be the original shape
-                    self.origin = np.zeros((self.dims[1], self.dims[2]), dtype=np.uint8)
-                    self.origin[output == (np.argmin(stats) + 1)] = 1
-                elif self.vars['appearance_detection_method'] == 'largest':
-                    self.origin = np.zeros((self.dims[1], self.dims[2]), dtype=np.uint8)
-                    self.origin[output == np.argmax(stats[1:, 4])] = 1
-            self.origin_idx = np.nonzero(self.origin)
-            self.substantial_growth = self.origin.sum() + 250
-        ##
-
-    def get_covering_duration(self, step):
-        logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Find a frame with a significant growth/motion and determine the number of frames necessary for a pixel to get covered")
-        ## Find the time at which growth reached a substantial growth.
-        self.substantial_time = self.start
-        # To avoid noisy images to have deleterious effects, make sure that area area reaches the threshold thrice.
-        occurrence = 0
-        if self.vars['drift_already_corrected']:
-            mask_coord = np.zeros((self.dims[0], 4), dtype=np.uint32)
-            for frame_i in np.arange(self.dims[0]):  # 100):#
-                true_pixels = np.nonzero(self.converted_video[frame_i, ...])
-                mask_coord[frame_i, :] = np.min(true_pixels[0]), np.max(true_pixels[0]), np.min(true_pixels[1]), np.max(
-                    true_pixels[1])
-        else:
-            mask_coord = None
-        while np.logical_and(occurrence < 3, self.substantial_time < (self.dims[0] - step - 1)):
-            self.substantial_time += step
-            growth_vision = self.frame_by_frame_segmentation(self.substantial_time, mask_coord)
-
-            # growth_vision = OneImageAnalysis(self.converted_video[self.substantial_time, :, :])
-            # # growth_vision.thresholding()
-            # if self.vars['convert_for_motion']['logical'] != 'None':
-            #     growth_vision.image2 = self.converted_video2[self.substantial_time, ...]
-            #
-            # growth_vision.segmentation(self.vars['convert_for_motion']['logical'], self.vars['color_number'],
-            #                            bio_label=self.vars["bio_label"], bio_label2=self.vars["bio_label2"],
-            #                            grid_segmentation=self.vars['grid_segmentation'],
-            #                            lighter_background=self.vars['lighter_background'])
-
-            surfarea = np.sum(growth_vision.binary_image * self.borders)
-            if surfarea > self.substantial_growth:
-                occurrence += 1
-        # get a rough idea of the area covered during this time
-        if (self.substantial_time - self.start) > 20:
-            if self.vars['lighter_background']:
-                growth = (np.sum(self.converted_video[self.start:(self.start + 10), :, :], 0) / 10) - (np.sum(self.converted_video[(self.substantial_time - 10):self.substantial_time, :, :], 0) / 10)
-            else:
-                growth = (np.sum(self.converted_video[(self.substantial_time - 10):self.substantial_time, :, :], 0) / 10) - (
-                            np.sum(self.converted_video[self.start:(self.start + 10), :, :], 0) / 10)
-        else:
-            if self.vars['lighter_background']:
-                growth = self.converted_video[self.start, ...] - self.converted_video[self.substantial_time, ...]
-            else:
-                growth = self.converted_video[self.substantial_time, ...] - self.converted_video[self.start, ...]
-        intensity_extent = np.ptp(self.converted_video[self.start:self.substantial_time, :, :], axis=0)
-        growth[np.logical_or(growth < 0, intensity_extent < np.median(intensity_extent))] = 0
-        growth = bracket_to_uint8_image_contrast(growth)
-        growth *= self.borders
-        growth_vision = OneImageAnalysis(growth)
-        growth_vision.thresholding()
-        self.substantial_image = cv2.erode(growth_vision.binary_image, cross_33, iterations=2)
-
-        if np.any(self.substantial_image):
-            natural_noise = np.nonzero(intensity_extent == np.min(intensity_extent))
-            natural_noise = self.converted_video[self.start:self.substantial_time, natural_noise[0][0], natural_noise[1][0]]
-            natural_noise = moving_average(natural_noise, 5)
-            natural_noise = np.ptp(natural_noise)
-            subst_idx = np.nonzero(self.substantial_image)
-            cover_lengths = np.zeros(len(subst_idx[0]), dtype=np.uint32)
-            for index in np.arange(len(subst_idx[0])):
-                vector = self.converted_video[self.start:self.substantial_time, subst_idx[0][index], subst_idx[1][index]]
-                left, right = find_major_incline(vector, natural_noise)
-                # If find_major_incline did find a major incline: (otherwise it put 0 to left and 1 to right)
-                if not np.logical_and(left == 0, right == 1):
-                    cover_lengths[index] = len(vector[left:-right])
-            # If this analysis fails put a deterministic step
-            if len(cover_lengths[cover_lengths > 0]) > 0:
-                self.step = (np.round(np.mean(cover_lengths[cover_lengths > 0])).astype(np.uint32) // 2) + 1
-                logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Pre-processing detection: the time for a pixel to get covered is set to {self.step}")
-            else:
-                logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Pre-processing detection: could not automatically find the time for a pixel to get covered. Default value is 1 for video length < 40 and 10 otherwise")
-
-            # Make sure to avoid a step overestimation
-            if self.step > self.dims[0] // 20:
-                self.step = self.dims[0] // 20
-
-            if self.step == 0:
-                self.step = 1
-        # When the first_move_threshold is not stringent enough the program may detect a movement due to noise
-        # In that case, the substantial_image is empty and there is no reason to proceed further
-        else:
-            self.start = None
-        ##
-
-    def detection(self, compute_all_possibilities=False):
-        # self.lost_frames = (self.step - 1) * self.vars['repeat_video_smoothing'] # relevant when smoothing did not use padding.
-        self.lost_frames = self.step
-        # I/ Image by image segmentation algorithms
-        # If images contain a drift correction (zeros at borders of the image,
-        # Replace these 0 by normal background values before segmenting
-        if self.vars['frame_by_frame_segmentation'] or compute_all_possibilities:
-            logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Detect cell motion and growth using the frame by frame segmentation algorithm")
-            self.segmentation = np.zeros(self.dims, dtype=np.uint8)
-            if self.vars['drift_already_corrected']:
-                logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Adjust images to drift correction and segment them")
-                # 1. Get the mask valid for a number of images around it (step).
-                mask_coord = np.zeros((self.dims[0], 4), dtype=np.uint32)
-                for frame_i in np.arange(self.dims[0]):#100):#
-                    true_pixels = np.nonzero(self.converted_video[frame_i, ...])
-                    mask_coord[frame_i, :] = np.min(true_pixels[0]), np.max(true_pixels[0]), np.min(true_pixels[1]), np.max(true_pixels[1])
-            else:
-                mask_coord = None
-
-            for t in np.arange(self.dims[0]):#20):#
-                analysisi = self.frame_by_frame_segmentation(t, mask_coord)
-                self.segmentation[t, ...] = analysisi.binary_image
-
-                if self.vars['lose_accuracy_to_save_memory']:
-                    self.converted_video[t, ...] = bracket_to_uint8_image_contrast(analysisi.image)
-                else:
-                    self.converted_video[t, ...] = analysisi.image
-                if self.vars['convert_for_motion']['logical'] != 'None':
-                    if self.vars['lose_accuracy_to_save_memory']:
-                        self.converted_video2[t, ...] = bracket_to_uint8_image_contrast(analysisi.image2)
-                    else:
-                        self.converted_video2[t, ...] = analysisi.image2
-
-        if self.vars['color_number'] == 2:
-            luminosity_segmentation, l_threshold_over_time = self.lum_value_segmentation(self.converted_video, do_threshold_segmentation=self.vars['do_threshold_segmentation'] or compute_all_possibilities)
-            self.converted_video = self.smooth_pixel_slopes(self.converted_video)
-            if self.vars['do_slope_segmentation'] or compute_all_possibilities:
-                gradient_segmentation = self.lum_slope_segmentation(self.converted_video)
-                gradient_segmentation[-self.lost_frames:, ...] = np.repeat(gradient_segmentation[-self.lost_frames, :, :][np.newaxis, :, :], self.lost_frames, axis=0)
-            if self.vars['convert_for_motion']['logical'] != 'None':
-                if self.vars['do_threshold_segmentation'] or compute_all_possibilities:
-                    luminosity_segmentation2, l_threshold_over_time2 = self.lum_value_segmentation(self.converted_video2, do_threshold_segmentation=True)
-                    if self.vars['convert_for_motion']['logical'] == 'Or':
-                        luminosity_segmentation = np.logical_or(luminosity_segmentation, luminosity_segmentation2)
-                    elif self.vars['convert_for_motion']['logical'] == 'And':
-                        luminosity_segmentation = np.logical_and(luminosity_segmentation, luminosity_segmentation2)
-                    elif self.vars['convert_for_motion']['logical'] == 'Xor':
-                        luminosity_segmentation = np.logical_xor(luminosity_segmentation, luminosity_segmentation2)
-                self.converted_video2 = self.smooth_pixel_slopes(self.converted_video2)
-                if self.vars['do_slope_segmentation'] or compute_all_possibilities:
-                    gradient_segmentation2 = self.lum_slope_segmentation(self.converted_video2)
-                    gradient_segmentation2[-self.lost_frames:, ...] = np.repeat(gradient_segmentation2[-self.lost_frames, :, :][np.newaxis, :, :], self.lost_frames, axis=0)
-                    if self.vars['convert_for_motion']['logical'] == 'Or':
-                        gradient_segmentation = np.logical_or(gradient_segmentation, gradient_segmentation2)
-                    elif self.vars['convert_for_motion']['logical'] == 'And':
-                        gradient_segmentation = np.logical_and(gradient_segmentation, gradient_segmentation2)
-                    elif self.vars['convert_for_motion']['logical'] == 'Xor':
-                        gradient_segmentation = np.logical_xor(gradient_segmentation, gradient_segmentation2)
-
-            if compute_all_possibilities:
-                logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Compute all options to detect cell motion and growth. Maximal growth per frame: {self.vars['maximal_growth_factor']}")
-                self.luminosity_segmentation = np.nonzero(luminosity_segmentation)
-                self.gradient_segmentation = np.nonzero(gradient_segmentation)
-                self.logical_and = np.nonzero(np.logical_and(luminosity_segmentation, gradient_segmentation))
-                self.logical_or = np.nonzero(np.logical_or(luminosity_segmentation, gradient_segmentation))
-            elif not self.vars['frame_by_frame_segmentation']:
-                if self.vars['do_threshold_segmentation'] and not self.vars['do_slope_segmentation']:
-                    logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Detect with luminosity threshold segmentation algorithm")
-                    self.segmentation = luminosity_segmentation
-                if self.vars['do_slope_segmentation']:# and not self.vars['do_threshold_segmentation']: NEW
-                    logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Detect with luminosity slope segmentation algorithm")
-                    # gradient_segmentation[:(self.lost_frames + 1), ...] = luminosity_segmentation[:(self.lost_frames + 1), ...]
-                    if not self.vars['do_threshold_segmentation']:# NEW
-                        self.segmentation = gradient_segmentation
-                if np.logical_and(self.vars['do_threshold_segmentation'], self.vars['do_slope_segmentation']):
-                    if self.vars['true_if_use_light_AND_slope_else_OR']:
-                        logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Detection resuts from threshold AND slope segmentation algorithms")
-                        self.segmentation = np.logical_and(luminosity_segmentation, gradient_segmentation)
-                    else:
-                        logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Detection resuts from threshold OR slope segmentation algorithms")
-                        self.segmentation = np.logical_or(luminosity_segmentation, gradient_segmentation)
-                self.segmentation = self.segmentation.astype(np.uint8)
-        self.converted_video2 = None
-
-
-    def frame_by_frame_segmentation(self, t, mask_coord=None):
-
-        contrasted_im = bracket_to_uint8_image_contrast(self.converted_video[t, :, :])
-        if self.vars['convert_for_motion']['logical'] != 'None':
-            contrasted_im2 = bracket_to_uint8_image_contrast(self.converted_video2[t, :, :])
-        # 1. Get the mask valid for a number of images around it (step).
-        if self.vars['drift_already_corrected']:
-            if t < self.step // 2:
-                t_start = 0
-                t_end = self.step
-            elif t > (self.dims[0] - self.step // 2):
-                t_start = self.dims[0] - self.step
-                t_end = self.dims[0]
-            else:
-                t_start = t - (self.step // 2)
-                t_end = t + (self.step // 2)
-            min_y, max_y = np.max(mask_coord[t_start:t_end, 0]), np.min(mask_coord[t_start:t_end, 1])
-            min_x, max_x = np.max(mask_coord[t_start:t_end, 2]), np.min(mask_coord[t_start:t_end, 3])
-            # 3. Bracket the focal image
-            image_i = contrasted_im[min_y:(max_y + 1), min_x:(max_x + 1)].astype(np.float64)
-            image_i /= np.mean(image_i)
-            image_i = OneImageAnalysis(image_i)
-            if self.vars['convert_for_motion']['logical'] != 'None':
-                image_i2 = contrasted_im2[min_y:(max_y + 1), min_x:(max_x + 1)]
-                image_i2 /= np.mean(image_i2)
-                image_i.image2 = image_i2
-            mask = (self.converted_video[t, ...] > 0).astype(np.uint8)
-        else:
-            mask = None
-        # 3. Bracket the focal image
-        if self.vars['grid_segmentation']:
-            int_variation_thresh = 100 - (np.ptp(contrasted_im) * 90 / 255)
-        else:
-            int_variation_thresh = None
-        analysisi = OneImageAnalysis(bracket_to_uint8_image_contrast(contrasted_im / np.mean(contrasted_im)))
-        if self.vars['convert_for_motion']['logical'] != 'None':
-            analysisi.image2 = bracket_to_uint8_image_contrast(contrasted_im2 / np.mean(contrasted_im2))
-
-        if t == 0:
-            analysisi.previous_binary_image = self.origin
-        else:
-            analysisi.previous_binary_image = deepcopy(self.segmentation[t - 1, ...])
-
-        analysisi.segmentation(self.vars['convert_for_motion']['logical'], self.vars['color_number'],
-                               bio_label=self.vars["bio_label"], bio_label2=self.vars["bio_label2"],
-                               grid_segmentation=self.vars['grid_segmentation'],
-                               lighter_background=self.vars['lighter_background'],
-                               side_length=20, step=5, int_variation_thresh=int_variation_thresh, mask=mask,
-                               filter_spec=None) # filtering already done when creating converted_video
-
-        return analysisi
-
-        # 1. Get the mask valid for a number of images around it (step).
-
-
-    def lum_value_segmentation(self, converted_video, do_threshold_segmentation):
-        shape_motion_failed: bool = False
-        if self.vars['lighter_background']:
-            covering_l_values = np.min(converted_video[:self.substantial_time, :, :],
-                                             0) * self.substantial_image
-        else:
-            covering_l_values = np.max(converted_video[:self.substantial_time, :, :],
-                                             0) * self.substantial_image
-        # Avoid errors by checking whether the covering values are nonzero
-        covering_l_values = covering_l_values[covering_l_values != 0]
-        if len(covering_l_values) == 0:
-            shape_motion_failed = True
-        if not shape_motion_failed:
-            value_segmentation_thresholds = np.arange(0.8, -0.7, -0.1)
-            validated_thresholds = np.zeros(value_segmentation_thresholds.shape, dtype=bool)
-            counter = 0
-            while_condition = True
-            max_motion_per_frame = (self.dims[1] * self.dims[2]) * self.vars['maximal_growth_factor'] * 2
-            if self.vars['lighter_background']:
-                basic_bckgrnd_values = np.quantile(converted_video[:(self.lost_frames + 1), ...], 0.9, axis=(1, 2))
-            else:
-                basic_bckgrnd_values = np.quantile(converted_video[:(self.lost_frames + 1), ...], 0.1, axis=(1, 2))
-            # Try different values of do_threshold_segmentation and keep the one that does not
-            # segment more than x percent of the image
-            while counter <= 14:
-                value_threshold = value_segmentation_thresholds[counter]
-                if self.vars['lighter_background']:
-                    l_threshold = (1 + value_threshold) * np.max(covering_l_values)
-                else:
-                    l_threshold = (1 - value_threshold) * np.min(covering_l_values)
-                starting_segmentation, l_threshold_over_time = segment_with_lum_value(converted_video[:(self.lost_frames + 1), ...],
-                                                               basic_bckgrnd_values, l_threshold,
-                                                               self.vars['lighter_background'])
-
-                changing_pixel_number = np.sum(np.absolute(np.diff(starting_segmentation.astype(np.int8), 1, 0)), (1, 2))
-                validation = np.max(np.sum(starting_segmentation, (1, 2))) < max_motion_per_frame and (
-                        np.max(changing_pixel_number) < max_motion_per_frame)
-                validated_thresholds[counter] = validation
-                if np.any(validated_thresholds):
-                    if not validation:
-                        break
-                counter += 1
-            # If any threshold is accepted, use their average to proceed the final thresholding
-            valid_number = validated_thresholds.sum()
-            if valid_number > 0:
-                if valid_number > 2:
-                    index_to_keep = 2
-                else:
-                    index_to_keep = valid_number - 1
-                value_threshold = value_segmentation_thresholds[
-                    np.uint8(np.floor(np.mean(np.nonzero(validated_thresholds)[0][index_to_keep])))]
-            else:
-                value_threshold = 0
-
-            if self.vars['lighter_background']:
-                l_threshold = (1 + value_threshold) * np.max(covering_l_values)
-            else:
-                l_threshold = (1 - value_threshold) * np.min(covering_l_values)
-            if do_threshold_segmentation:
-                if self.vars['lighter_background']:
-                    basic_bckgrnd_values = np.quantile(converted_video, 0.9, axis=(1, 2))
-                else:
-                    basic_bckgrnd_values = np.quantile(converted_video, 0.1, axis=(1, 2))
-                luminosity_segmentation, l_threshold_over_time = segment_with_lum_value(converted_video, basic_bckgrnd_values,
-                                                                 l_threshold, self.vars['lighter_background'])
-            else:
-                luminosity_segmentation, l_threshold_over_time = segment_with_lum_value(converted_video[:(self.lost_frames + 1), ...],
-                                                               basic_bckgrnd_values, l_threshold,
-                                                               self.vars['lighter_background'])
-        else:
-            luminosity_segmentation = None
-
-        return luminosity_segmentation, l_threshold_over_time
-
-    def smooth_pixel_slopes(self, converted_video):
-        # smoothed_video = np.zeros(
-        #     (self.dims[0] - self.lost_frames, self.dims[1], self.dims[2]),
-        #     dtype=np.float64)
-        try:
-            if self.vars['lose_accuracy_to_save_memory']:
-                smoothed_video = np.zeros(self.dims, dtype=np.float16)
-                smooth_kernel = np.ones(self.step) / self.step
-                for i in np.arange(converted_video.shape[1]):
-                    for j in np.arange(converted_video.shape[2]):
-                        padded = np.pad(converted_video[:, i, j] / self.mean_intensity_per_frame,
-                                     (self.step // 2, self.step - 1 - self.step // 2), mode='edge')
-                        moving_average = np.convolve(padded, smooth_kernel, mode='valid')
-                        if self.vars['repeat_video_smoothing'] > 1:
-                            for it in np.arange(1, self.vars['repeat_video_smoothing']):
-                                padded = np.pad(moving_average,
-                                             (self.step // 2, self.step - 1 - self.step // 2), mode='edge')
-                                moving_average = np.convolve(padded, smooth_kernel, mode='valid')
-                        smoothed_video[:, i, j] = moving_average.astype(np.float16)
-            else:
-                smoothed_video = np.zeros(self.dims, dtype=np.float64)
-                smooth_kernel = np.ones(self.step) / self.step
-                for i in np.arange(converted_video.shape[1]):
-                    for j in np.arange(converted_video.shape[2]):
-                        padded = np.pad(converted_video[:, i, j] / self.mean_intensity_per_frame,
-                                     (self.step // 2, self.step - 1 - self.step // 2), mode='edge')
-                        moving_average = np.convolve(padded, smooth_kernel, mode='valid')
-                        if self.vars['repeat_video_smoothing'] > 1:
-                            for it in np.arange(1, self.vars['repeat_video_smoothing']):
-                                padded = np.pad(moving_average,
-                                             (self.step // 2, self.step - 1 - self.step // 2), mode='edge')
-                                moving_average = np.convolve(padded, smooth_kernel, mode='valid')
-                        smoothed_video[:, i, j] = moving_average
-            return smoothed_video
-
-        except MemoryError:
-            logging.error("Not enough RAM available to smooth pixel curves. Detection may fail.")
-            smoothed_video = converted_video
-            return smoothed_video
-
-    def lum_slope_segmentation(self, converted_video):
-        shape_motion_failed : bool = False
-        gradient_segmentation = np.zeros(self.dims, np.uint8)
-        # 2) Contrast increase
-        oridx = np.nonzero(self.origin)
-        notoridx = np.nonzero(1 - self.origin)
-        do_increase_contrast = np.mean(converted_video[0, oridx[0], oridx[1]]) * 10 > np.mean(
-                converted_video[0, notoridx[0], notoridx[1]])
-        necessary_memory = self.dims[0] * self.dims[1] * self.dims[2] * 64 * 2 * 1.16415e-10
-        available_memory = (virtual_memory().available >> 30) - self.vars['min_ram_free']
-        if self.vars['lose_accuracy_to_save_memory']:
-            derive = converted_video.astype(np.float16)
-        else:
-            derive = converted_video.astype(np.float64)
-        if necessary_memory > available_memory:
-            converted_video = None
-
-        if do_increase_contrast:
-            derive = np.square(derive)
-
-        # 3) Get the gradient
-        necessary_memory = derive.size * 64 * 4 * 1.16415e-10
-        available_memory = (virtual_memory().available >> 30) - self.vars['min_ram_free']
-        if necessary_memory > available_memory:
-            for cy in np.arange(self.dims[1]):
-                for cx in np.arange(self.dims[2]):
-                    if self.vars['lose_accuracy_to_save_memory']:
-                        derive[:, cy, cx] = np.gradient(derive[:, cy, cx], self.step).astype(np.float16)
-                    else:
-                        derive[:, cy, cx] = np.gradient(derive[:, cy, cx], self.step)
-        else:
-            if self.vars['lose_accuracy_to_save_memory']:
-                derive = np.gradient(derive, self.step, axis=0).astype(np.float16)
-            else:
-                derive = np.gradient(derive, self.step, axis=0)
-
-        # 4) Segment
-        if self.vars['lighter_background']:
-            covering_slopes = np.min(derive[:self.substantial_time, :, :], 0) * self.substantial_image
-        else:
-            covering_slopes = np.max(derive[:self.substantial_time, :, :], 0) * self.substantial_image
-        covering_slopes = covering_slopes[covering_slopes != 0]
-        if len(covering_slopes) == 0:
-            shape_motion_failed = True
-
-        if not shape_motion_failed:
-            ####
-            # ease_slope_segmentation = 0.8
-            value_segmentation_thresholds = np.arange(0.8, -0.7, -0.1)
-            validated_thresholds = np.zeros(value_segmentation_thresholds.shape, dtype=bool)
-            counter = 0
-            while_condition = True
-            max_motion_per_frame = (self.dims[1] * self.dims[2]) * self.vars['maximal_growth_factor']
-            # Try different values of do_slope_segmentation and keep the one that does not
-            # segment more than x percent of the image
-            while counter <= 14:
-                ease_slope_segmentation = value_segmentation_thresholds[counter]
-                if self.vars['lighter_background']:
-                    gradient_threshold = (1 + ease_slope_segmentation) * np.max(covering_slopes)
-                    sample = np.less(derive[:self.substantial_time], gradient_threshold)
-                else:
-                    gradient_threshold = (1 - ease_slope_segmentation) * np.min(covering_slopes)
-                    sample = np.greater(derive[:self.substantial_time], gradient_threshold)
-                changing_pixel_number = np.sum(np.absolute(np.diff(sample.astype(np.int8), 1, 0)), (1, 2))
-                validation = np.max(np.sum(sample, (1, 2))) < max_motion_per_frame and (
-                        np.max(changing_pixel_number) < max_motion_per_frame)
-                validated_thresholds[counter] = validation
-                if np.any(validated_thresholds):
-                    if not validation:
-                        break
-                counter += 1
-                # If any threshold is accepted, use their average to proceed the final thresholding
-            valid_number = validated_thresholds.sum()
-            if valid_number > 0:
-                if valid_number > 2:
-                    index_to_keep = 2
-                else:
-                    index_to_keep = valid_number - 1
-                ease_slope_segmentation = value_segmentation_thresholds[
-                    np.uint8(np.floor(np.mean(np.nonzero(validated_thresholds)[0][index_to_keep])))]
-            else:
-                ease_slope_segmentation = 0
-
-            if self.vars['lighter_background']:
-                gradient_threshold = (1 - ease_slope_segmentation) * np.max(covering_slopes)
-                gradient_segmentation[:-self.lost_frames, :, :] = np.less(derive, gradient_threshold)[self.lost_frames:, :, :]
-            else:
-                gradient_threshold = (1 - ease_slope_segmentation) * np.min(covering_slopes)
-                gradient_segmentation[:-self.lost_frames, :, :] = np.greater(derive, gradient_threshold)[self.lost_frames:, :, :]
-        else:
-            gradient_segmentation = None
-        return gradient_segmentation
-
-    def update_ring_width(self):
-        # Make sure that self.pixels_depths are odd and greater than 3
-        if self.pixel_ring_depth <= 3:
-            self.pixel_ring_depth = 3
-        if self.pixel_ring_depth % 2 == 0:
-            self.pixel_ring_depth = self.pixel_ring_depth + 1
-        self.erodila_disk = Ellipse((self.pixel_ring_depth, self.pixel_ring_depth)).create().astype(np.uint8)
-        self.max_distance = self.pixel_ring_depth * self.vars['detection_range_factor']
-
-    def initialize_post_processing(self):
-        ## Initialization
-        logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Starting Post_processing. Fading detection: {self.vars['do_fading']}: {self.vars['fading']}, Subtract background: {self.vars['subtract_background']}, Correct errors around initial shape: {self.vars['correct_errors_around_initial']}, Connect distant shapes: {self.vars['detection_range_factor'] > 0}, How to select appearing cell(s): {self.vars['appearance_detection_method']}")
-
-        self.binary = np.zeros(self.dims[:3], dtype=np.uint8)
-        if self.origin.shape[0] != self.binary[self.start - 1, :, :].shape[0] or self.origin.shape[1] != self.binary[self.start - 1, :, :].shape[1]:
-            logging.error("Unaltered videos deprecated, they have been created with different settings.\nDelete .npy videos and Data to run Cellects quickly.pkl and re-run")
-
-        if self.vars['origin_state'] == "invisible":
-            self.binary[self.start - 1, :, :] = deepcopy(self.origin)
-            self.covering_intensity[self.origin_idx[0], self.origin_idx[1]] = self.converted_video[self.start, self.origin_idx[0], self.origin_idx[1]]
-        else:
-            if self.vars['origin_state'] == "fluctuating":
-                self.covering_intensity[self.origin_idx[0], self.origin_idx[1]] = np.median(self.converted_video[:self.start, self.origin_idx[0], self.origin_idx[1]], axis=0)
-
-            self.binary[:self.start, :, :] = np.repeat(np.expand_dims(self.origin, 0), self.start, axis=0)
-            if self.start < self.step:
-                frames_to_assess = self.step
-                self.segmentation[self.start - 1, ...] = self.binary[self.start - 1, :, :]
-                for t in np.arange(self.start, self.lost_frames):
-                    # Only keep pixels that are always detected
-                    always_found = np.sum(self.segmentation[t:(t + frames_to_assess), ...], 0)
-                    always_found = always_found == frames_to_assess
-                    # Remove too small shapes
-                    without_small, stats, centro = cc(always_found.astype(np.uint8))
-                    large_enough = np.nonzero(stats[1:, 4] > ((self.vars['first_move_threshold'] + 1) // 2))[0]
-                    if len(large_enough) > 0:
-                        always_found *= np.isin(always_found, large_enough + 1)
-                        always_found = np.logical_or(always_found, self.segmentation[t - 1, ...])
-                        self.segmentation[t, ...] *= always_found
-                    else:
-                        self.segmentation[t, ...] = 0
-                    self.segmentation[t, ...] = np.logical_or(self.segmentation[t - 1, ...], self.segmentation[t, ...])
-        self.mean_distance_per_frame = None
-        self.surfarea = np.zeros(self.dims[0], dtype =np.uint64)
-        self.surfarea[:self.start] = np.sum(self.binary[:self.start, :, :], (1, 2))
-        self.gravity_field = inverted_distance_transform(self.binary[(self.start - 1), :, :],
-                                           np.sqrt(np.sum(self.binary[(self.start - 1), :, :])))
-        if self.vars['correct_errors_around_initial']:
-            self.rays, self.sun = draw_me_a_sun(self.binary[(self.start - 1), :, :], ray_length_coef=1.25)  # plt.imshow(sun)
-            self.holes = np.zeros(self.dims[1:], dtype=np.uint8)
-            self.pixel_ring_depth += 2
-            self.update_ring_width()
-
-        if self.vars['prevent_fast_growth_near_periphery']:
-            self.near_periphery = np.zeros(self.dims[1:])
-            if self.vars['arena_shape'] == 'circle':
-                periphery_width = self.vars['periphery_width'] * 2
-                elliperiphery = Ellipse((self.dims[1] - periphery_width, self.dims[2] - periphery_width)).create()
-                half_width = periphery_width // 2
-                if periphery_width % 2 == 0:
-                    self.near_periphery[half_width:-half_width, half_width:-half_width] = elliperiphery
-                else:
-                    self.near_periphery[half_width:-half_width - 1, half_width:-half_width - 1] = elliperiphery
-                self.near_periphery = 1 - self.near_periphery
-            else:
-                self.near_periphery[:self.vars['periphery_width'], :] = 1
-                self.near_periphery[-self.vars['periphery_width']:, :] = 1
-                self.near_periphery[:, :self.vars['periphery_width']] = 1
-                self.near_periphery[:, -self.vars['periphery_width']:] = 1
-            self.near_periphery = np.nonzero(self.near_periphery)
-            # near_periphery = np.zeros(self.dims[1:])
-            # near_periphery[self.near_periphery] = 1
-
-    def update_shape(self, show_seg):
-
-        # Get from gradients, a 2D matrix of potentially covered pixels
-        # I/ dilate the shape made with covered pixels to assess for covering
-
-        # I/ 1) Only keep pixels that have been detected at least two times in the three previous frames
-        if self.dims[0] < 100:
-            new_potentials = self.segmentation[self.t, :, :]
-        else:
-            if self.t > 1:
-                new_potentials = np.sum(self.segmentation[(self.t - 2): (self.t + 1), :, :], 0, dtype=np.uint8)
-            else:
-                new_potentials = np.sum(self.segmentation[: (self.t + 1), :, :], 0, dtype=np.uint8)
-            new_potentials[new_potentials == 1] = 0
-            new_potentials[new_potentials > 1] = 1
-
-        # I/ 2) If an image displays more new potential pixels than 50% of image pixels,
-        # one of these images is considered noisy and we try taking only one.
-        frame_counter = -1
-        maximal_size = 0.5 * new_potentials.size
-        if (self.vars["do_threshold_segmentation"] or self.vars["frame_by_frame_segmentation"]) and self.t > np.max((self.start + self.step, 6)):
-           maximal_size = np.min((np.max(self.binary[:self.t].sum((1, 2))) * (1 + self.vars['maximal_growth_factor']), self.borders.sum()))
-        while np.logical_and(np.sum(new_potentials) > maximal_size,
-                             frame_counter <= 5):  # np.logical_and(np.sum(new_potentials > 0) > 5 * np.sum(dila_ring), frame_counter <= 5):
-            frame_counter += 1
-            if frame_counter > self.t:
-                break
-            else:
-                if frame_counter < 5:
-                    new_potentials = self.segmentation[self.t - frame_counter, :, :]
-                else:
-                # If taking only one image is not enough, use the inverse of the fadinged matrix as new_potentials
-                # Given it haven't been processed by any slope calculation, it should be less noisy
-                    new_potentials = np.sum(self.segmentation[(self.t - 5): (self.t + 1), :, :], 0, dtype=np.uint8)
-                    new_potentials[new_potentials < 6] = 0
-                    new_potentials[new_potentials == 6] = 1
-
-
-        new_shape = deepcopy(self.binary[self.t - 1, :, :])
-        new_potentials = cv2.morphologyEx(new_potentials, cv2.MORPH_CLOSE, cross_33)
-        new_potentials = cv2.morphologyEx(new_potentials, cv2.MORPH_OPEN, cross_33) * self.borders
-        new_shape = np.logical_or(new_shape, new_potentials).astype(np.uint8)
-        # Add distant shapes within a radius, score every added pixels according to their distance
-        if not self.vars['several_blob_per_arena']:
-            if new_shape.sum() == 0:
-                new_shape = deepcopy(new_potentials)
-            else:
-                pads = ProgressivelyAddDistantShapes(new_potentials, new_shape, self.max_distance)
-                r = weakref.ref(pads)
-                # If max_distance is non nul look for distant shapes
-                pads.consider_shapes_sizes(self.vars['min_size_for_connection'],
-                                                     self.vars['max_size_for_connection'])
-                pads.connect_shapes(only_keep_connected_shapes=True, rank_connecting_pixels=True)
-
-                new_shape = deepcopy(pads.expanded_shape)
-                new_shape[new_shape > 1] = 1
-                if np.logical_and(self.t > self.step, self.t < self.dims[0]):
-                    if np.any(pads.expanded_shape > 5):
-                        # Add distant shapes back in time at the covering speed of neighbors
-                        self.binary[self.t][np.nonzero(new_shape)] = 1
-                        self.binary[(self.step):(self.t + 1), :, :] = \
-                            pads.modify_past_analysis(self.binary[(self.step):(self.t + 1), :, :],
-                                                      self.segmentation[(self.step):(self.t + 1), :, :])
-                        new_shape = deepcopy(self.binary[self.t, :, :])
-                pads = None
-
-            # Fill holes
-            new_shape = cv2.morphologyEx(new_shape, cv2.MORPH_CLOSE, cross_33)
-
-        if self.vars['do_fading'] and (self.t > self.step + self.lost_frames):
-            # Shape Erosion
-            # I/ After a substantial growth, erode the shape made with covered pixels to assess for fading
-            # Use the newly covered pixels to calculate their mean covering intensity
-            new_idx = np.nonzero(np.logical_xor(new_shape, self.binary[self.t - 1, :, :]))
-            start_intensity_monitoring = self.t - self.lost_frames - self.step
-            end_intensity_monitoring = self.t - self.lost_frames
-            self.covering_intensity[new_idx[0], new_idx[1]] = np.median(self.converted_video[start_intensity_monitoring:end_intensity_monitoring, new_idx[0], new_idx[1]], axis=0)
-            previous_binary = self.binary[self.t - 1, :, :]
-            greyscale_image = self.converted_video[self.t - self.lost_frames, :, :]
-            protect_from_fading = None
-            if self.vars['origin_state'] == 'constant':
-                protect_from_fading = self.origin
-            new_shape, self.covering_intensity = cell_leaving_detection(new_shape, self.covering_intensity, previous_binary, greyscale_image, self.vars['fading'], self.vars['lighter_background'], self.vars['several_blob_per_arena'], self.erodila_disk, protect_from_fading)
-
-        self.covering_intensity *= new_shape
-        self.binary[self.t, :, :] = new_shape * self.borders
-        self.surfarea[self.t] = np.sum(self.binary[self.t, :, :])
-
-        # Calculate the mean distance covered per frame and correct for a ring of not really fading pixels
-        if self.mean_distance_per_frame is None:
-            if self.vars['correct_errors_around_initial'] and not self.vars['several_blob_per_arena']:
-                if np.logical_and((self.t % 20) == 0,
-                                  np.logical_and(self.surfarea[self.t] > self.substantial_growth,
-                                                 self.surfarea[self.t] < self.substantial_growth * 2)):
-                    shape = self.binary[self.t, :, :] * self.sun
-                    back = (1 - self.binary[self.t, :, :]) * self.sun
-                    for ray in self.rays:
-                        # For each sun's ray, see how they cross the shape/back and
-                        # store the gravity_field value of these pixels (distance to the original shape).
-                        ray_through_shape = (shape == ray) * self.gravity_field
-                        ray_through_back = (back == ray) * self.gravity_field
-                        if np.any(ray_through_shape):
-                            if np.any(ray_through_back):
-                                # If at least one back pixel is nearer to the original shape than a shape pixel,
-                                # there is a hole to fill.
-                                if np.any(ray_through_back > np.min(ray_through_shape[ray_through_shape > 0])):
-                                    # Check if the nearest pixels are shape, if so, supress them until the nearest pixel
-                                    # becomes back
-                                    while np.max(ray_through_back) <= np.max(ray_through_shape):
-                                        ray_through_shape[ray_through_shape == np.max(ray_through_shape)] = 0
-                                    # Now, all back pixels that are nearer than the closest shape pixel should get filled
-                                    # To do so, replace back pixels further than the nearest shape pixel by 0
-                                    ray_through_back[ray_through_back < np.max(ray_through_shape)] = 0
-                                    self.holes[np.nonzero(ray_through_back)] = 1
-                            else:
-                                self.rays = np.concatenate((self.rays[:(ray - 2)], self.rays[(ray - 1):]))
-                        ray_through_shape = None
-                        ray_through_back = None
-            if np.any(self.surfarea[:self.t] > self.substantial_growth * 2):
-
-                if self.vars['correct_errors_around_initial'] and not self.vars['several_blob_per_arena']:
-                    # Apply the hole correction
-                    self.holes = cv2.morphologyEx(self.holes, cv2.MORPH_CLOSE, cross_33, iterations=10)
-                    # If some holes are not covered by now
-                    if np.any(self.holes * (1 - self.binary[self.t, :, :])):
-                        self.binary[:(self.t + 1), :, :], holes_time_end, distance_against_time = \
-                            dynamically_expand_to_fill_holes(self.binary[:(self.t + 1), :, :], self.holes)
-                        if holes_time_end is not None:
-                            self.binary[holes_time_end:(self.t + 1), :, :] += self.binary[holes_time_end, :, :]
-                            self.binary[holes_time_end:(self.t + 1), :, :][
-                                self.binary[holes_time_end:(self.t + 1), :, :] > 1] = 1
-                            self.surfarea[:(self.t + 1)] = np.sum(self.binary[:(self.t + 1), :, :], (1, 2))
-
-                    else:
-                        distance_against_time = [1, 2]
-                else:
-                    distance_against_time = [1, 2]
-                distance_against_time = np.diff(distance_against_time)
-                if len(distance_against_time) > 0:
-                    self.mean_distance_per_frame = np.mean(- distance_against_time)
-                else:
-                    self.mean_distance_per_frame = 1
-
-        if self.vars['prevent_fast_growth_near_periphery']:
-            # growth_near_periphery = np.diff(self.binary[self.t-1:self.t+1, :, :] * self.near_periphery, axis=0)
-            growth_near_periphery = np.diff(self.binary[self.t-1:self.t+1, self.near_periphery[0], self.near_periphery[1]], axis=0)
-            if (growth_near_periphery == 1).sum() > self.vars['max_periphery_growth']:
-                # self.binary[self.t, self.near_periphery[0], self.near_periphery[1]] = self.binary[self.t - 1, self.near_periphery[0], self.near_periphery[1]]
-                periphery_to_remove = np.zeros(self.dims[1:], dtype=np.uint8)
-                periphery_to_remove[self.near_periphery[0], self.near_periphery[1]] = self.binary[self.t, self.near_periphery[0], self.near_periphery[1]]
-                shapes, stats, centers = cc(periphery_to_remove)
-                periphery_to_remove = np.nonzero(np.isin(shapes, np.nonzero(stats[:, 4] > self.vars['max_periphery_growth'])[0][1:]))
-                self.binary[self.t, periphery_to_remove[0], periphery_to_remove[1]] = self.binary[self.t - 1, periphery_to_remove[0], periphery_to_remove[1]]
-                if not self.vars['several_blob_per_arena']:
-                    shapes, stats, centers = cc(self.binary[self.t, ...])
-                    shapes[shapes != 1] = 0
-                    self.binary[self.t, ...] = shapes
-
-        # Display
-
-        if show_seg:
-            if self.visu is not None:
-                im_to_display = deepcopy(self.visu[self.t, ...])
-                contours = np.nonzero(cv2.morphologyEx(self.binary[self.t, :, :], cv2.MORPH_GRADIENT, cross_33))
-                if self.vars['lighter_background']:
-                    im_to_display[contours[0], contours[1]] = 0
-                else:
-                    im_to_display[contours[0], contours[1]] = 255
-            else:
-                im_to_display = self.binary[self.t, :, :] * 255
-            imtoshow = cv2.resize(im_to_display, (540, 540))
-            cv2.imshow("shape_motion", imtoshow)
-            cv2.waitKey(1)
-        self.t += 1
-
-    def save_coord_specimen_and_contour(self):
-        if self.vars['save_coord_specimen']:
-             np.save(f"coord_specimen{self.one_descriptor_per_arena['arena']}_t{self.dims[0]}_y{self.dims[1]}_x{self.dims[2]}.npy",
-                 smallest_memory_array(np.nonzero(self.binary), "uint"))
-        if self.vars['save_coord_contour']:
-            contours = np.zeros(self.dims[:3], np.uint8)
-            for frame in range(self.dims[0]):
-                eroded_binary = cv2.erode(self.binary[frame, ...], cross_33, borderType=cv2.BORDER_CONSTANT, borderValue=0)
-                contours[frame, ...] = self.binary[frame, ...] - eroded_binary
-                np.save(f"coord_contour{self.one_descriptor_per_arena['arena']}_t{self.dims[0]}_y{self.dims[1]}_x{self.dims[2]}.npy",
-                 smallest_memory_array(np.nonzero(contours), "uint"))
-
-    def get_descriptors_from_binary(self, release_memory=True):
-        ##
-        if release_memory:
-            self.substantial_image = None
-            self.covering_intensity = None
-            self.segmentation = None
-            self.gravity_field = None
-            self.sun = None
-            self.rays = None
-            self.holes = None
-            collect()
-        self.save_coord_specimen_and_contour()
-        if self.vars['do_fading']:
-            self.newly_explored_area = np.zeros(self.dims[0], dtype =np.uint64)
-            self.already_explored_area = deepcopy(self.origin)
-            for self.t in range(self.dims[0]):
-                self.newly_explored_area[self.t] = ((self.binary[self.t, :, :] - self.already_explored_area) == 1).sum()
-                self.already_explored_area = np.logical_or(self.already_explored_area, self.binary[self.t, :, :])
-
-        self.surfarea = self.binary.sum((1, 2))
-        timings = self.vars['exif']
-        if len(timings) < self.dims[0]:
-            timings = np.arange(self.dims[0])
-        if np.any(timings > 0):
-            self.time_interval = np.mean(np.diff(timings))
-        timings = timings[:self.dims[0]]
-        available_descriptors_in_sd = list(from_shape_descriptors_class.keys())
-        # ["area", "perimeter", "circularity", "rectangularity", "total_hole_area", "solidity",
-        #                          "convexity", "eccentricity", "euler_number", "standard_deviation_y",
-        #                          "standard_deviation_x", "skewness_y", "skewness_x", "kurtosis_y", "kurtosis_x",
-        #                          "major_axis_len", "minor_axis_len", "axes_orientation"]
-        all_descriptors = []
-        to_compute_from_sd = []
-        for name, do_compute in self.vars['descriptors'].items():
-            if do_compute:# and
-                all_descriptors.append(name)
-                if np.isin(name, available_descriptors_in_sd):
-                    to_compute_from_sd.append(name)
-        self.compute_solidity_separately: bool = self.vars['iso_digi_analysis'] and not self.vars['several_blob_per_arena'] and not np.isin("solidity", to_compute_from_sd)
-        if self.compute_solidity_separately:
-            self.solidity = np.zeros(self.dims[0], dtype=np.float64)
-        if not self.vars['several_blob_per_arena']:
-            self.one_row_per_frame = pd.DataFrame(np.zeros((self.dims[0], 2 + len(all_descriptors))),
-                                              columns=['arena', 'time'] + all_descriptors)
-            self.one_row_per_frame['arena'] = [self.one_descriptor_per_arena['arena']] * self.dims[0]
-            self.one_row_per_frame['time'] = timings
-            # solidity must be added if detect growth transition is computed
-            origin = self.binary[0, :, :]
-            self.one_descriptor_per_arena["first_move"] = pd.NA
-
-            for t in np.arange(self.dims[0]):
-                SD = ShapeDescriptors(self.binary[t, :, :], to_compute_from_sd)
-
-
-                # NEW
-                for descriptor in to_compute_from_sd:
-                    self.one_row_per_frame.loc[t, descriptor] = SD.descriptors[descriptor]
-                # Old
-                # self.one_row_per_frame.iloc[t, 2: 2 + len(descriptors)] = SD.descriptors.values()
-
-
-                if self.compute_solidity_separately:
-                    solidity = ShapeDescriptors(self.binary[t, :, :], ["solidity"])
-                    self.solidity[t] = solidity.descriptors["solidity"]
-                    # self.solidity[t] = list(solidity.descriptors.values())[0]
-                # I) Find a first pseudopod [aim: time]
-                if pd.isna(self.one_descriptor_per_arena["first_move"]):
-                    if self.surfarea[t] >= (origin.sum() + self.vars['first_move_threshold']):
-                        self.one_descriptor_per_arena["first_move"] = t
-
-            # Apply the scale to the variables
-            if self.vars['output_in_mm']:
-                if np.isin('area', to_compute_from_sd):
-                    self.one_row_per_frame['area'] *= self.vars['average_pixel_size']
-                if np.isin('total_hole_area', to_compute_from_sd):
-                    self.one_row_per_frame['total_hole_area'] *= self.vars['average_pixel_size']
-                if np.isin('perimeter', to_compute_from_sd):
-                    self.one_row_per_frame['perimeter'] *= np.sqrt(self.vars['average_pixel_size'])
-                if np.isin('major_axis_len', to_compute_from_sd):
-                    self.one_row_per_frame['major_axis_len'] *= np.sqrt(self.vars['average_pixel_size'])
-                if np.isin('minor_axis_len', to_compute_from_sd):
-                    self.one_row_per_frame['minor_axis_len'] *= np.sqrt(self.vars['average_pixel_size'])
-        else:
-            # Objective: create a matrix with 4 columns (time, y, x, colony) containing the coordinates of all colonies
-            # against time
-            self.one_descriptor_per_arena["first_move"] = 1
-            max_colonies = 0
-            for t in np.arange(self.dims[0]):
-                nb, shapes = cv2.connectedComponents(self.binary[t, :, :])
-                max_colonies = np.max((max_colonies, nb))
-
-            time_descriptor_colony = np.zeros((self.dims[0], len(to_compute_from_sd) * max_colonies * self.dims[0]),
-                                              dtype=np.float32)  # Adjust max_colonies
-            colony_number = 0
-            colony_id_matrix = np.zeros(self.dims[1:], dtype =np.uint64)
-            coord_colonies = []
-            centroids = []
-
-            pat_tracker = PercentAndTimeTracker(self.dims[0], compute_with_elements_number=True)
-            for t in np.arange(self.dims[0]):  #21):#
-                # t=0
-                # t+=1
-                # We rank colonies in increasing order to make sure that the larger colony issued from a colony division
-                # keeps the previous colony name.
-                shapes, stats, centers = cc(self.binary[t, :, :])
-
-                # Consider that shapes bellow 3 pixels are noise. The loop will stop at nb and not compute them
-                nb = stats[stats[:, 4] >= 4].shape[0]
-
-                # nb = stats.shape[0]
-                current_percentage, eta = pat_tracker.get_progress(t, element_number=nb)
-                logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}, Colony descriptors computation: {current_percentage}%{eta}")
-
-                updated_colony_names = np.zeros(1, dtype=np.uint32)
-                for colony in (np.arange(nb - 1) + 1):  # 120)):# #92
-                    # colony = 1
-                    # colony+=1
-                    # logging.info(f'Colony number {colony}')
-                    current_colony_img = (shapes == colony).astype(np.uint8)
-
-                    # I/ Find out which names the current colony had at t-1
-                    colony_previous_names = np.unique(current_colony_img * colony_id_matrix)
-                    colony_previous_names = colony_previous_names[colony_previous_names != 0]
-                    # II/ Find out if the current colony name had already been analyzed at t
-                    # If there no match with the saved colony_id_matrix, assign colony ID
-                    if t == 0 or len(colony_previous_names) == 0:
-                        # logging.info("New colony")
-                        colony_number += 1
-                        colony_names = [colony_number]
-                    # If there is at least 1 match with the saved colony_id_matrix, we keep the colony_previous_name(s)
-                    else:
-                        colony_names = colony_previous_names.tolist()
-                    # Handle colony division if necessary
-                    if np.any(np.isin(updated_colony_names, colony_names)):
-                        colony_number += 1
-                        colony_names = [colony_number]
-
-                    # Update colony ID matrix for the current frame
-                    coords = np.nonzero(current_colony_img)
-                    colony_id_matrix[coords[0], coords[1]] = colony_names[0]
-
-                    # Add coordinates to coord_colonies
-                    time_column = np.full(coords[0].shape, t, dtype=np.uint32)
-                    colony_column = np.full(coords[0].shape, colony_names[0], dtype=np.uint32)
-                    coord_colonies.append(np.column_stack((time_column, colony_column, coords[0], coords[1])))
-
-                    # Calculate centroid and add to centroids list
-                    centroid_x, centroid_y = centers[colony, :]
-                    centroids.append((t, colony_names[0], centroid_y, centroid_x))
-
-                    # Compute shape descriptors
-                    SD = ShapeDescriptors(current_colony_img, to_compute_from_sd)
-                    descriptors = list(SD.descriptors.values())
-                    # Adjust descriptors if output_in_mm is specified
-                    if self.vars['output_in_mm']:
-                        if 'area' in to_compute_from_sd:
-                            descriptors['area'] *= self.vars['average_pixel_size']
-                        if 'total_hole_area' in to_compute_from_sd:
-                            descriptors['total_hole_area'] *= self.vars['average_pixel_size']
-                        if 'perimeter' in to_compute_from_sd:
-                            descriptors['perimeter'] *= np.sqrt(self.vars['average_pixel_size'])
-                        if 'major_axis_len' in to_compute_from_sd:
-                            descriptors['major_axis_len'] *= np.sqrt(self.vars['average_pixel_size'])
-                        if 'minor_axis_len' in to_compute_from_sd:
-                            descriptors['minor_axis_len'] *= np.sqrt(self.vars['average_pixel_size'])
-
-                    # Store descriptors in time_descriptor_colony
-                    descriptor_index = (colony_names[0] - 1) * len(to_compute_from_sd)
-                    time_descriptor_colony[t, descriptor_index:(descriptor_index + len(descriptors))] = descriptors
-
-                    updated_colony_names = np.append(updated_colony_names, colony_names)
-
-                # Reset colony_id_matrix for the next frame
-                colony_id_matrix *= self.binary[t, :, :]
-
-            coord_colonies = np.vstack(coord_colonies)
-            centroids = np.array(centroids, dtype=np.float32)
-            time_descriptor_colony = time_descriptor_colony[:, :(colony_number*len(to_compute_from_sd))]
-
-            if self.vars['save_coord_specimen']:
-                coord_colonies = pd.DataFrame(coord_colonies, columns=["time", "colony", "y", "x"])
-                coord_colonies.to_csv(f"coord_colonies{self.one_descriptor_per_arena['arena']}_t{self.dims[0]}_col{colony_number}_y{self.dims[1]}_x{self.dims[2]}.csv", sep=';', index=False, lineterminator='\n')
-                
-            centroids = pd.DataFrame(centroids, columns=["time", "colony", "y", "x"])
-            centroids.to_csv(f"colony_centroids{self.one_descriptor_per_arena['arena']}_t{self.dims[0]}_col{colony_number}_y{self.dims[1]}_x{self.dims[2]}.csv", sep=';', index=False, lineterminator='\n')
-
-            # Format the final dataframe to have one row per time frame, and one column per descriptor_colony_name
-            self.one_row_per_frame = pd.DataFrame({'arena': self.one_descriptor_per_arena['arena'], 'time': timings, 'area_total': self.surfarea.astype(np.float64)})
-            if self.vars['output_in_mm']:
-                self.one_row_per_frame['area_total'] *= self.vars['average_pixel_size']
-            column_names = np.char.add(np.repeat(to_compute_from_sd, colony_number),
-                                    np.tile((np.arange(colony_number) + 1).astype(str), len(to_compute_from_sd)))
-            time_descriptor_colony = pd.DataFrame(time_descriptor_colony, columns=column_names)
-            self.one_row_per_frame = pd.concat([self.one_row_per_frame, time_descriptor_colony], axis=1)
-
-
-        if self.vars['do_fading']:
-            self.one_row_per_frame['newly_explored_area'] = self.newly_explored_area
-            if self.vars['output_in_mm']:
-                self.one_row_per_frame['newly_explored_area'] *= self.vars['average_pixel_size']
-
-    def detect_growth_transitions(self):
-        ##
-        if self.vars['iso_digi_analysis'] and not self.vars['several_blob_per_arena']:
-            self.one_descriptor_per_arena["iso_digi_transi"] = pd.NA
-            if not pd.isna(self.one_descriptor_per_arena["first_move"]):
-                logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Starting growth transition analysis.")
-
-                # II) Once a pseudopod is deployed, look for a disk/ around the original shape
-                growth_begining = self.surfarea < ((self.surfarea[0] * 1.2) + ((self.dims[1] / 4) * (self.dims[2] / 4)))
-                dilated_origin = cv2.dilate(self.binary[self.one_descriptor_per_arena["first_move"], :, :], kernel=cross_33, iterations=10, borderType=cv2.BORDER_CONSTANT, borderValue=0)
-                isisotropic = np.sum(self.binary[:, :, :] * dilated_origin, (1, 2))
-                isisotropic *= growth_begining
-                # Ask if the dilated origin area is 90% covered during the growth beginning
-                isisotropic = isisotropic > 0.9 * dilated_origin.sum()
-                if np.any(isisotropic):
-                    self.one_descriptor_per_arena["is_growth_isotropic"] = 1
-                    # Determine a solidity reference to look for a potential breaking of the isotropic growth
-                    if self.compute_solidity_separately:
-                        solidity_reference = np.mean(self.solidity[:self.one_descriptor_per_arena["first_move"]])
-                        different_solidity = self.solidity < (0.9 * solidity_reference)
-                        del self.solidity
-                    else:
-                        solidity_reference = np.mean(
-                            self.one_row_per_frame.iloc[:(self.one_descriptor_per_arena["first_move"]), :]["solidity"])
-                        different_solidity = self.one_row_per_frame["solidity"].values < (0.9 * solidity_reference)
-                    # Make sure that isotropic breaking not occur before isotropic growth
-                    if np.any(different_solidity):
-                        self.one_descriptor_per_arena["iso_digi_transi"] = np.nonzero(different_solidity)[0][0] * self.time_interval
-                else:
-                    self.one_descriptor_per_arena["is_growth_isotropic"] = 0
-            else:
-                self.one_descriptor_per_arena["is_growth_isotropic"] = pd.NA
-                
-
-    def check_converted_video_type(self):
-        if self.converted_video.dtype != "uint8":
-            self.converted_video -= np.min(self.converted_video)
-            self.converted_video = np.round((255 * (self.converted_video / np.max(self.converted_video)))).astype(np.uint8)
-
-
-    def networks_detection(self, show_seg=False):
-        if not pd.isna(self.one_descriptor_per_arena["first_move"]) and not self.vars['several_blob_per_arena'] and (self.vars['save_coord_network'] or self.vars['network_analysis']):
-            logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Starting network detection.")
-            smooth_segmentation_over_time = True
-            detect_pseudopods = True
-            pseudopod_min_size = 50
-            self.check_converted_video_type()
-            if detect_pseudopods:
-                pseudopod_vid = np.zeros_like(self.binary, dtype=bool)
-            potential_network = np.zeros_like(self.binary, dtype=bool)
-            self.network_dynamics = np.zeros_like(self.binary, dtype=np.uint8)
-            greyscale = self.visu[-1, ...].mean(axis=-1)
-            NetDet = NetworkDetection(greyscale, possibly_filled_pixels=self.binary[-1, ...],
-                                      origin_to_add=self.origin)
-            NetDet.get_best_network_detection_method()
-            NetDet.change_greyscale(self.visu[-1, ...], c_space_dict=self.vars['convert_for_motion'])
-            lighter_background = NetDet.greyscale_image[self.binary[-1, ...] > 0].mean() < NetDet.greyscale_image[self.binary[-1, ...] == 0].mean()
-
-
-            for t in np.arange(self.one_descriptor_per_arena["first_move"], self.dims[0]):  # 20):#
-                greyscale = self.visu[t, ...].mean(axis=-1)
-                NetDet_fast = NetworkDetection(greyscale, possibly_filled_pixels=self.binary[t, ...],
-                                          origin_to_add=self.origin, best_result=NetDet.best_result)
-                NetDet_fast.detect_network()
-                if detect_pseudopods:
-                    NetDet_fast.detect_pseudopods(lighter_background, pseudopod_min_size=pseudopod_min_size)
-                    NetDet_fast.merge_network_with_pseudopods()
-                    pseudopod_vid[t, ...] = NetDet_fast.pseudopods
-                potential_network[t, ...] = NetDet_fast.complete_network
-            for t in np.arange(self.one_descriptor_per_arena["first_move"], self.dims[0]):  # 20):#
-                if smooth_segmentation_over_time:
-                    if 2 <= t <= (self.dims[0] - 2):
-                        computed_network = potential_network[(t - 2):(t + 3), :, :].sum(axis=0)
-                        computed_network[computed_network == 1] = 0
-                        computed_network[computed_network > 1] = 1
-                    else:
-                        if t < 2:
-                            computed_network = potential_network[:2, :, :].sum(axis=0)
-                        else:
-                            computed_network = potential_network[-2:, :, :].sum(axis=0)
-                        computed_network[computed_network > 0] = 1
-                else:
-                    computed_network = computed_network[t, :, :].copy()
-
-                if self.origin is not None:
-                    computed_network = computed_network * (1 - self.origin)
-                    origin_contours = get_contours(self.origin)
-                    complete_network = np.logical_or(origin_contours, computed_network).astype(np.uint8)
-                complete_network = keep_one_connected_component(complete_network)
-
-                if detect_pseudopods:
-                    # Make sure that removing pseudopods do not cut the network:
-                    without_pseudopods = complete_network * (1 - pseudopod_vid[t])
-                    only_connected_network = keep_one_connected_component(without_pseudopods)
-                    # # Option A: To add these cutting regions to the pseudopods do:
-                    pseudopods = (1 - only_connected_network) * complete_network
-                    pseudopod_vid[t] = pseudopods
-                self.network_dynamics[t] = complete_network
-
-                # # Option B: To add these cutting regions to the network:
-                # # Differentiate pseudopods that cut the network from the 'true ones'
-                # # Dilate pseudopods and restrein them to the
-                # pseudopods = cv2.dilate(pseudopod_vid[t], kernel=Ellipse((15, 15)).create().astype(np.uint8),
-                #                         iterations=1) * self.binary[t, :, :]
-                # nb, numbered_pseudopods = cv2.connectedComponents(pseudopods)
-                # pseudopods = np.zeros_like(pseudopod_vid[t])
-                # for p_i in range(1, nb + 1):
-                #     pseudo_i = numbered_pseudopods == p_i
-                #     nb_i, remainings, stats, centro = cv2.connectedComponentsWithStats(
-                #         complete_network * (1 - pseudo_i.astype(np.uint8)))
-                #     if (stats[:, 4] > pseudopod_min_size).sum() == 2:
-                #         pseudopods[pseudo_i] = 1
-                #         fragmented = np.nonzero(stats[:, 4] <= pseudopod_min_size)[0]
-                #         pseudopods[np.isin(remainings, fragmented)] = 1
-                # pseudopod_vid[t] = pseudopods
-                # complete_network[pseudopods > 0] = 1
-                # self.network_dynamics[t] = complete_network
-
-
-                imtoshow = self.visu[t, ...]
-                eroded_binary = cv2.erode(self.network_dynamics[t, ...], cross_33)
-                net_coord = np.nonzero(self.network_dynamics[t, ...] - eroded_binary)
-                imtoshow[net_coord[0], net_coord[1], :] = (34, 34, 158)
-                if show_seg:
-                    cv2.imshow("", cv2.resize(imtoshow, (1000, 1000)))
-                    cv2.waitKey(1)
-                else:
-                    self.visu[t, ...] = imtoshow
-                if show_seg:
-                    cv2.destroyAllWindows()
-
-            network_coord = smallest_memory_array(np.nonzero(self.network_dynamics), "uint")
-
-            if detect_pseudopods:
-                self.network_dynamics[pseudopod_vid > 0] = 2
-                pseudopod_coord = smallest_memory_array(np.nonzero(pseudopod_vid), "uint")
-            if self.vars['save_coord_network']:
-                 np.save(
-                    f"coord_tubular_network{self.one_descriptor_per_arena['arena']}_t{self.dims[0]}_y{self.dims[1]}_x{self.dims[2]}.npy",
-                    network_coord)
-
-                 if detect_pseudopods:
-                     np.save(
-                        f"coord_pseudopods{self.one_descriptor_per_arena['arena']}_t{self.dims[0]}_y{self.dims[1]}_x{self.dims[2]}.npy",
-                        pseudopod_coord)
-
-    def graph_extraction(self):
-        if self.vars['graph_extraction'] and not self.vars['network_analysis'] and not self.vars['save_coord_network']:
-            self.network_dynamics = self.binary
-        _, _, _, origin_centroid = cv2.connectedComponentsWithStats(self.origin)
-        origin_centroid = np.round((origin_centroid[1, 1], origin_centroid[1, 0])).astype(np.uint64)
-        for t in np.arange(self.one_descriptor_per_arena["first_move"], self.dims[0]):  # 20):#
-
-
-            if self.origin is not None:
-                computed_network = self.network_dynamics[t, ...] * (1 - self.origin)
-                origin_contours = get_contours(self.origin)
-                computed_network = np.logical_or(origin_contours, computed_network).astype(np.uint8)
-            else:
-                origin_contours = None
-                computed_network = self.network_dynamics[t, ...].astype(np.uint8)
-            computed_network = keep_one_connected_component(computed_network)
-            pad_network, pad_origin = add_padding([computed_network, self.origin])
-            pad_origin_centroid = origin_centroid + 1
-            pad_skeleton, pad_distances, pad_origin_contours = get_skeleton_and_widths(pad_network, pad_origin,
-                                                                                       pad_origin_centroid)
-            edge_id = EdgeIdentification(pad_skeleton, pad_distances)
-            edge_id.run_edge_identification()
-            if pad_origin_contours is not None:
-                origin_contours = remove_padding([pad_origin_contours])[0]
-            edge_id.make_vertex_table(origin_contours, self.network_dynamics[t, ...] == 2)
-            edge_id.make_edge_table(self.converted_video[:, t])
-
-
-            edge_id.vertex_table = np.hstack((np.repeat(t, edge_id.vertex_table.shape[0])[:, None], edge_id.vertex_table))
-            edge_id.edge_table = np.hstack((np.repeat(t, edge_id.edge_table.shape[0])[:, None], edge_id.edge_table))
-            if t == self.one_descriptor_per_arena["first_move"]:
-                vertex_table = edge_id.vertex_table.copy()
-                edge_table = edge_id.edge_table.copy()
-            else:
-                vertex_table = np.vstack((vertex_table, edge_id.vertex_table))
-                edge_table = np.vstack((edge_table, edge_id.edge_table))
-
-        vertex_table = pd.DataFrame(vertex_table, columns=["t", "y", "x", "vertex_id", "is_tip", "origin",
-                                                 "vertex_connected"])
-        edge_table = pd.DataFrame(edge_table,
-                        columns=["t", "edge_id", "vertex1", "vertex2", "length", "average_width", "intensity", "betweenness_centrality"])
-        vertex_table.to_csv(
-            f"vertex_table{self.one_descriptor_per_arena['arena']}_t{self.dims[0]}_y{self.dims[1]}_x{self.dims[2]}.csv")
-        edge_table.to_csv(
-            f"edge_table{self.one_descriptor_per_arena['arena']}_t{self.dims[0]}_y{self.dims[1]}_x{self.dims[2]}.csv")
-
-
-    def memory_allocation_for_cytoscillations(self):
-        try:
-            period_in_frame_nb = int(self.vars['expected_oscillation_period'] / self.time_interval)
-            if period_in_frame_nb < 2:
-                period_in_frame_nb = 2
-            necessary_memory = self.converted_video.shape[0] * self.converted_video.shape[1] * \
-                               self.converted_video.shape[2] * 64 * 4 * 1.16415e-10
-            available_memory = (virtual_memory().available >> 30) - self.vars['min_ram_free']
-            if len(self.converted_video.shape) == 4:
-                self.converted_video = self.converted_video[:, :, :, 0]
-            average_intensities = np.mean(self.converted_video, (1, 2))
-            if self.vars['lose_accuracy_to_save_memory'] or (necessary_memory > available_memory):
-                oscillations_video = np.zeros(self.converted_video.shape, dtype=np.float16)
-                for cy in np.arange(self.converted_video.shape[1]):
-                    for cx in np.arange(self.converted_video.shape[2]):
-                        oscillations_video[:, cy, cx] = np.round(np.gradient(self.converted_video[:, cy, cx, ...]/average_intensities,
-                                                                      period_in_frame_nb), 3).astype(np.float16)
-            else:
-                oscillations_video = np.gradient(self.converted_video/average_intensities, period_in_frame_nb, axis=0)
-            # check if conv change here
-            self.check_converted_video_type()
-            if len(self.converted_video.shape) == 3:
-                self.converted_video = np.stack((self.converted_video, self.converted_video, self.converted_video), axis=3)
-            oscillations_video = np.sign(oscillations_video)
-            return oscillations_video
-        except Exception as exc:
-            logging.error(f"{exc}. Retrying to allocate for 10 minutes before crashing. ")
-            return None
-
-
-    def study_cytoscillations(self, show_seg):
-        if pd.isna(self.one_descriptor_per_arena["first_move"]):
-            if not self.vars['lose_accuracy_to_save_memory']:
-                self.check_converted_video_type()
-            if self.vars['oscilacyto_analysis']:
-                self.one_row_per_frame['mean_cluster_area'] = pd.NA
-                self.one_row_per_frame['cluster_number'] = pd.NA
-        else:
-            if self.vars['save_coord_thickening_slimming'] or self.vars['oscilacyto_analysis']:
-                logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Starting oscillation analysis.")
-                oscillations_video = None
-                staring_time = default_timer()
-                current_time = staring_time
-                while oscillations_video is None and (current_time - staring_time) < 600:
-                    oscillations_video = self.memory_allocation_for_cytoscillations()
-                    if oscillations_video is None:
-                        sleep(30)
-                        current_time = default_timer()
-
-                within_range = (1 - self.binary[0, :, :]) * self.borders
-                within_range = self.binary * within_range
-                oscillations_video *= within_range
-                del within_range
-                oscillations_video += 1
-                oscillations_video = oscillations_video.astype(np.uint8)
-
-                dotted_image = np.ones(self.converted_video.shape[1:3], np.uint8)
-                for cy in np.arange(dotted_image.shape[0]):
-                    if cy % 2 != 0:
-                        dotted_image[cy, :] = 0
-                for cx in np.arange(dotted_image.shape[1]):
-                    if cx % 2 != 0:
-                        dotted_image[:, cx] = 0
-
-                if self.start is None:
-                    self.start = 0
-
-                for t in np.arange(self.dims[0]):
-                    eroded_binary = cv2.erode(self.binary[t, :, :], cross_33)
-                    contours = self.binary[t, :, :] - eroded_binary
-                    contours_idx = np.nonzero(contours)
-                    imtoshow = deepcopy(self.converted_video[t, ...])
-                    imtoshow[contours_idx[0], contours_idx[1], :] = self.vars['contour_color']
-                    if self.vars['iso_digi_analysis'] and not self.vars['several_blob_per_arena'] and not pd.isna(self.one_descriptor_per_arena["iso_digi_transi"]):
-                        if self.one_descriptor_per_arena["is_growth_isotropic"] == 1:
-                            if t < self.one_descriptor_per_arena["iso_digi_transi"]:
-                                imtoshow[contours_idx[0], contours_idx[1], 2] = 255
-                    oscillations_image = np.zeros(self.dims[1:], np.uint8)
-                    if t >= self.start:
-                        # Add in or ef if a pixel has at least 4 neighbor in or ef
-                        neigh_comp = CompareNeighborsWithValue(oscillations_video[t, :, :], connectivity=8, data_type=np.int8)
-                        neigh_comp.is_inf(1, and_itself=False)
-                        neigh_comp.is_sup(1, and_itself=False)
-                        # Not verified if influx is really influx (resp efflux)
-                        influx = neigh_comp.sup_neighbor_nb
-                        efflux = neigh_comp.inf_neighbor_nb
-
-                        # Only keep pixels having at least 4 positive (resp. negative) neighbors
-                        influx[influx <= 4] = 0
-                        efflux[efflux <= 4] = 0
-                        influx[influx > 4] = 1
-                        efflux[efflux > 4] = 1
-                        if np.any(influx) or np.any(efflux):
-                            influx, in_stats, in_centroids = cc(influx)
-                            efflux, ef_stats, ef_centroids = cc(efflux)
-                            # Only keep clusters larger than 'minimal_oscillating_cluster_size' pixels (smaller are considered as noise
-                            in_smalls = np.nonzero(in_stats[:, 4] < self.vars['minimal_oscillating_cluster_size'])[0]
-                            if len(in_smalls) > 0:
-                                influx[np.isin(influx, in_smalls)] = 0
-                                in_stats = in_stats[:in_smalls[0], :]
-                                in_centroids = in_centroids[:in_smalls[0], :]
-                            ef_smalls = np.nonzero(ef_stats[:, 4] < self.vars['minimal_oscillating_cluster_size'])[0]
-                            if len(ef_smalls) > 0:
-                                efflux[np.isin(efflux, ef_smalls)] = 0
-                                ef_stats = ef_stats[:(ef_smalls[0]), :]
-                                ef_centroids = ef_centroids[:(ef_smalls[0]), :]
-                            in_idx = np.nonzero(influx)  # NEW
-                            ef_idx = np.nonzero(efflux)  # NEW
-                            oscillations_image[in_idx[0], in_idx[1]] = 1  # NEW
-                            oscillations_image[ef_idx[0], ef_idx[1]] = 2  # NEW
-                            # Prepare the image for display
-                            influx *= dotted_image
-                            efflux *= dotted_image
-                            in_idx = np.nonzero(influx)
-                            ef_idx = np.nonzero(efflux)
-                            imtoshow[in_idx[0], in_idx[1], :2] = 153  # Green: influx, intensity increase
-                            imtoshow[in_idx[0], in_idx[1], 2] = 0
-                            imtoshow[ef_idx[0], ef_idx[1], 1:] = 0  # Blue: efflux, intensity decrease
-                            imtoshow[ef_idx[0], ef_idx[1], 0] = 204
-                    oscillations_video[t, :, :] = oscillations_image
-                    self.converted_video[t, ...] = deepcopy(imtoshow)
-                    if show_seg:
-                        im_to_show = cv2.resize(imtoshow, (540, 540))
-                        cv2.imshow("shape_motion", im_to_show)
-                        cv2.waitKey(1)
-                if show_seg:
-                    cv2.destroyAllWindows()
-                if self.vars['save_coord_thickening_slimming']:
-                     np.save(f"coord_thickening{self.one_descriptor_per_arena['arena']}_t{self.dims[0]}_y{self.dims[1]}_x{self.dims[2]}.npy", smallest_memory_array(np.nonzero(oscillations_video == 1), "uint"))
-                     np.save(f"coord_slimming{self.one_descriptor_per_arena['arena']}_t{self.dims[0]}_y{self.dims[1]}_x{self.dims[2]}.npy", smallest_memory_array(np.nonzero(oscillations_video == 2), "uint"))
-
-
-                if self.vars['oscilacyto_analysis']:
-                    # To get the median oscillatory period of each oscillating cluster,
-                    # we create a dict containing two lists (for influx and efflux)
-                    # Each list element correspond to a cluster and stores :
-                    # All pixel coordinates of that cluster, their corresponding lifespan, their time of disappearing
-                    # Row number will give the size. Euclidean distance between pix coord, the wave distance
-                    self.clusters_final_data = np.empty((0, 6),
-                                                     dtype=np.float32)  # ["mean_pixel_period", "phase", "total_size", "edge_distance", cy, cx]
-                    period_tracking = np.zeros(self.converted_video.shape[1:3], dtype=np.uint32)
-                    efflux_study = ClusterFluxStudy(self.converted_video.shape[:3])
-                    influx_study = ClusterFluxStudy(self.converted_video.shape[:3])
-
-                    if self.start is None:
-                        self.start = 0
-                    if self.vars['fractal_analysis']:
-                        if os.path.exists(f"oscillating_clusters_temporal_dynamics.h5"):
-                            remove_h5_key(f"oscillating_clusters_temporal_dynamics.h5",
-                                          f"arena{self.one_descriptor_per_arena['arena']}")
-                    cluster_id_matrix = np.zeros(self.dims[1:], dtype =np.uint64)
-                    named_cluster_number = 0
-                    mean_cluster_area = np.zeros(oscillations_video.shape[0])
-                    pat_tracker = PercentAndTimeTracker(self.dims[0], compute_with_elements_number=True)
-                    for t in np.arange(np.max((self.start, self.lost_frames)), self.dims[0]):  # np.arange(21): #
-                        eroded_binary = cv2.erode(self.binary[t, :, :], cross_33)
-                        contours = self.binary[t, :, :] - eroded_binary
-                        oscillations_image = oscillations_video[t, ...]
-                        influx = (oscillations_image == 1).astype(np.uint8)
-                        efflux = (oscillations_image == 2).astype(np.uint8)
-                        in_idx = np.nonzero(influx)  # NEW
-                        ef_idx = np.nonzero(efflux)
-                        influx, in_stats, in_centroids = cc(influx)
-                        efflux, ef_stats, ef_centroids = cc(efflux)
-                        in_stats = in_stats[1:]
-                        in_centroids = in_centroids[1:]
-                        ef_stats = ef_stats[1:]
-                        ef_centroids = ef_centroids[1:]
-                        # Sum the number of connected components minus the background to get the number of clusters
-                        oscillating_cluster_number = in_stats.shape[0] + ef_stats.shape[0]
-                        updated_cluster_names = [0]
-                        if oscillating_cluster_number > 0:
-                            current_percentage, eta = pat_tracker.get_progress(t, element_number=oscillating_cluster_number)
-                            logging.info(
-                                f"Arena n°{self.one_descriptor_per_arena['arena']}, Oscillatory cluster computation: {current_percentage}%{eta}")
-                            if self.vars['fractal_analysis']:
-                                # New analysis to get the surface dynamic of every oscillatory cluster: Part 2 openning:
-                                network_at_t = np.zeros(self.dims[1:], dtype=np.uint8)
-                                network_idx = self.network_dynamics[:, self.network_dynamics[0, :] == t]
-                                network_at_t[network_idx[1, :], network_idx[2, :]] = 1
-                                shapes = np.zeros(self.dims[1:], dtype=np.uint32)
-                                shapes[in_idx[0], in_idx[1]] = influx[in_idx[0], in_idx[1]]
-                                max_in = in_stats.shape[0]
-                                shapes[ef_idx[0], ef_idx[1]] = max_in + efflux[ef_idx[0], ef_idx[1]]
-                                centers = np.vstack((in_centroids, ef_centroids))
-                                cluster_dynamic = np.zeros((int(oscillating_cluster_number) - 1, 13), dtype=np.float64)
-                                for clust_i in np.arange(oscillating_cluster_number - 1, dtype=np.uint32):  # 120)):# #92
-                                    cluster = clust_i + 1
-                                    # cluster = 1
-                                    # print(cluster)
-                                    current_cluster_img = (shapes == cluster).astype(np.uint8)
-                                    # I/ Find out which names the current cluster had at t-1
-                                    cluster_previous_names = np.unique(current_cluster_img * cluster_id_matrix)
-                                    cluster_previous_names = cluster_previous_names[cluster_previous_names != 0]
-                                    # II/ Find out if the current cluster name had already been analyzed at t
-                                    # If there no match with the saved cluster_id_matrix, assign cluster ID
-                                    if t == 0 or len(cluster_previous_names) == 0:
-                                        # logging.info("New cluster")
-                                        named_cluster_number += 1
-                                        cluster_names = [named_cluster_number]
-                                    # If there is at least 1 match with the saved cluster_id_matrix, we keep the cluster_previous_name(s)
-                                    else:
-                                        cluster_names = cluster_previous_names.tolist()
-                                    # Handle cluster division if necessary
-                                    if np.any(np.isin(updated_cluster_names, cluster_names)):
-                                        named_cluster_number += 1
-                                        cluster_names = [named_cluster_number]
-
-                                    # Get flow direction:
-                                    if np.unique(oscillations_image * current_cluster_img)[1] == 1:
-                                        flow = 1
-                                    else:
-                                        flow = - 1
-                                    # Update cluster ID matrix for the current frame
-                                    coords = np.nonzero(current_cluster_img)
-                                    cluster_id_matrix[coords[0], coords[1]] = cluster_names[0]
-
-                                    # Save the current cluster areas:
-                                    inner_network = current_cluster_img * network_at_t
-                                    inner_network_area = inner_network.sum()
-                                    zoomed_binary, side_lengths = prepare_box_counting(current_cluster_img,
-                                                                                       side_threshold=self.vars[
-                                                                                           'fractal_box_side_threshold'],
-                                                                                       zoom_step=self.vars[
-                                                                                           'fractal_zoom_step'],
-                                                                                       contours=True)
-                                    box_count_dim, r_value, box_nb = box_counting_dimension(zoomed_binary, side_lengths)
-
-                                    if np.any(inner_network):
-                                        zoomed_binary, side_lengths = prepare_box_counting(inner_network,
-                                                                                           side_threshold=self.vars[
-                                                                                               'fractal_box_side_threshold'],
-                                                                                           zoom_step=self.vars[
-                                                                                               'fractal_zoom_step'],
-                                                                                           contours=False)
-                                        inner_network_box_count_dim, inner_net_r_value, inner_net_box_nb = box_counting_dimension(
-                                            zoomed_binary, side_lengths)
-                                    else:
-                                        inner_network_box_count_dim, inner_net_r_value, inner_net_box_nb = 0, 0, 0
-                                    # Calculate centroid and add to centroids list
-                                    centroid_x, centroid_y = centers[cluster, :]
-                                    if self.vars['output_in_mm']:
-                                        cluster_dynamic[clust_i, :] = np.array(
-                                            (t * self.time_interval, cluster_names[0], flow, centroid_y, centroid_x,
-                                             current_cluster_img.sum() * self.vars['average_pixel_size'],
-                                             inner_network_area * self.vars['average_pixel_size'], box_count_dim, r_value,
-                                             box_nb, inner_network_box_count_dim, inner_net_r_value, inner_net_box_nb),
-                                            dtype=np.float64)
-                                    else:
-                                        cluster_dynamic[clust_i, :] = np.array((t, cluster_names[0], flow, centroid_y,
-                                                                             centroid_x, current_cluster_img.sum(),
-                                                                             inner_network_area, box_count_dim, r_value,
-                                                                             box_nb, inner_network_box_count_dim,
-                                                                             inner_net_r_value, inner_net_box_nb),
-                                                                            dtype=np.float64)
-
-                                    updated_cluster_names = np.append(updated_cluster_names, cluster_names)
-                                vstack_h5_array(f"oscillating_clusters_temporal_dynamics.h5",
-                                                cluster_dynamic, key=f"arena{self.one_descriptor_per_arena['arena']}")
-
-                                # Reset cluster_id_matrix for the next frame
-                                cluster_id_matrix *= self.binary[t, :, :]
-
-                            period_tracking, self.clusters_final_data = efflux_study.update_flux(t, contours, efflux,
-                                                                                                 period_tracking,
-                                                                                                 self.clusters_final_data)
-                            period_tracking, self.clusters_final_data = influx_study.update_flux(t, contours, influx,
-                                                                                                 period_tracking,
-                                                                                                 self.clusters_final_data)
-                            
-                            mean_cluster_area[t] = np.mean(np.concatenate((in_stats[:, 4], ef_stats[:, 4])))
-                    if self.vars['output_in_mm']:
-                        self.clusters_final_data[:, 1] *= self.time_interval # phase
-                        self.clusters_final_data[:, 2] *= self.vars['average_pixel_size']  # size
-                        self.clusters_final_data[:, 3] *= np.sqrt(self.vars['average_pixel_size'])  # distance
-                        self.one_row_per_frame['mean_cluster_area'] = mean_cluster_area * self.vars['average_pixel_size']
-                    self.one_row_per_frame['cluster_number'] = named_cluster_number
-
-                del oscillations_video
-
-
-    def fractal_descriptions(self):
-        if not pd.isna(self.one_descriptor_per_arena["first_move"]) and self.vars['fractal_analysis']:
-            logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Starting fractal analysis.")
-
-            if self.vars['network_analysis']:
-                box_counting_dimensions = np.zeros((self.dims[0], 7), dtype=np.float64)
-            else:
-                box_counting_dimensions = np.zeros((self.dims[0], 3), dtype=np.float64)
-
-            for t in np.arange(self.dims[0]):
-                if self.vars['network_analysis']:
-                    box_counting_dimensions[t, 0] = self.network_dynamics[t, ...].sum()
-                    zoomed_binary, side_lengths = prepare_box_counting(self.binary[t, ...], side_threshold=self.vars[
-                        'fractal_box_side_threshold'], zoom_step=self.vars['fractal_zoom_step'], contours=True)
-                    box_counting_dimensions[t, 1], box_counting_dimensions[t, 2], box_counting_dimensions[
-                        t, 3] = box_counting_dimension(zoomed_binary, side_lengths)
-                    zoomed_binary, side_lengths = prepare_box_counting(self.network_dynamics[t, ...],
-                                                                       side_threshold=self.vars[
-                                                                           'fractal_box_side_threshold'],
-                                                                       zoom_step=self.vars['fractal_zoom_step'],
-                                                                       contours=False)
-                    box_counting_dimensions[t, 4], box_counting_dimensions[t, 5], box_counting_dimensions[
-                        t, 6] = box_counting_dimension(zoomed_binary, side_lengths)
-                else:
-                    zoomed_binary, side_lengths = prepare_box_counting(self.binary[t, ...],
-                                                                       side_threshold=self.vars['fractal_box_side_threshold'],
-                                                                       zoom_step=self.vars['fractal_zoom_step'], contours=True)
-                    box_counting_dimensions[t, :] = box_counting_dimension(zoomed_binary, side_lengths)
-
-            if self.vars['network_analysis']:
-                self.one_row_per_frame["inner_network_size"] = box_counting_dimensions[:, 0]
-                self.one_row_per_frame["fractal_dimension"] = box_counting_dimensions[:, 1]
-                self.one_row_per_frame["fractal_r_value"] = box_counting_dimensions[:, 2]
-                self.one_row_per_frame["fractal_box_nb"] = box_counting_dimensions[:, 3]
-                self.one_row_per_frame["inner_network_fractal_dimension"] = box_counting_dimensions[:, 4]
-                self.one_row_per_frame["inner_network_fractal_r_value"] = box_counting_dimensions[:, 5]
-                self.one_row_per_frame["inner_network_fractal_box_nb"] = box_counting_dimensions[:, 6]
-                if self.vars['output_in_mm']:
-                    self.one_row_per_frame["inner_network_size"] *= self.vars['average_pixel_size']
-            else:
-                self.one_row_per_frame["fractal_dimension"] = box_counting_dimensions[:, 0]
-                self.one_row_per_frame["fractal_box_nb"] = box_counting_dimensions[:, 1]
-                self.one_row_per_frame["fractal_r_value"] = box_counting_dimensions[:, 2]
-
-            if self.vars['network_analysis'] or self.vars['save_coord_network']:
-                del self.network_dynamics
-
-    def get_descriptors_summary(self):
-        potential_descriptors = ["area", "perimeter", "circularity", "rectangularity", "total_hole_area", "solidity",
-                                 "convexity", "eccentricity", "euler_number", "standard_deviation_y",
-                                 "standard_deviation_x", "skewness_y", "skewness_x", "kurtosis_y", "kurtosis_x",
-                                 "major_axis_len", "minor_axis_len", "axes_orientation"]
-
-        self.one_descriptor_per_arena["final_area"] = self.binary[-1, :, :].sum()
-
-    def save_efficiency_tests(self):
-        # Provide images allowing to assess the analysis efficiency
-        if self.dims[0] > 1:
-            after_one_tenth_of_time = np.ceil(self.dims[0] / 10).astype(np.uint64)
-        else:
-            after_one_tenth_of_time = 0
-
-        last_good_detection = self.dims[0] - 1
-        if self.dims[0] > self.lost_frames:
-            if self.vars['do_threshold_segmentation']:
-                last_good_detection -= self.lost_frames
-        else:
-            last_good_detection = 0
-        if self.visu is None:
-            if len(self.converted_video.shape) == 3:
-                self.converted_video = np.stack((self.converted_video, self.converted_video, self.converted_video),
-                                             axis=3)
-            self.efficiency_test_1 = deepcopy(self.converted_video[after_one_tenth_of_time, ...])
-            self.efficiency_test_2 = deepcopy(self.converted_video[last_good_detection, ...])
-        else:
-            self.efficiency_test_1 = deepcopy(self.visu[after_one_tenth_of_time, :, :, :])
-            self.efficiency_test_2 = deepcopy(self.visu[last_good_detection, :, :, :])
-
-        position = (25, self.dims[1] // 2)
-        text = str(self.one_descriptor_per_arena['arena'])
-        eroded_binary = cv2.erode(self.binary[after_one_tenth_of_time, :, :], cross_33)
-        contours = np.nonzero(self.binary[after_one_tenth_of_time, :, :] - eroded_binary)
-        self.efficiency_test_1[contours[0], contours[1], :] = self.vars['contour_color']
-        self.efficiency_test_1 = cv2.putText(self.efficiency_test_1, text, position, cv2.FONT_HERSHEY_SIMPLEX, 1,
-                                        (self.vars["contour_color"], self.vars["contour_color"],
-                                         self.vars["contour_color"], 255), 3)
-
-        eroded_binary = cv2.erode(self.binary[last_good_detection, :, :], cross_33)
-        contours = np.nonzero(self.binary[last_good_detection, :, :] - eroded_binary)
-        self.efficiency_test_2[contours[0], contours[1], :] = self.vars['contour_color']
-        self.efficiency_test_2 = cv2.putText(self.efficiency_test_2, text, position, cv2.FONT_HERSHEY_SIMPLEX, 1,
-                                         (self.vars["contour_color"], self.vars["contour_color"],
-                                          self.vars["contour_color"], 255), 3)
-
-    def save_video(self):
-
-        if self.vars['save_processed_videos']:
-            self.check_converted_video_type()
-            if len(self.converted_video.shape) == 3:
-                self.converted_video = np.stack((self.converted_video, self.converted_video, self.converted_video),
-                                                axis=3)
-            for t in np.arange(self.dims[0]):
-
-                eroded_binary = cv2.erode(self.binary[t, :, :], cross_33)
-                contours = np.nonzero(self.binary[t, :, :] - eroded_binary)
-                self.converted_video[t, contours[0], contours[1], :] = self.vars['contour_color']
-                if "iso_digi_transi" in self.one_descriptor_per_arena.keys():
-                    if self.vars['iso_digi_analysis']  and not self.vars['several_blob_per_arena'] and not pd.isna(self.one_descriptor_per_arena["iso_digi_transi"]):
-                        if self.one_descriptor_per_arena["is_growth_isotropic"] == 1:
-                            if t < self.one_descriptor_per_arena["iso_digi_transi"]:
-                                self.converted_video[t, contours[0], contours[1], :] = 0, 0, 255
-            del self.binary
-            del self.surfarea
-            del self.borders
-            del self.origin
-            del self.origin_idx
-            del self.mean_intensity_per_frame
-            del self.erodila_disk
-            collect()
-            if self.visu is None:
-                true_frame_width = self.dims[2]
-                if len(self.vars['background_list']) == 0:
-                    self.background = None
-                else:
-                    self.background = self.vars['background_list'][self.one_descriptor_per_arena['arena'] - 1]
-                self.visu = video2numpy(f"ind_{self.one_descriptor_per_arena['arena']}.npy", None, self.background, true_frame_width)
-                if len(self.visu.shape) == 3:
-                    self.visu = np.stack((self.visu, self.visu, self.visu), axis=3)
-            self.converted_video = np.concatenate((self.visu, self.converted_video), axis=2)
-            # self.visu = None
-
-            if np.any(self.one_row_per_frame['time'] > 0):
-                position = (5, self.dims[1] - 5)
-                for t in np.arange(self.dims[0]):
-                    image = self.converted_video[t, ...]
-                    text = str(self.one_row_per_frame['time'][t]) + " min"
-                    image = cv2.putText(image,  # numpy array on which text is written
-                                    text,  # text
-                                    position,  # position at which writing has to start
-                                    cv2.FONT_HERSHEY_SIMPLEX,  # font family
-                                    1,  # font size
-                                    (self.vars["contour_color"], self.vars["contour_color"], self.vars["contour_color"], 255),  #(209, 80, 0, 255),  
-                                    2)  # font stroke
-                    self.converted_video[t, ...] = image
-            vid_name = f"ind_{self.one_descriptor_per_arena['arena']}{self.vars['videos_extension']}"
-            write_video(self.converted_video, vid_name, is_color=True, fps=self.vars['video_fps'])
-            # self.converted_video = None
-
-    def save_results(self):
-        self.save_efficiency_tests()
-        self.save_video()
-        if self.vars['several_blob_per_arena']:
-            try:
-                with open(f"one_row_per_frame_arena{self.one_descriptor_per_arena['arena']}.csv", 'w') as file:
-                    self.one_row_per_frame.to_csv(file, sep=';', index=False, lineterminator='\n')
-            except PermissionError:
-                logging.error(f"Never let one_row_per_frame_arena{self.one_descriptor_per_arena['arena']}.csv open when Cellects runs")
-
-            create_new_csv: bool = False
-            if os.path.isfile("one_row_per_arena.csv"):
-                try:
-                    with open(f"one_row_per_arena.csv", 'r') as file:
-                        stats = pd.read_csv(file, header=0, sep=";")
-                except PermissionError:
-                    logging.error("Never let one_row_per_arena.csv open when Cellects runs")
-
-                if len(self.one_descriptor_per_arena) == len(stats.columns) - 1:
-                    try:
-                        with open(f"one_row_per_arena.csv", 'w') as file:
-                            stats.iloc[(self.one_descriptor_per_arena['arena'] - 1), 1:] = self.one_descriptor_per_arena.values()
-                            # if len(self.vars['analyzed_individuals']) == 1:
-                            #     stats = pd.DataFrame(self.one_descriptor_per_arena, index=[0])
-                            # else:
-                            #     stats = pd.DataFrame.from_dict(self.one_descriptor_per_arena)
-                        # stats.to_csv("stats.csv", sep=';', index=False, lineterminator='\n')
-                            stats.to_csv(file, sep=';', index=False, lineterminator='\n')
-                    except PermissionError:
-                        logging.error("Never let one_row_per_arena.csv open when Cellects runs")
-                else:
-                    create_new_csv = True
-            else:
-                create_new_csv = True
-            if create_new_csv:
-                with open(f"one_row_per_arena.csv", 'w') as file:
-                    stats = pd.DataFrame(np.zeros((len(self.vars['analyzed_individuals']), len(self.one_descriptor_per_arena))),
-                               columns=list(self.one_descriptor_per_arena.keys()))
-                    stats.iloc[(self.one_descriptor_per_arena['arena'] - 1), :] = np.array(list(self.one_descriptor_per_arena.values()), dtype=np.uint32)
-                    stats.to_csv(file, sep=';', index=False, lineterminator='\n')
-        if not self.vars['keep_unaltered_videos'] and os.path.isfile(f"ind_{self.one_descriptor_per_arena['arena']}.npy"):
-            os.remove(f"ind_{self.one_descriptor_per_arena['arena']}.npy")
-
-    def change_results_of_one_arena(self):
-        self.save_video()
-        # I/ Update/Create one_row_per_arena.csv
-        create_new_csv: bool = False
-        if os.path.isfile("one_row_per_arena.csv"):
-            try:
-                with open(f"one_row_per_arena.csv", 'r') as file:
-                    stats = pd.read_csv(file, header=0, sep=";")
-                for stat_name, stat_value in self.one_descriptor_per_arena.items():
-                    if stat_name in stats.columns:
-                        stats.loc[(self.one_descriptor_per_arena['arena'] - 1), stat_name] = np.uint32(self.one_descriptor_per_arena[stat_name])
-                with open(f"one_row_per_arena.csv", 'w') as file:
-                    stats.to_csv(file, sep=';', index=False, lineterminator='\n')
-            except PermissionError:
-                logging.error("Never let one_row_per_arena.csv open when Cellects runs")
-            except Exception as e:
-                logging.error(f"{e}")
-                create_new_csv = True
-            # if len(self.one_descriptor_per_arena) == len(stats.columns):
-            #     try:
-            #         with open(f"one_row_per_arena.csv", 'w') as file:
-            #             stats.iloc[(self.one_descriptor_per_arena['arena'] - 1), :] = self.one_descriptor_per_arena.values()
-            #             # stats.to_csv("stats.csv", sep=';', index=False, lineterminator='\n')
-            #             stats.to_csv(file, sep=';', index=False, lineterminator='\n')
-            #     except PermissionError:
-            #         logging.error("Never let one_row_per_arena.csv open when Cellects runs")
-            # else:
-            #     create_new_csv = True
-        else:
-            create_new_csv = True
-        if create_new_csv:
-            logging.info("Create a new one_row_per_arena.csv file")
-            try:
-                with open(f"one_row_per_arena.csv", 'w') as file:
-                    stats = pd.DataFrame(np.zeros((len(self.vars['analyzed_individuals']), len(self.one_descriptor_per_arena))),
-                               columns=list(self.one_descriptor_per_arena.keys()))
-                    stats.iloc[(self.one_descriptor_per_arena['arena'] - 1), :] = np.array(list(self.one_descriptor_per_arena.values()), dtype=np.uint32)
-                    stats.to_csv(file, sep=';', index=False, lineterminator='\n')
-            except PermissionError:
-                logging.error("Never let one_row_per_arena.csv open when Cellects runs")
-
-        # II/ Update/Create one_row_per_frame.csv
-        create_new_csv = False
-        if os.path.isfile("one_row_per_frame.csv"):
-            try:
-                with open(f"one_row_per_frame.csv", 'r') as file:
-                    descriptors = pd.read_csv(file, header=0, sep=";")
-                for stat_name, stat_value in self.one_row_per_frame.items():
-                    if stat_name in descriptors.columns:
-                        descriptors.loc[((self.one_descriptor_per_arena['arena'] - 1) * self.dims[0]):((self.one_descriptor_per_arena['arena']) * self.dims[0] - 1), stat_name] = self.one_row_per_frame.loc[:, stat_name].values[:]
-                with open(f"one_row_per_frame.csv", 'w') as file:
-                    descriptors.to_csv(file, sep=';', index=False, lineterminator='\n')
-                # with open(f"one_row_per_frame.csv", 'w') as file:
-                #     for descriptor in descriptors.keys():
-                #         descriptors.loc[
-                #         ((self.one_descriptor_per_arena['arena'] - 1) * self.dims[0]):((self.one_descriptor_per_arena['arena']) * self.dims[0]),
-                #         descriptor] = self.one_row_per_frame[descriptor]
-                #     descriptors.to_csv(file, sep=';', index=False, lineterminator='\n')
-
-
-
-                # if len(self.one_row_per_frame.columns) == len(descriptors.columns):
-                #     with open(f"one_row_per_frame.csv", 'w') as file:
-                #         # NEW
-                #         for descriptor in descriptors.keys():
-                #             descriptors.loc[((self.one_descriptor_per_arena['arena'] - 1) * self.dims[0]):((self.one_descriptor_per_arena['arena']) * self.dims[0]), descriptor] = self.one_row_per_frame[descriptor]
-                #         # Old
-                #         # descriptors.iloc[((self.one_descriptor_per_arena['arena'] - 1) * self.dims[0]):((self.one_descriptor_per_arena['arena']) * self.dims[0]), :] = self.one_row_per_frame
-                #         descriptors.to_csv(file, sep=';', index=False, lineterminator='\n')
-                # else:
-                #     create_new_csv = True
-            except PermissionError:
-                logging.error("Never let one_row_per_frame.csv open when Cellects runs")
-            except Exception as e:
-                logging.error(f"{e}")
-                create_new_csv = True
-        else:
-            create_new_csv = True
-        if create_new_csv:
-            logging.info("Create a new one_row_per_frame.csv file")
-            try:
-                with open(f"one_row_per_frame.csv", 'w') as file:
-                    descriptors = pd.DataFrame(np.zeros((len(self.vars['analyzed_individuals']) * self.dims[0], len(self.one_row_per_frame.columns))),
-                               columns=list(self.one_row_per_frame.keys()))
-                    descriptors.iloc[((self.one_descriptor_per_arena['arena'] - 1) * self.dims[0]):((self.one_descriptor_per_arena['arena']) * self.dims[0]), :] = self.one_row_per_frame
-                    descriptors.to_csv(file, sep=';', index=False, lineterminator='\n')
-            except PermissionError:
-                logging.error("Never let one_row_per_frame.csv open when Cellects runs")
-
-        # III/ Update/Create one_row_per_oscillating_cluster.csv
-        if not pd.isna(self.one_descriptor_per_arena["first_move"]) and self.vars['oscilacyto_analysis']:
-            oscil_i = pd.DataFrame(
-                np.c_[np.repeat(self.one_descriptor_per_arena['arena'], self.clusters_final_data.shape[0]), self.clusters_final_data],
-                columns=['arena', 'mean_pixel_period', 'phase', 'cluster_size', 'edge_distance', 'coord_y', 'coord_x'])
-            if os.path.isfile("one_row_per_oscillating_cluster.csv"):
-                try:
-                    with open(f"one_row_per_oscillating_cluster.csv", 'r') as file:
-                        one_row_per_oscillating_cluster = pd.read_csv(file, header=0, sep=";")
-                    with open(f"one_row_per_oscillating_cluster.csv", 'w') as file:
-                        one_row_per_oscillating_cluster_before = one_row_per_oscillating_cluster[one_row_per_oscillating_cluster['arena'] < self.one_descriptor_per_arena['arena']]
-                        one_row_per_oscillating_cluster_after = one_row_per_oscillating_cluster[one_row_per_oscillating_cluster['arena'] > self.one_descriptor_per_arena['arena']]
-                        one_row_per_oscillating_cluster = pd.concat((one_row_per_oscillating_cluster_before, oscil_i, one_row_per_oscillating_cluster_after))
-                        one_row_per_oscillating_cluster.to_csv(file, sep=';', index=False, lineterminator='\n')
-
-                        # one_row_per_oscillating_cluster = one_row_per_oscillating_cluster[one_row_per_oscillating_cluster['arena'] != self.one_descriptor_per_arena['arena']]
-                        # one_row_per_oscillating_cluster = pd.concat((one_row_per_oscillating_cluster, oscil_i))
-                        # one_row_per_oscillating_cluster.to_csv(file, sep=';', index=False, lineterminator='\n')
-                except PermissionError:
-                    logging.error("Never let one_row_per_oscillating_cluster.csv open when Cellects runs")
-            else:
-                try:
-                    with open(f"one_row_per_oscillating_cluster.csv", 'w') as file:
-                        oscil_i.to_csv(file, sep=';', index=False, lineterminator='\n')
-                except PermissionError:
-                    logging.error("Never let one_row_per_oscillating_cluster.csv open when Cellects runs")
-
+#!/usr/bin/env python3
+"""Module for analyzing motion, growth patterns, and structural properties of biological specimens in video data.
+
+This module provides comprehensive tools to analyze videos of biological samples (e.g., cell colonies) by:
+1. Loading and converting RGB videos to grayscale using configurable color space combinations
+2. Performing multi-strategy segmentation (frame-by-frame, intensity thresholding, derivative-based detection)
+3. Applying post-processing steps including error correction algorithms for shape continuity
+4. Computing morphological descriptors over time (area, perimeter, fractal dimension, etc.)
+5. Detecting network structures and oscillatory behavior in dynamic biological systems
+
+Classes
+-------
+MotionAnalysis : Processes video data to analyze specimen motion, growth patterns, and structural properties.
+    Provides methods for loading videos, performing segmentation using multiple algorithms,
+    post-processing results with error correction, extracting morphological descriptors,
+    detecting network structures, analyzing oscillations, and saving processed outputs.
+
+Functions
+---------
+load_images_and_videos : Loads and converts video files to appropriate format for analysis.
+get_converted_video : Converts RGB video to grayscale based on specified color space parameters.
+detection : Performs multi-strategy segmentation of the specimen across all frames.
+update_shape : Updates segmented shape with post-processing steps like noise filtering and hole filling.
+save_results : Saves processed data, efficiency tests, and annotated videos.
+
+Notes
+-----
+The features of this module include:
+- Processes large video datasets with memory optimization strategies including typed arrays (NumPy)
+  and progressive processing techniques.
+- The module supports both single-specimen and multi-specimen analysis through configurable parameters.
+- Segmentation strategies include intensity-based thresholding, gradient detection, and combinations thereof.
+- Post-processing includes morphological operations to refine segmented regions and error correction for specific use cases (e.g., Physarum polycephalum).
+- Biological network detection and graph extraction is available to represent network structures as vertex-edge tables.
+- Biological oscillatory pattern detection
+- Fractal dimension calculation
+"""
+
+import weakref
+from gc import collect
+import numpy as np
+from numba.typed import Dict as TDict
+from psutil import virtual_memory
+from cellects.core.one_image_analysis import OneImageAnalysis
+from cellects.image_analysis.cell_leaving_detection import cell_leaving_detection
+from cellects.image_analysis.oscillations_functions import detect_oscillations_dynamics
+from cellects.image_analysis.image_segmentation import segment_with_lum_value, convert_subtract_and_filter_video
+from cellects.image_analysis.morphological_operations import (find_major_incline, create_ellipse, draw_me_a_sun,
+                                                              inverted_distance_transform, dynamically_expand_to_fill_holes,
+                                                              box_counting_dimension, prepare_box_counting, cc)
+from cellects.image_analysis.network_functions import *
+from cellects.image_analysis.progressively_add_distant_shapes import ProgressivelyAddDistantShapes
+from cellects.image_analysis.shape_descriptors import compute_one_descriptor_per_frame, compute_one_descriptor_per_colony, scale_descriptors, ShapeDescriptors, from_shape_descriptors_class
+from cellects.utils.utilitarian import smallest_memory_array
+from cellects.utils.formulas import detect_first_move
+
+
+class MotionAnalysis:
+
+    def __init__(self, l: list):
+
+        """
+        Analyzes motion in a given arena using video data.
+
+        This class processes video frames to analyze motion within a specified area,
+        detecting shapes, covering durations, and generating descriptors for further
+        analysis.
+
+        Args:
+            l (list): A list containing various parameters and flags necessary for the motion
+                analysis.
+
+        Args:
+            l[0] (int): Arena index.
+            l[1] (str): Arena identifier or name, stored in one_descriptor_per_arena['arena'].
+            l[2] (dict): Variables required for the analysis, stored in vars.
+            l[3] (bool): Flag to detect shape.
+            l[4] (bool): Flag to analyze shape.
+            l[5] (bool): Flag to show segmentation.
+            l[6] (None or list): Videos already in RAM.
+
+        Attributes:
+            vars (dict): Variables required for the analysis.
+            visu (None): Placeholder for visualization data.
+            binary (None): Placeholder for binary segmentation data.
+            origin_idx (None): Placeholder for the index of the first frame.
+            smoothing_flag (bool): Flag to indicate if smoothing should be applied.
+            dims (tuple): Dimensions of the converted video.
+            segmentation (ndarray): Array to store segmentation data.
+            covering_intensity (ndarray): Intensity values for covering analysis.
+            mean_intensity_per_frame (ndarray): Mean intensity per frame.
+            borders (object): Borders of the arena.
+            pixel_ring_depth (int): Depth of the pixel ring for analysis, default is 9.
+            step (int): Step size for processing, default is 10.
+            lost_frames (int): Number of lost frames to account for, default is 10.
+            start (None or int): Starting frame index for the analysis.
+
+        Methods:
+            load_images_and_videos(videos_already_in_ram, arena_idx): Loads images and videos
+                for the specified arena index.
+            update_ring_width(): Updates the width of the pixel ring for analysis.
+            get_origin_shape(): Detects the origin shape in the video frames.
+            get_covering_duration(step): Calculates the covering duration based on a step size.
+            detection(): Performs motion detection within the arena.
+            initialize_post_processing(): Initializes post-processing steps.
+            update_shape(show_seg): Updates the shape based on segmentation and visualization flags.
+            get_descriptors_from_binary(): Extracts descriptors from binary data.
+            detect_growth_transitions(): Detects growth transitions in the data.
+            networks_analysis(show_seg): Detected networks within the arena based on segmentation
+                visualization.
+            study_cytoscillations(show_seg): Studies cytoscillations within the arena with
+                segmentation visualization.
+            fractal_descriptions(): Generates fractal descriptions of the analyzed data.
+            get_descriptors_summary(): Summarizes the descriptors obtained from the analysis.
+            save_results(): Saves the results of the analysis.
+
+        """
+        self.one_descriptor_per_arena = {}
+        self.one_descriptor_per_arena['arena'] = l[1]
+        vars = l[2]
+        detect_shape = l[3]
+        analyse_shape = l[4]
+        show_seg = l[5]
+        videos_already_in_ram = l[6]
+        self.visu = None
+        self.binary = None
+        self.origin_idx = None
+        self.smoothing_flag: bool = False
+        self.drift_mask_coord = None
+        self.coord_network = None
+        logging.info(f"Start the motion analysis of the arena n°{self.one_descriptor_per_arena['arena']}")
+
+        self.vars = vars
+        if not 'contour_color' in self.vars:
+            self.vars['contour_color']: np.uint8 = 0
+        if not 'background_list' in self.vars:
+            self.vars['background_list'] = []
+        self.load_images_and_videos(videos_already_in_ram, l[0])
+
+        self.dims = self.converted_video.shape
+        self.segmented = np.zeros(self.dims, dtype=np.uint8)
+
+        self.covering_intensity = np.zeros(self.dims[1:], dtype=np.float64)
+        self.mean_intensity_per_frame = np.mean(self.converted_video, (1, 2))
+
+        self.borders = image_borders(self.dims[1:], shape=self.vars['arena_shape'])
+        self.pixel_ring_depth = 9
+        self.step: int = 10
+        self.lost_frames = 10
+        self.update_ring_width()
+
+        self.start = None
+        if detect_shape:
+            self.start = None
+            # Here to conditional layers allow to detect if an expansion/exploration occured
+            self.get_origin_shape()
+            # The first, user-defined is the 'first_move_threshold' and the second is the detection of the
+            # substantial image: if any of them is not detected, the program considers there is not exp.
+            if self.dims[0] >= 40:
+                step = self.dims[0] // 20
+            else:
+                step = 1
+            if self.dims[0] == 1 or self.start >= (self.dims[0] - step - 1):
+                self.start = None
+            else:
+                self.get_covering_duration(step)
+                if self.start is not None:
+                    self.detection()
+                    self.initialize_post_processing()
+                    self.t = self.start
+                    while self.t < self.dims[0]:  #200:
+                        self.update_shape(show_seg)
+                #
+            if self.start is None:
+                self.binary = np.repeat(np.expand_dims(self.origin, 0), self.converted_video.shape[0], axis=0)
+
+            if analyse_shape:
+                self.get_descriptors_from_binary()
+                self.detect_growth_transitions()
+                self.networks_analysis(show_seg)
+                self.study_cytoscillations(show_seg)
+                self.fractal_descriptions()
+                if videos_already_in_ram is None:
+                    self.save_results()
+
+    def load_images_and_videos(self, videos_already_in_ram, i: int):
+        """
+
+        Load images and videos from disk or RAM.
+
+        Parameters
+        ----------
+        videos_already_in_ram : numpy.ndarray or None
+            Video data that is already loaded into RAM. If `None`, videos will be
+            loaded from disk.
+        i : int
+            Index used to select the origin and background data.
+
+        Notes
+        -----
+        This method logs information about the arena number and loads necessary data
+        from disk or RAM based on whether videos are already in memory. It sets various
+        attributes like `self.origin`, `self.background`, and `self.converted_video`.
+
+        """
+        logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Load images and videos")
+        self.origin = self.vars['origin_list'][i]  # self.vars['origins_list'][i]
+        true_frame_width = self.origin.shape[1]
+        vid_name = None
+        if self.vars['video_list'] is not None:
+            vid_name = self.vars['video_list'][i]
+        self.background = None
+        if len(self.vars['background_list']) > 0:
+            self.background = self.vars['background_list'][i]
+        self.background2 = None
+        if 'background_list2' in self.vars and len(self.vars['background_list2']) > 0:
+            self.background2 = self.vars['background_list2'][i]
+        vids = read_one_arena(self.one_descriptor_per_arena['arena'], self.vars['already_greyscale'],
+                              self.vars['convert_for_motion'], videos_already_in_ram, true_frame_width, vid_name,
+                              self.background, self.background2)
+        self.visu, self.converted_video, self.converted_video2 = vids
+        if self.converted_video is None:
+            logging.info(
+                f"Arena n°{self.one_descriptor_per_arena['arena']}. Convert the RGB visu video into a greyscale image using the color space combination: {self.vars['convert_for_motion']}")
+            vids = convert_subtract_and_filter_video(self.visu, self.vars['convert_for_motion'],
+                                                     self.background, self.background2,
+                                                     self.vars['lose_accuracy_to_save_memory'],
+                                                     self.vars['filter_spec'])
+            self.converted_video, self.converted_video2 = vids
+
+    def get_origin_shape(self):
+        """
+        Determine the origin shape and initialize variables based on the state of the current analysis.
+
+        This method analyzes the initial frame or frames to determine the origin shape
+        of an object in a video, initializing necessary variables and matrices for
+        further processing.
+
+
+        Attributes Modified:
+            start: (int) Indicates the starting frame index.
+            origin_idx: (np.ndarray) The indices of non-zero values in the origin matrix.
+            covering_intensity: (np.ndarray) Matrix used for pixel fading intensity.
+            substantial_growth: (int) Represents a significant growth measure based on the origin.
+
+        Notes:
+            - The method behavior varies if 'origin_state' is set to "constant" or not.
+            - If the background is lighter, 'covering_intensity' matrix is initialized.
+            - Uses connected components to determine which shape is closest to the center
+              or largest, based on 'appearance_detection_method'.
+        """
+        logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Make sure of origin shape")
+        if self.vars['drift_already_corrected']:
+            self.drift_mask_coord = np.zeros((self.dims[0], 4), dtype=np.uint32)
+            for frame_i in np.arange(self.dims[0]):  # 100):#
+                true_pixels = np.nonzero(self.converted_video[frame_i, ...])
+                self.drift_mask_coord[frame_i, :] = np.min(true_pixels[0]), np.max(true_pixels[0]) + 1, np.min(true_pixels[1]), np.max(true_pixels[1]) + 1
+            if np.all(self.drift_mask_coord[:, 0] == 0) and np.all(self.drift_mask_coord[:, 1] == self.dims[1] - 1) and np.all(
+                    self.drift_mask_coord[:, 2] == 0) and np.all(self.drift_mask_coord[:, 3] == self.dims[2] - 1):
+                logging.error(f"Drift correction has been wrongly detected. Images do not contain zero-valued pixels")
+                self.vars['drift_already_corrected'] = False
+        if self.vars['origin_state'] == "constant":
+            self.start = 1
+            if self.vars['lighter_background']:
+                # Initialize the covering_intensity matrix as a reference for pixel fading
+                self.covering_intensity[self.origin_idx[0], self.origin_idx[1]] = 200
+        else:
+            self.start = 0
+            analysisi = self.frame_by_frame_segmentation(self.start, self.origin)
+            while np.logical_and(np.sum(analysisi.binary_image) < self.vars['first_move_threshold'], self.start < self.dims[0]):
+                self.start += 1
+                analysisi = self.frame_by_frame_segmentation(self.start, self.origin)
+
+            # Use connected components to find which shape is the nearest from the image center.
+            if self.vars['several_blob_per_arena']:
+                self.origin = analysisi.binary_image
+            else:
+                nb_components, output, stats, centroids = cv2.connectedComponentsWithStats(analysisi.binary_image,
+                                                                                           connectivity=8)
+                if self.vars['appearance_detection_method'] == 'most_central':
+                    center = np.array((self.dims[2] // 2, self.dims[1] // 2))
+                    stats = np.zeros(nb_components - 1)
+                    for shape_i in np.arange(1, nb_components):
+                        stats[shape_i - 1] = eudist(center, centroids[shape_i, :])
+                    # The shape having the minimal euclidean distance from the center will be the original shape
+                    self.origin = np.zeros((self.dims[1], self.dims[2]), dtype=np.uint8)
+                    self.origin[output == (np.argmin(stats) + 1)] = 1
+                elif self.vars['appearance_detection_method'] == 'largest':
+                    self.origin = np.zeros((self.dims[1], self.dims[2]), dtype=np.uint8)
+                    self.origin[output == np.argmax(stats[1:, 4])] = 1
+        self.origin_idx = np.nonzero(self.origin)
+        self.substantial_growth = np.min((1.2 * self.origin.sum(), self.origin.sum() + 250))
+
+    def get_covering_duration(self, step: int):
+        """
+        Determine the number of frames necessary for a pixel to get covered.
+
+        This function identifies the time when significant growth or motion occurs
+        in a video and calculates the number of frames needed for a pixel to be
+        completely covered. It also handles noise and ensures that the calculated
+        step value is reasonable.
+
+        Parameters
+        ----------
+        step : int
+            The initial step size for frame analysis.
+
+        Raises
+        ------
+        Exception
+            If an error occurs during the calculation process.
+
+        Notes
+        -----
+        This function may modify several instance attributes including
+        `substantial_time`, `step`, and `start`.
+        """
+        logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Find a frame with a significant growth/motion and determine the number of frames necessary for a pixel to get covered")
+        ## Find the time at which growth reached a substantial growth.
+        self.substantial_time = self.start
+        # To avoid noisy images to have deleterious effects, make sure that area area reaches the threshold thrice.
+        occurrence = 0
+        allowed_window = None
+        if self.vars['drift_already_corrected']:
+            allowed_window = self.drift_mask_coord[:, 0].max(), self.drift_mask_coord[:, 1].min(), self.drift_mask_coord[:, 2].max(), self.drift_mask_coord[:, 3].min()
+        prev_bin_im = self.origin
+        while np.logical_and(occurrence < 3, self.substantial_time < (self.dims[0] - step - 1)):
+            self.substantial_time += step
+            growth_vision = self.frame_by_frame_segmentation(self.substantial_time, prev_bin_im)
+            prev_bin_im = growth_vision.binary_image * self.borders
+            surfarea = np.sum(prev_bin_im)
+            prev_bin_im = np.logical_or(prev_bin_im, self.origin).astype(np.uint8)
+            if surfarea > self.substantial_growth:
+                occurrence += 1
+        # get a rough idea of the area covered during this time
+        if (self.substantial_time - self.start) > 20:
+            if self.vars['lighter_background']:
+                growth = (np.sum(self.converted_video[self.start:(self.start + 10), :, :], 0) / 10) - (np.sum(self.converted_video[(self.substantial_time - 10):self.substantial_time, :, :], 0) / 10)
+            else:
+                growth = (np.sum(self.converted_video[(self.substantial_time - 10):self.substantial_time, :, :], 0) / 10) - (
+                            np.sum(self.converted_video[self.start:(self.start + 10), :, :], 0) / 10)
+        else:
+            if self.vars['lighter_background']:
+                growth = self.converted_video[self.start, ...] - self.converted_video[self.substantial_time, ...]
+            else:
+                growth = self.converted_video[self.substantial_time, ...] - self.converted_video[self.start, ...]
+        intensity_extent = np.ptp(self.converted_video[self.start:self.substantial_time, :, :], axis=0)
+        growth[np.logical_or(growth < 0, intensity_extent < np.median(intensity_extent))] = 0
+        growth = bracket_to_uint8_image_contrast(growth)
+        growth *= self.borders
+        growth_vision = OneImageAnalysis(growth)
+        growth_vision.segmentation(allowed_window=allowed_window)
+        if self.vars['several_blob_per_arena']:
+            _, _, stats, _ = cv2.connectedComponentsWithStats(self.origin)
+            do_erode = np.any(stats[1:, 4] > 50)
+        else:
+            do_erode = self.origin.sum() > 50
+        if do_erode:
+            self.substantial_image = cv2.erode(growth_vision.binary_image, cross_33, iterations=2)
+        else:
+            self.substantial_image = growth_vision.binary_image
+
+        if np.any(self.substantial_image):
+            natural_noise = np.nonzero(intensity_extent == np.min(intensity_extent))
+            natural_noise = self.converted_video[self.start:self.substantial_time, natural_noise[0][0], natural_noise[1][0]]
+            natural_noise = moving_average(natural_noise, 5)
+            natural_noise = np.ptp(natural_noise)
+            subst_idx = np.nonzero(self.substantial_image)
+            cover_lengths = np.zeros(len(subst_idx[0]), dtype=np.uint32)
+            for index in np.arange(len(subst_idx[0])):
+                vector = self.converted_video[self.start:self.substantial_time, subst_idx[0][index], subst_idx[1][index]]
+                left, right = find_major_incline(vector, natural_noise)
+                # If find_major_incline did find a major incline: (otherwise it put 0 to left and 1 to right)
+                if not np.logical_and(left == 0, right == 1):
+                    cover_lengths[index] = len(vector[left:-right])
+            # If this analysis fails put a deterministic step
+            if len(cover_lengths[cover_lengths > 0]) > 0:
+                self.step = (np.round(np.mean(cover_lengths[cover_lengths > 0])).astype(int) // 2) + 1
+                logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Pre-processing detection: the time for a pixel to get covered is set to {self.step}")
+            else:
+                logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Pre-processing detection: could not automatically find the time for a pixel to get covered. Default value is 1 for video length < 40 and 10 otherwise")
+
+            # Make sure to avoid a step overestimation
+            if self.step > self.dims[0] // 20:
+                self.step: int = self.dims[0] // 20
+
+            if self.step == 0:
+                self.step: int = 1
+        # When the first_move_threshold is not stringent enough the program may detect a movement due to noise
+        # In that case, the substantial_image is empty and there is no reason to proceed further
+        else:
+            self.start = None
+
+    def detection(self, compute_all_possibilities: bool=False):
+        """
+
+            Perform frame-by-frame or luminosity-based segmentation on video data to detect cell motion and growth.
+
+            This function processes video frames using either frame-by-frame segmentation or luminosity-based
+            segmentation algorithms to detect cell motion and growth. It handles drift correction, adjusts parameters
+            based on configuration settings, and applies logical operations to combine results from different segmentation
+            methods.
+
+            Parameters
+            ----------
+            compute_all_possibilities : bool, optional
+                Flag to determine if all segmentation possibilities should be computed, by default False
+
+            Returns
+            -------
+            None
+
+            Notes
+            -----
+            This function modifies the instance variables `self.segmented`, `self.converted_video`,
+            and potentially `self.luminosity_segmentation` and `self.gradient_segmentation`.
+            Depending on the configuration settings, it performs various segmentation algorithms and updates
+            the instance variables accordingly.
+
+        """
+        if self.start is None:
+            self.start = 1
+        else:
+            self.start = np.max((self.start, 1))
+        self.lost_frames = np.min((self.step, self.dims[0] // 4))
+        # I/ Image by image segmentation algorithms
+        # If images contain a drift correction (zeros at borders of the image,
+        # Replace these 0 by normal background values before segmenting
+        if self.vars['frame_by_frame_segmentation'] or compute_all_possibilities:
+            logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Detect cell motion and growth using the frame by frame segmentation algorithm")
+            self.segmented = np.zeros(self.dims, dtype=np.uint8)
+            for t in np.arange(self.dims[0]):#20):#
+                analysisi = self.frame_by_frame_segmentation(t, self.segmented[t - 1, ...])
+                self.segmented[t, ...] = analysisi.binary_image
+
+                if self.vars['lose_accuracy_to_save_memory']:
+                    self.converted_video[t, ...] = bracket_to_uint8_image_contrast(analysisi.image)
+                else:
+                    self.converted_video[t, ...] = analysisi.image
+                if self.vars['convert_for_motion']['logical'] != 'None':
+                    if self.vars['lose_accuracy_to_save_memory']:
+                        self.converted_video2[t, ...] = bracket_to_uint8_image_contrast(analysisi.image2)
+                    else:
+                        self.converted_video2[t, ...] = analysisi.image2
+
+        if self.vars['color_number'] == 2:
+            luminosity_segmentation, l_threshold_over_time = self.lum_value_segmentation(self.converted_video, do_threshold_segmentation=self.vars['do_threshold_segmentation'] or compute_all_possibilities)
+            self.converted_video = self.smooth_pixel_slopes(self.converted_video)
+            gradient_segmentation = None
+            if self.vars['do_slope_segmentation'] or compute_all_possibilities:
+                gradient_segmentation = self.lum_slope_segmentation(self.converted_video)
+                if gradient_segmentation is not None:
+                    gradient_segmentation[-self.lost_frames:, ...] = np.repeat(gradient_segmentation[-self.lost_frames, :, :][np.newaxis, :, :], self.lost_frames, axis=0)
+            if self.vars['convert_for_motion']['logical'] != 'None':
+                if self.vars['do_threshold_segmentation'] or compute_all_possibilities:
+                    luminosity_segmentation2, l_threshold_over_time2 = self.lum_value_segmentation(self.converted_video2, do_threshold_segmentation=True)
+                    if luminosity_segmentation is None:
+                        luminosity_segmentation = luminosity_segmentation2
+                    if luminosity_segmentation is not None:
+                        if self.vars['convert_for_motion']['logical'] == 'Or':
+                            luminosity_segmentation = np.logical_or(luminosity_segmentation, luminosity_segmentation2)
+                        elif self.vars['convert_for_motion']['logical'] == 'And':
+                            luminosity_segmentation = np.logical_and(luminosity_segmentation, luminosity_segmentation2)
+                        elif self.vars['convert_for_motion']['logical'] == 'Xor':
+                            luminosity_segmentation = np.logical_xor(luminosity_segmentation, luminosity_segmentation2)
+                self.converted_video2 = self.smooth_pixel_slopes(self.converted_video2)
+                if self.vars['do_slope_segmentation'] or compute_all_possibilities:
+                    gradient_segmentation2 = self.lum_slope_segmentation(self.converted_video2)
+                    if gradient_segmentation2 is not None:
+                        gradient_segmentation2[-self.lost_frames:, ...] = np.repeat(gradient_segmentation2[-self.lost_frames, :, :][np.newaxis, :, :], self.lost_frames, axis=0)
+                    if gradient_segmentation is None:
+                        gradient_segmentation = gradient_segmentation2
+                    if gradient_segmentation is not None:
+                        if self.vars['convert_for_motion']['logical'] == 'Or':
+                            gradient_segmentation = np.logical_or(gradient_segmentation, gradient_segmentation2)
+                        elif self.vars['convert_for_motion']['logical'] == 'And':
+                            gradient_segmentation = np.logical_and(gradient_segmentation, gradient_segmentation2)
+                        elif self.vars['convert_for_motion']['logical'] == 'Xor':
+                            gradient_segmentation = np.logical_xor(gradient_segmentation, gradient_segmentation2)
+
+            if compute_all_possibilities:
+                logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Compute all options to detect cell motion and growth. Maximal growth per frame: {self.vars['maximal_growth_factor']}")
+                if luminosity_segmentation is not None:
+                    self.luminosity_segmentation = np.nonzero(luminosity_segmentation)
+                if gradient_segmentation is not None:
+                    self.gradient_segmentation = np.nonzero(gradient_segmentation)
+                if luminosity_segmentation is not None and gradient_segmentation is not None:
+                    self.logical_and = np.nonzero(np.logical_and(luminosity_segmentation, gradient_segmentation))
+                    self.logical_or = np.nonzero(np.logical_or(luminosity_segmentation, gradient_segmentation))
+            elif not self.vars['frame_by_frame_segmentation']:
+                if self.vars['do_threshold_segmentation'] and not self.vars['do_slope_segmentation']:
+                    logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Detect with luminosity threshold segmentation algorithm")
+                    self.segmented = luminosity_segmentation
+                if self.vars['do_slope_segmentation']:
+                    logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Detect with luminosity slope segmentation algorithm")
+                    self.segmented = gradient_segmentation
+                if np.logical_and(self.vars['do_threshold_segmentation'], self.vars['do_slope_segmentation']):
+                    if self.vars['true_if_use_light_AND_slope_else_OR']:
+                        logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Detection resuts from threshold AND slope segmentation algorithms")
+                        if luminosity_segmentation is not None and gradient_segmentation is not None:
+                            self.segmented = np.logical_and(luminosity_segmentation, gradient_segmentation)
+                    else:
+                        logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Detection resuts from threshold OR slope segmentation algorithms")
+                        if luminosity_segmentation is not None and gradient_segmentation is not None:
+                            self.segmented = np.logical_or(luminosity_segmentation, gradient_segmentation)
+                self.segmented = self.segmented.astype(np.uint8)
+
+
+    def frame_by_frame_segmentation(self, t: int, previous_binary_image: NDArray=None):
+        """
+
+        Frame-by-frame segmentation of a video.
+
+        Parameters
+        ----------
+        t : int
+            The time index of the frame to process.
+        previous_binary_image : NDArray, optional
+            The binary image from the previous frame. Default is `None`.
+
+        Returns
+        -------
+        OneImageAnalysis
+            An object containing the analysis of the current frame.
+        """
+        contrasted_im = bracket_to_uint8_image_contrast(self.converted_video[t, :, :])
+        # 1. Get the mask valid for a number of images around it (step).
+        allowed_window = None
+        if self.vars['drift_already_corrected']:
+            half_step = np.ceil(self.step / 2).astype(int)
+            t_start = t - half_step
+            t_end = t + half_step
+            t_start = np.max((t_start, 0))
+            t_end = np.min((t_end, self.dims[0]))
+            min_y, max_y = np.max(self.drift_mask_coord[t_start:t_end, 0]), np.min(self.drift_mask_coord[t_start:t_end, 1])
+            min_x, max_x = np.max(self.drift_mask_coord[t_start:t_end, 2]), np.min(self.drift_mask_coord[t_start:t_end, 3])
+            allowed_window = min_y, max_y, min_x, max_x
+
+        analysisi = OneImageAnalysis(contrasted_im)
+        if self.vars['convert_for_motion']['logical'] != 'None':
+            contrasted_im2 = bracket_to_uint8_image_contrast(self.converted_video2[t, :, :])
+            analysisi.image2 = contrasted_im2
+
+        if previous_binary_image is None or t == 0:
+            analysisi.previous_binary_image = self.origin
+        else:
+            analysisi.previous_binary_image = previous_binary_image
+
+        analysisi.segmentation(self.vars['convert_for_motion']['logical'], self.vars['color_number'],
+                               bio_label=self.vars["bio_label"], bio_label2=self.vars["bio_label2"],
+                               rolling_window_segmentation=self.vars['rolling_window_segmentation'],
+                               lighter_background=self.vars['lighter_background'],
+                               allowed_window=allowed_window, filter_spec=self.vars['filter_spec']) # filtering already done when creating converted_video
+
+        return analysisi
+
+    def lum_value_segmentation(self, converted_video: NDArray, do_threshold_segmentation: bool) -> Tuple[NDArray, NDArray]:
+        """
+        Perform segmentation based on luminosity values from a video.
+
+        Parameters
+        ----------
+        converted_video : NDArray
+            The input video data in a NumPy array format.
+        do_threshold_segmentation : bool
+            Flag to determine whether threshold segmentation should be applied.
+
+        Returns
+        -------
+        Tuple[NDArray, NDArray]
+            A tuple containing two NumPy arrays:
+            - The first array is the luminosity segmentation of the video.
+            - The second array represents the luminosity threshold over time.
+
+        Notes
+        -----
+        This function operates under the assumption that there is sufficient motion in the video data.
+        If no valid thresholds are found for segmentation, the function returns None for
+        `luminosity_segmentation`.
+        """
+        shape_motion_failed: bool = False
+        if self.vars['lighter_background']:
+            covering_l_values = np.min(converted_video[:self.substantial_time, :, :],
+                                             0) * self.substantial_image
+        else:
+            covering_l_values = np.max(converted_video[:self.substantial_time, :, :],
+                                             0) * self.substantial_image
+        # Avoid errors by checking whether the covering values are nonzero
+        covering_l_values = covering_l_values[covering_l_values != 0]
+        if len(covering_l_values) == 0:
+            shape_motion_failed = True
+
+        luminosity_segmentation = None
+        l_threshold_over_time = None
+        if not shape_motion_failed:
+            value_segmentation_thresholds = np.arange(0.8, -0.7, -0.1)
+            validated_thresholds = np.zeros(value_segmentation_thresholds.shape, dtype=bool)
+            counter = 0
+            while_condition = True
+            max_motion_per_frame = (self.dims[1] * self.dims[2]) * self.vars['maximal_growth_factor'] * 2
+            if self.vars['lighter_background']:
+                basic_bckgrnd_values = np.quantile(converted_video[:(self.lost_frames + 1), ...], 0.9, axis=(1, 2))
+            else:
+                basic_bckgrnd_values = np.quantile(converted_video[:(self.lost_frames + 1), ...], 0.1, axis=(1, 2))
+            # Try different values of do_threshold_segmentation and keep the one that does not
+            # segment more than x percent of the image
+            while counter <= 14:
+                value_threshold = value_segmentation_thresholds[counter]
+                if self.vars['lighter_background']:
+                    l_threshold = (1 + value_threshold) * np.max(covering_l_values)
+                else:
+                    l_threshold = (1 - value_threshold) * np.min(covering_l_values)
+                starting_segmentation, l_threshold_over_time = segment_with_lum_value(converted_video[:(self.lost_frames + 1), ...],
+                                                               basic_bckgrnd_values, l_threshold,
+                                                               self.vars['lighter_background'])
+
+                changing_pixel_number = np.sum(np.absolute(np.diff(starting_segmentation.astype(np.int8), 1, 0)), (1, 2))
+                validation = np.max(np.sum(starting_segmentation, (1, 2))) < max_motion_per_frame and (
+                        np.max(changing_pixel_number) < max_motion_per_frame)
+                validated_thresholds[counter] = validation
+                if np.any(validated_thresholds):
+                    if not validation:
+                        break
+                counter += 1
+            # If any threshold is accepted, use their average to proceed the final thresholding
+            valid_number = validated_thresholds.sum()
+            if valid_number > 0:
+                if valid_number > 2:
+                    index_to_keep = 2
+                else:
+                    index_to_keep = valid_number - 1
+                value_threshold = value_segmentation_thresholds[
+                    np.uint8(np.floor(np.mean(np.nonzero(validated_thresholds)[0][index_to_keep])))]
+            else:
+                value_threshold = 0
+
+            if self.vars['lighter_background']:
+                l_threshold = (1 + value_threshold) * np.max(covering_l_values)
+            else:
+                l_threshold = (1 - value_threshold) * np.min(covering_l_values)
+            if do_threshold_segmentation:
+                if self.vars['lighter_background']:
+                    basic_bckgrnd_values = np.quantile(converted_video, 0.9, axis=(1, 2))
+                else:
+                    basic_bckgrnd_values = np.quantile(converted_video, 0.1, axis=(1, 2))
+                luminosity_segmentation, l_threshold_over_time = segment_with_lum_value(converted_video, basic_bckgrnd_values,
+                                                                 l_threshold, self.vars['lighter_background'])
+            else:
+                luminosity_segmentation, l_threshold_over_time = segment_with_lum_value(converted_video[:(self.lost_frames + 1), ...],
+                                                               basic_bckgrnd_values, l_threshold,
+                                                               self.vars['lighter_background'])
+        return luminosity_segmentation, l_threshold_over_time
+
+    def smooth_pixel_slopes(self, converted_video: NDArray) -> NDArray:
+        """
+        Apply smoothing to pixel slopes in a video by convolving with a moving average kernel.
+
+        Parameters
+        ----------
+        converted_video : NDArray
+            The input video array to be smoothed.
+
+        Returns
+        -------
+        NDArray
+            Smoothed video array with pixel slopes averaged using a moving average kernel.
+
+        Raises
+        ------
+        MemoryError
+            If there is not enough RAM available to perform the smoothing operation.
+
+        Notes
+        -----
+        This function applies a moving average kernel to each pixel across the frames of
+        the input video. The smoothing operation can be repeated based on user-defined settings.
+        The precision of the output array is controlled by a flag that determines whether to
+        save memory at the cost of accuracy.
+
+        Examples
+        --------
+        >>> smoothed = smooth_pixel_slopes(converted_video)
+        >>> print(smoothed.shape)  # Expected output will vary depending on the input video shape
+        """
+        try:
+            if self.vars['lose_accuracy_to_save_memory']:
+                smoothed_video = np.zeros(self.dims, dtype=np.float32)
+                smooth_kernel = np.ones(self.step, dtype=np.float64) / self.step
+                for i in np.arange(converted_video.shape[1]):
+                    for j in np.arange(converted_video.shape[2]):
+                        padded = np.pad(converted_video[:, i, j] / self.mean_intensity_per_frame,
+                                     (self.step // 2, self.step - 1 - self.step // 2), mode='edge')
+                        moving_average = np.convolve(padded, smooth_kernel, mode='valid')
+                        if self.vars['repeat_video_smoothing'] > 1:
+                            for it in np.arange(1, self.vars['repeat_video_smoothing']):
+                                padded = np.pad(moving_average,
+                                             (self.step // 2, self.step - 1 - self.step // 2), mode='edge')
+                                moving_average = np.convolve(padded, smooth_kernel, mode='valid')
+                        smoothed_video[:, i, j] = moving_average.astype(np.float32)
+            else:
+                smoothed_video = np.zeros(self.dims, dtype=np.float64)
+                smooth_kernel = np.ones(self.step) / self.step
+                for i in np.arange(converted_video.shape[1]):
+                    for j in np.arange(converted_video.shape[2]):
+                        padded = np.pad(converted_video[:, i, j] / self.mean_intensity_per_frame,
+                                     (self.step // 2, self.step - 1 - self.step // 2), mode='edge')
+                        moving_average = np.convolve(padded, smooth_kernel, mode='valid')
+                        if self.vars['repeat_video_smoothing'] > 1:
+                            for it in np.arange(1, self.vars['repeat_video_smoothing']):
+                                padded = np.pad(moving_average,
+                                             (self.step // 2, self.step - 1 - self.step // 2), mode='edge')
+                                moving_average = np.convolve(padded, smooth_kernel, mode='valid')
+                        smoothed_video[:, i, j] = moving_average
+            return smoothed_video
+
+        except MemoryError:
+            logging.error("Not enough RAM available to smooth pixel curves. Detection may fail.")
+            smoothed_video = converted_video
+            return smoothed_video
+
+    def lum_slope_segmentation(self, converted_video: NDArray) -> NDArray:
+        """
+        Perform lum slope segmentation on the given video.
+
+        Parameters
+        ----------
+        converted_video : NDArray
+            The input video array for segmentation processing.
+
+        Returns
+        -------
+        NDArray
+            Segmented gradient array of the video. If segmentation fails,
+            returns `None` for the corresponding frames.
+
+        Notes
+        -----
+        This function may consume significant memory and adjusts
+        data types (float32 or float64) based on available RAM.
+
+        Examples
+        --------
+        >>> result = lum_slope_segmentation(converted_video)
+        """
+        shape_motion_failed : bool = False
+        # 2) Contrast increase
+        oridx = np.nonzero(self.origin)
+        notoridx = np.nonzero(1 - self.origin)
+        do_increase_contrast = np.mean(converted_video[0, oridx[0], oridx[1]]) * 10 > np.mean(
+                converted_video[0, notoridx[0], notoridx[1]])
+        necessary_memory = self.dims[0] * self.dims[1] * self.dims[2] * 64 * 2 * 1.16415e-10
+        available_memory = (virtual_memory().available >> 30) - self.vars['min_ram_free']
+        if self.vars['lose_accuracy_to_save_memory']:
+            derive = converted_video.astype(np.float32)
+        else:
+            derive = converted_video.astype(np.float64)
+        if necessary_memory > available_memory:
+            converted_video = None
+
+        if do_increase_contrast:
+            derive = np.square(derive)
+
+        # 3) Get the gradient
+        necessary_memory = derive.size * 64 * 4 * 1.16415e-10
+        available_memory = (virtual_memory().available >> 30) - self.vars['min_ram_free']
+        if necessary_memory > available_memory:
+            for cy in np.arange(self.dims[1]):
+                for cx in np.arange(self.dims[2]):
+                    if self.vars['lose_accuracy_to_save_memory']:
+                        derive[:, cy, cx] = np.gradient(derive[:, cy, cx], self.step).astype(np.float32)
+                    else:
+                        derive[:, cy, cx] = np.gradient(derive[:, cy, cx], self.step)
+        else:
+            if self.vars['lose_accuracy_to_save_memory']:
+                derive = np.gradient(derive, self.step, axis=0).astype(np.float32)
+            else:
+                derive = np.gradient(derive, self.step, axis=0)
+
+        # 4) Segment
+        if self.vars['lighter_background']:
+            covering_slopes = np.min(derive[:self.substantial_time, :, :], 0) * self.substantial_image
+        else:
+            covering_slopes = np.max(derive[:self.substantial_time, :, :], 0) * self.substantial_image
+        covering_slopes = covering_slopes[covering_slopes != 0]
+        if len(covering_slopes) == 0:
+            shape_motion_failed = True
+
+        gradient_segmentation = None
+        if not shape_motion_failed:
+            gradient_segmentation = np.zeros(self.dims, np.uint8)
+            ####
+            # ease_slope_segmentation = 0.8
+            value_segmentation_thresholds = np.arange(0.8, -0.7, -0.1)
+            validated_thresholds = np.zeros(value_segmentation_thresholds.shape, dtype=bool)
+            counter = 0
+            while_condition = True
+            max_motion_per_frame = (self.dims[1] * self.dims[2]) * self.vars['maximal_growth_factor']
+            # Try different values of do_slope_segmentation and keep the one that does not
+            # segment more than x percent of the image
+            while counter < value_segmentation_thresholds.shape[0]:
+                ease_slope_segmentation = value_segmentation_thresholds[counter]
+                if self.vars['lighter_background']:
+                    gradient_threshold = (1 + ease_slope_segmentation) * np.max(covering_slopes)
+                    sample = np.less(derive[:self.substantial_time], gradient_threshold)
+                else:
+                    gradient_threshold = (1 - ease_slope_segmentation) * np.min(covering_slopes)
+                    sample = np.greater(derive[:self.substantial_time], gradient_threshold)
+                changing_pixel_number = np.sum(np.absolute(np.diff(sample.astype(np.int8), 1, 0)), (1, 2))
+                validation = np.max(np.sum(sample, (1, 2))) < max_motion_per_frame and (
+                        np.max(changing_pixel_number) < max_motion_per_frame)
+                validated_thresholds[counter] = validation
+                if np.any(validated_thresholds):
+                    if not validation:
+                        break
+                counter += 1
+                # If any threshold is accepted, use their average to proceed the final thresholding
+            valid_number = validated_thresholds.sum()
+            if valid_number > 0:
+                if valid_number > 2:
+                    index_to_keep = 2
+                else:
+                    index_to_keep = valid_number - 1
+                ease_slope_segmentation = value_segmentation_thresholds[
+                    np.uint8(np.floor(np.mean(np.nonzero(validated_thresholds)[0][index_to_keep])))]
+
+                if self.vars['lighter_background']:
+                    gradient_threshold = (1 - ease_slope_segmentation) * np.max(covering_slopes)
+                    gradient_segmentation[:-self.lost_frames, :, :] = np.less(derive, gradient_threshold)[
+                        self.lost_frames:, :, :]
+                else:
+                    gradient_threshold = (1 - ease_slope_segmentation) * np.min(covering_slopes)
+                    gradient_segmentation[:-self.lost_frames, :, :] = np.greater(derive, gradient_threshold)[
+                        self.lost_frames:, :, :]
+            else:
+                if self.vars['lighter_background']:
+                    gradient_segmentation[:-self.lost_frames, :, :] = (derive < (np.min(derive, (1, 2)) * 1.1)[:, None, None])[self.lost_frames:, :, :]
+                else:
+                    gradient_segmentation[:-self.lost_frames, :, :] = (derive > (np.max(derive, (1, 2)) * 0.1)[:, None, None])[self.lost_frames:, :, :]
+        return gradient_segmentation
+
+    def update_ring_width(self):
+        """
+
+        Update the `pixel_ring_depth` and create an erodila disk.
+
+        This method ensures that the pixel ring depth is odd and at least 3,
+        then creates an erodila disk of that size.
+        """
+        # Make sure that self.pixels_depths are odd and greater than 3
+        if self.pixel_ring_depth <= 3:
+            self.pixel_ring_depth = 3
+        if self.pixel_ring_depth % 2 == 0:
+            self.pixel_ring_depth = self.pixel_ring_depth + 1
+        self.erodila_disk = create_ellipse(self.pixel_ring_depth, self.pixel_ring_depth).astype(np.uint8)
+        self.max_distance = self.pixel_ring_depth * self.vars['detection_range_factor']
+
+    def initialize_post_processing(self):
+        """
+
+        Initialize post-processing for video analysis.
+
+        This function initializes various parameters and prepares the binary
+        representation used in post-processing of video data. It logs information about
+        the settings, handles initial origin states, sets up segmentation data,
+        calculates surface areas, and optionally corrects errors around the initial
+        shape or prevents fast growth near the periphery.
+
+        Notes
+        -----
+        This function performs several initialization steps and logs relevant information,
+        including handling different origin states, updating segmentation data, and
+        calculating the gravity field based on binary representation.
+
+        """
+        ## Initialization
+        logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Starting Post_processing. Fading detection: {self.vars['do_fading']}: {self.vars['fading']}, Subtract background: {self.vars['subtract_background']}, Correct errors around initial shape: {self.vars['correct_errors_around_initial']}, Connect distant shapes: {self.vars['detection_range_factor'] > 0}, How to select appearing cell(s): {self.vars['appearance_detection_method']}")
+        self.binary = np.zeros(self.dims[:3], dtype=np.uint8)
+        if self.origin.shape[0] != self.binary[self.start - 1, :, :].shape[0] or self.origin.shape[1] != self.binary[self.start - 1, :, :].shape[1]:
+            logging.error("Unaltered videos deprecated, they have been created with different settings.\nDelete .npy videos and Data to run Cellects quickly.pkl and re-run")
+
+        if self.vars['origin_state'] == "invisible":
+            self.binary[self.start - 1, :, :] = deepcopy(self.origin)
+            self.covering_intensity[self.origin_idx[0], self.origin_idx[1]] = self.converted_video[self.start, self.origin_idx[0], self.origin_idx[1]]
+        else:
+            if self.vars['origin_state'] == "fluctuating":
+                self.covering_intensity[self.origin_idx[0], self.origin_idx[1]] = np.median(self.converted_video[:self.start, self.origin_idx[0], self.origin_idx[1]], axis=0)
+
+            self.binary[:self.start, :, :] = np.repeat(np.expand_dims(self.origin, 0), self.start, axis=0)
+            if self.start < self.step:
+                frames_to_assess = self.step
+                self.segmented[self.start - 1, ...] = self.binary[self.start - 1, :, :]
+                for t in np.arange(self.start, self.lost_frames):
+                    # Only keep pixels that are always detected
+                    always_found = np.sum(self.segmented[t:(t + frames_to_assess), ...], 0)
+                    always_found = always_found == frames_to_assess
+                    # Remove too small shapes
+                    without_small, stats, centro = cc(always_found.astype(np.uint8))
+                    large_enough = np.nonzero(stats[1:, 4] > ((self.vars['first_move_threshold'] + 1) // 2))[0]
+                    if len(large_enough) > 0:
+                        always_found *= np.isin(always_found, large_enough + 1)
+                        always_found = np.logical_or(always_found, self.segmented[t - 1, ...])
+                        self.segmented[t, ...] *= always_found
+                    else:
+                        self.segmented[t, ...] = 0
+                    self.segmented[t, ...] = np.logical_or(self.segmented[t - 1, ...], self.segmented[t, ...])
+        self.mean_distance_per_frame = None
+        self.surfarea = np.zeros(self.dims[0], dtype =np.uint64)
+        self.surfarea[:self.start] = np.sum(self.binary[:self.start, :, :], (1, 2))
+        self.gravity_field = inverted_distance_transform(self.binary[(self.start - 1), :, :],
+                                           np.sqrt(np.sum(self.binary[(self.start - 1), :, :])))
+        if self.vars['correct_errors_around_initial']:
+            self.rays, self.sun = draw_me_a_sun(self.binary[(self.start - 1), :, :], ray_length_coef=1)  # plt.imshow(sun)
+            self.holes = np.zeros(self.dims[1:], dtype=np.uint8)
+            self.pixel_ring_depth += 2
+            self.update_ring_width()
+
+        if self.vars['prevent_fast_growth_near_periphery']:
+            self.near_periphery = np.zeros(self.dims[1:])
+            if self.vars['arena_shape'] == 'circle':
+                periphery_width = self.vars['periphery_width'] * 2
+                elliperiphery = create_ellipse(self.dims[1] - periphery_width, self.dims[2] - periphery_width)
+                half_width = periphery_width // 2
+                if periphery_width % 2 == 0:
+                    self.near_periphery[half_width:-half_width, half_width:-half_width] = elliperiphery
+                else:
+                    self.near_periphery[half_width:-half_width - 1, half_width:-half_width - 1] = elliperiphery
+                self.near_periphery = 1 - self.near_periphery
+            else:
+                self.near_periphery[:self.vars['periphery_width'], :] = 1
+                self.near_periphery[-self.vars['periphery_width']:, :] = 1
+                self.near_periphery[:, :self.vars['periphery_width']] = 1
+                self.near_periphery[:, -self.vars['periphery_width']:] = 1
+            self.near_periphery = np.nonzero(self.near_periphery)
+
+    def update_shape(self, show_seg: bool):
+        """
+        Update the shape of detected objects in the current frame by analyzing
+        segmentation potentials and applying morphological operations.
+
+        Parameters
+        ----------
+        show_seg : bool
+            Flag indicating whether to display segmentation results.
+
+        Notes
+        -----
+        This function performs several operations to update the shape of detected objects:
+        - Analyzes segmentation potentials from previous frames.
+        - Applies morphological operations to refine the shape.
+        - Updates internal state variables such as `binary` and `covering_intensity`.
+
+        """
+        # Get from gradients, a 2D matrix of potentially covered pixels
+        # I/ dilate the shape made with covered pixels to assess for covering
+
+        # I/ 1) Only keep pixels that have been detected at least two times in the three previous frames
+        if self.dims[0] < 100:
+            new_potentials = self.segmented[self.t, :, :]
+        else:
+            if self.t > 1:
+                new_potentials = np.sum(self.segmented[(self.t - 2): (self.t + 1), :, :], 0, dtype=np.uint8)
+            else:
+                new_potentials = np.sum(self.segmented[: (self.t + 1), :, :], 0, dtype=np.uint8)
+            new_potentials[new_potentials == 1] = 0
+            new_potentials[new_potentials > 1] = 1
+
+        # I/ 2) If an image displays more new potential pixels than 50% of image pixels,
+        # one of these images is considered noisy and we try taking only one.
+        frame_counter = -1
+        maximal_size = 0.5 * new_potentials.size
+        if (self.vars["do_threshold_segmentation"] or self.vars["frame_by_frame_segmentation"]) and self.t > np.max((self.start + self.step, 6)):
+           maximal_size = np.min((np.max(self.binary[:self.t].sum((1, 2))) * (1 + self.vars['maximal_growth_factor']), self.borders.sum()))
+        while np.logical_and(np.sum(new_potentials) > maximal_size,
+                             frame_counter <= 5):  # np.logical_and(np.sum(new_potentials > 0) > 5 * np.sum(dila_ring), frame_counter <= 5):
+            frame_counter += 1
+            if frame_counter > self.t:
+                break
+            else:
+                if frame_counter < 5:
+                    new_potentials = self.segmented[self.t - frame_counter, :, :]
+                else:
+                # If taking only one image is not enough, use the inverse of the fadinged matrix as new_potentials
+                # Given it haven't been processed by any slope calculation, it should be less noisy
+                    new_potentials = np.sum(self.segmented[(self.t - 5): (self.t + 1), :, :], 0, dtype=np.uint8)
+                    new_potentials[new_potentials < 6] = 0
+                    new_potentials[new_potentials == 6] = 1
+
+
+        new_shape = deepcopy(self.binary[self.t - 1, :, :])
+        new_potentials = cv2.morphologyEx(new_potentials, cv2.MORPH_CLOSE, cross_33)
+        new_potentials = cv2.morphologyEx(new_potentials, cv2.MORPH_OPEN, cross_33) * self.borders
+        new_shape = np.logical_or(new_shape, new_potentials).astype(np.uint8)
+        # Add distant shapes within a radius, score every added pixels according to their distance
+        if not self.vars['several_blob_per_arena']:
+            if new_shape.sum() == 0:
+                new_shape = deepcopy(new_potentials)
+            else:
+                pads = ProgressivelyAddDistantShapes(new_potentials, new_shape, self.max_distance)
+                r = weakref.ref(pads)
+                # If max_distance is non nul look for distant shapes
+                pads.consider_shapes_sizes(self.vars['min_size_for_connection'],
+                                                     self.vars['max_size_for_connection'])
+                pads.connect_shapes(only_keep_connected_shapes=True, rank_connecting_pixels=True)
+
+                new_shape = deepcopy(pads.expanded_shape)
+                new_shape[new_shape > 1] = 1
+                if np.logical_and(self.t > self.step, self.t < self.dims[0]):
+                    if np.any(pads.expanded_shape > 5):
+                        # Add distant shapes back in time at the covering speed of neighbors
+                        self.binary[self.t][np.nonzero(new_shape)] = 1
+                        self.binary[(self.step):(self.t + 1), :, :] = \
+                            pads.modify_past_analysis(self.binary[(self.step):(self.t + 1), :, :],
+                                                      self.segmented[(self.step):(self.t + 1), :, :])
+                        new_shape = deepcopy(self.binary[self.t, :, :])
+                pads = None
+
+            # Fill holes
+            new_shape = cv2.morphologyEx(new_shape, cv2.MORPH_CLOSE, cross_33)
+
+        if self.vars['do_fading'] and (self.t > self.step + self.lost_frames):
+            # Shape Erosion
+            # I/ After a substantial growth, erode the shape made with covered pixels to assess for fading
+            # Use the newly covered pixels to calculate their mean covering intensity
+            new_idx = np.nonzero(np.logical_xor(new_shape, self.binary[self.t - 1, :, :]))
+            start_intensity_monitoring = self.t - self.lost_frames - self.step
+            end_intensity_monitoring = self.t - self.lost_frames
+            self.covering_intensity[new_idx[0], new_idx[1]] = np.median(self.converted_video[start_intensity_monitoring:end_intensity_monitoring, new_idx[0], new_idx[1]], axis=0)
+            previous_binary = self.binary[self.t - 1, :, :]
+            greyscale_image = self.converted_video[self.t - self.lost_frames, :, :]
+            protect_from_fading = None
+            if self.vars['origin_state'] == 'constant':
+                protect_from_fading = self.origin
+            new_shape, self.covering_intensity = cell_leaving_detection(new_shape, self.covering_intensity, previous_binary, greyscale_image, self.vars['fading'], self.vars['lighter_background'], self.vars['several_blob_per_arena'], self.erodila_disk, protect_from_fading)
+
+        self.covering_intensity *= new_shape
+        self.binary[self.t, :, :] = new_shape * self.borders
+        self.surfarea[self.t] = np.sum(self.binary[self.t, :, :])
+
+        # Calculate the mean distance covered per frame and correct for a ring of not really fading pixels
+        if self.mean_distance_per_frame is None:
+            if self.vars['correct_errors_around_initial'] and not self.vars['several_blob_per_arena']:
+                if np.logical_and((self.t % 20) == 0,
+                                  np.logical_and(self.surfarea[self.t] > self.substantial_growth,
+                                                 self.surfarea[self.t] < self.substantial_growth * 2)):
+                    shape = self.binary[self.t, :, :] * self.sun
+                    back = (1 - self.binary[self.t, :, :]) * self.sun
+                    for ray in self.rays:
+                        # For each sun's ray, see how they cross the shape/back and
+                        # store the gravity_field value of these pixels (distance to the original shape).
+                        ray_through_shape = (shape == ray) * self.gravity_field
+                        ray_through_back = (back == ray) * self.gravity_field
+                        if np.any(ray_through_shape):
+                            if np.any(ray_through_back):
+                                # If at least one back pixel is nearer to the original shape than a shape pixel,
+                                # there is a hole to fill.
+                                if np.any(ray_through_back > np.min(ray_through_shape[ray_through_shape > 0])):
+                                    # Check if the nearest pixels are shape, if so, supress them until the nearest pixel
+                                    # becomes back
+                                    while np.max(ray_through_back) <= np.max(ray_through_shape):
+                                        ray_through_shape[ray_through_shape == np.max(ray_through_shape)] = 0
+                                    # Now, all back pixels that are nearer than the closest shape pixel should get filled
+                                    # To do so, replace back pixels further than the nearest shape pixel by 0
+                                    ray_through_back[ray_through_back < np.max(ray_through_shape)] = 0
+                                    self.holes[np.nonzero(ray_through_back)] = 1
+                            else:
+                                self.rays = np.concatenate((self.rays[:(ray - 2)], self.rays[(ray - 1):]))
+                        ray_through_shape = None
+                        ray_through_back = None
+            if np.any(self.surfarea[:self.t] > self.substantial_growth * 2):
+
+                if self.vars['correct_errors_around_initial'] and not self.vars['several_blob_per_arena']:
+                    # Apply the hole correction
+                    self.holes = cv2.morphologyEx(self.holes, cv2.MORPH_CLOSE, cross_33, iterations=10)
+                    # If some holes are not covered by now
+                    if np.any(self.holes * (1 - self.binary[self.t, :, :])):
+                        self.binary[:(self.t + 1), :, :], holes_time_end, distance_against_time = \
+                            dynamically_expand_to_fill_holes(self.binary[:(self.t + 1), :, :], self.holes)
+                        if holes_time_end is not None:
+                            self.binary[holes_time_end:(self.t + 1), :, :] += self.binary[holes_time_end, :, :]
+                            self.binary[holes_time_end:(self.t + 1), :, :][
+                                self.binary[holes_time_end:(self.t + 1), :, :] > 1] = 1
+                            self.surfarea[:(self.t + 1)] = np.sum(self.binary[:(self.t + 1), :, :], (1, 2))
+
+                    else:
+                        distance_against_time = [1, 2]
+                else:
+                    distance_against_time = [1, 2]
+                distance_against_time = np.diff(distance_against_time)
+                if len(distance_against_time) > 0:
+                    self.mean_distance_per_frame = np.mean(- distance_against_time)
+                else:
+                    self.mean_distance_per_frame = 1
+
+        if self.vars['prevent_fast_growth_near_periphery']:
+            # growth_near_periphery = np.diff(self.binary[self.t-1:self.t+1, :, :] * self.near_periphery, axis=0)
+            growth_near_periphery = np.diff(self.binary[self.t-1:self.t+1, self.near_periphery[0], self.near_periphery[1]], axis=0)
+            if (growth_near_periphery == 1).sum() > self.vars['max_periphery_growth']:
+                # self.binary[self.t, self.near_periphery[0], self.near_periphery[1]] = self.binary[self.t - 1, self.near_periphery[0], self.near_periphery[1]]
+                periphery_to_remove = np.zeros(self.dims[1:], dtype=np.uint8)
+                periphery_to_remove[self.near_periphery[0], self.near_periphery[1]] = self.binary[self.t, self.near_periphery[0], self.near_periphery[1]]
+                shapes, stats, centers = cc(periphery_to_remove)
+                periphery_to_remove = np.nonzero(np.isin(shapes, np.nonzero(stats[:, 4] > self.vars['max_periphery_growth'])[0][1:]))
+                self.binary[self.t, periphery_to_remove[0], periphery_to_remove[1]] = self.binary[self.t - 1, periphery_to_remove[0], periphery_to_remove[1]]
+                if not self.vars['several_blob_per_arena']:
+                    shapes, stats, centers = cc(self.binary[self.t, ...])
+                    shapes[shapes != 1] = 0
+                    self.binary[self.t, ...] = shapes
+
+        # Display
+        if show_seg:
+            if self.visu is not None:
+                im_to_display = deepcopy(self.visu[self.t, ...])
+                contours = np.nonzero(cv2.morphologyEx(self.binary[self.t, :, :], cv2.MORPH_GRADIENT, cross_33))
+                if self.vars['lighter_background']:
+                    im_to_display[contours[0], contours[1]] = 0
+                else:
+                    im_to_display[contours[0], contours[1]] = 255
+            else:
+                im_to_display = self.binary[self.t, :, :] * 255
+            imtoshow = cv2.resize(im_to_display, (540, 540))
+            cv2.imshow("shape_motion", imtoshow)
+            cv2.waitKey(1)
+        self.t += 1
+
+    def get_descriptors_from_binary(self, release_memory: bool=True):
+        """
+
+        Methods: get_descriptors_from_binary
+
+        Summary
+        -------
+        Generates shape descriptors for binary images, computes these descriptors for each frame and handles colony
+        tracking. This method can optionally release memory to reduce usage, apply scaling factors to descriptors
+        in millimeters and computes solidity separately if requested.
+
+        Parameters
+        ----------
+        release_memory : bool, optional
+            Flag to determine whether memory should be released after computation. Default is True.
+
+        Other Parameters
+        ----------------
+        **self.one_row_per_frame**
+            DataFrame to store one row of descriptors per frame.
+            - **'arena'**: Arena identifier, repeated for each frame.
+            - **'time'**: Array of time values corresponding to frames.
+
+        **self.binary**
+            3D array representing binary images over time.
+            - **t,x,y**: Time index, x-coordinate, and y-coordinate.
+
+        **self.dims**
+            Tuple containing image dimensions.
+            - **0**: Number of time frames.
+            - **1,2**: Image width and height respectively.
+
+        **self.surfarea**
+            Array containing surface areas for each frame.
+
+        **self.time_interval**
+            Time interval between frames, calculated only if provided timings are non-zero.
+
+        Notes
+        -----
+        This method uses various helper methods and classes like `ShapeDescriptors` for computing shape descriptors,
+        `PercentAndTimeTracker` for progress tracking, and other image processing techniques such as connected components analysis.
+
+        """
+        ##
+        if release_memory:
+            self.substantial_image = None
+            self.covering_intensity = None
+            self.segmented = None
+            self.gravity_field = None
+            self.sun = None
+            self.rays = None
+            self.holes = None
+            collect()
+        self.surfarea = self.binary.sum((1, 2))
+        timings = self.vars['exif']
+        if len(timings) < self.dims[0]:
+            timings = np.arange(self.dims[0])
+        if np.any(timings > 0):
+            self.time_interval = np.mean(np.diff(timings))
+        else:
+            self.time_interval = 1.
+        timings = timings[:self.dims[0]]
+
+        # Detect first motion
+        self.one_descriptor_per_arena['first_move'] = detect_first_move(self.surfarea, self.vars['first_move_threshold'])
+
+        self.compute_solidity_separately: bool = self.vars['iso_digi_analysis'] and not self.vars['several_blob_per_arena'] and not self.vars['descriptors']['solidity']
+        if self.compute_solidity_separately:
+            self.solidity = np.zeros(self.dims[0], dtype=np.float64)
+        if not self.vars['several_blob_per_arena']:
+            # solidity must be added if detect growth transition is computed
+            if self.compute_solidity_separately:
+                for t in np.arange(self.dims[0]):
+                    solidity = ShapeDescriptors(self.binary[t, :, :], ["solidity"])
+                    self.solidity[t] = solidity.descriptors["solidity"]
+            self.one_row_per_frame = compute_one_descriptor_per_frame(self.binary,
+                                                                      self.one_descriptor_per_arena['arena'], timings,
+                                                                      self.vars['descriptors'],
+                                                                      self.vars['output_in_mm'],
+                                                                      self.vars['average_pixel_size'],
+                                                                      self.vars['do_fading'],
+                                                                       self.vars['save_coord_specimen'])
+        else:
+            self.one_row_per_frame = compute_one_descriptor_per_colony(self.binary,
+                                                                       self.one_descriptor_per_arena['arena'], timings,
+                                                                       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'])
+        self.one_descriptor_per_arena["final_area"] = self.binary[-1, :, :].sum()
+        if self.vars['output_in_mm']:
+            self.one_descriptor_per_arena = scale_descriptors(self.one_descriptor_per_arena, self.vars['average_pixel_size'])
+
+    def detect_growth_transitions(self):
+        """
+        Detect growth transitions in a biological image processing context.
+
+        Analyzes the growth transitions of a shape within an arena, determining
+        whether growth is isotropic and identifying any breaking points.
+
+        Notes:
+            This method modifies the `one_descriptor_per_arena` dictionary in place
+            to include growth transition information.
+
+        """
+        if self.vars['iso_digi_analysis'] and not self.vars['several_blob_per_arena']:
+            self.one_descriptor_per_arena['iso_digi_transi'] = pd.NA
+            if not pd.isna(self.one_descriptor_per_arena['first_move']):
+                logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Starting growth transition analysis.")
+
+                # II) Once a pseudopod is deployed, look for a disk/ around the original shape
+                growth_begining = self.surfarea < ((self.surfarea[0] * 1.2) + ((self.dims[1] / 4) * (self.dims[2] / 4)))
+                dilated_origin = cv2.dilate(self.binary[self.one_descriptor_per_arena['first_move'], :, :], kernel=cross_33, iterations=10, borderType=cv2.BORDER_CONSTANT, borderValue=0)
+                isisotropic = np.sum(self.binary[:, :, :] * dilated_origin, (1, 2))
+                isisotropic *= growth_begining
+                # Ask if the dilated origin area is 90% covered during the growth beginning
+                isisotropic = isisotropic > 0.9 * dilated_origin.sum()
+                if np.any(isisotropic):
+                    self.one_descriptor_per_arena['is_growth_isotropic'] = 1
+                    # Determine a solidity reference to look for a potential breaking of the isotropic growth
+                    if self.compute_solidity_separately:
+                        solidity_reference = np.mean(self.solidity[:self.one_descriptor_per_arena['first_move']])
+                        different_solidity = self.solidity < (0.9 * solidity_reference)
+                        del self.solidity
+                    else:
+                        solidity_reference = np.mean(
+                            self.one_row_per_frame.iloc[:(self.one_descriptor_per_arena['first_move']), :]["solidity"])
+                        different_solidity = self.one_row_per_frame["solidity"].values < (0.9 * solidity_reference)
+                    # Make sure that isotropic breaking not occur before isotropic growth
+                    if np.any(different_solidity):
+                        self.one_descriptor_per_arena["iso_digi_transi"] = np.nonzero(different_solidity)[0][0] * self.time_interval
+                else:
+                    self.one_descriptor_per_arena['is_growth_isotropic'] = 0
+            else:
+                self.one_descriptor_per_arena['is_growth_isotropic'] = pd.NA
+                
+
+    def check_converted_video_type(self):
+        """
+        Check if the converted video type is uint8 and normalize it if necessary.
+        """
+        if self.converted_video.dtype != "uint8":
+            self.converted_video = bracket_to_uint8_image_contrast(self.converted_video)
+
+    def networks_analysis(self, show_seg: bool=False):
+        """
+        Perform network detection within a given arena.
+
+        This function carries out the task of detecting networks in an arena
+        based on several parameters and variables. It involves checking video
+        type, performing network detection over time, potentially detecting
+        pseudopods, and smoothing segmentation. The results can be visualized or saved.
+Extract and analyze graphs from a binary representation of network dynamics, producing vertex
+        and edge tables that represent the graph structure over time.
+
+        Args:
+            None
+
+        Attributes:
+            vars (dict): Dictionary of variables that control the graph extraction process.
+                - 'save_graph': Boolean indicating if graph extraction should be performed.
+                - 'save_coord_network': Boolean indicating if the coordinate network should be saved.
+
+            one_descriptor_per_arena (dict): Dictionary containing descriptors for each arena.
+
+            dims (tuple): Tuple containing dimension information.
+                - [0]: Integer representing the number of time steps.
+                - [1]: Integer representing the y-dimension size.
+                - [2]: Integer representing the x-dimension size.
+
+            origin (np.ndarray): Binary image representing the origin of the network.
+
+            binary (np.ndarray): Binary representation of network dynamics over time.
+                Shape: (time_steps, y_dimension, x_dimension).
+
+            converted_video (np.ndarray): Converted video data.
+                Shape: (y_dimension, x_dimension, time_steps).
+
+            network_dynamics (np.ndarray): Network dynamics representation.
+                Shape: (time_steps, y_dimension, x_dimension).
+
+        Notes:
+            - This method performs graph extraction and saves the vertex and edge tables to CSV files.
+            - The CSV files are named according to the arena, time steps, and dimensions.
+
+        Args:
+            show_seg: bool = False
+                A flag that determines whether to display the segmentation visually.
+        """
+        coord_pseudopods = None
+        if not self.vars['several_blob_per_arena'] and self.vars['save_coord_network']:
+            self.check_converted_video_type()
+
+            if self.vars['origin_state'] == "constant":
+                self.coord_network, coord_pseudopods = detect_network_dynamics(self.converted_video, self.binary,
+                                                           self.one_descriptor_per_arena['arena'], 0,
+                                                           self.visu, self.origin, True, True,
+                                                           self.vars['save_coord_network'], show_seg)
+            else:
+                self.coord_network, coord_pseudopods = detect_network_dynamics(self.converted_video, self.binary,
+                                                           self.one_descriptor_per_arena['arena'], 0,
+                                                           self.visu, None, True, True,
+                                                           self.vars['save_coord_network'], show_seg)
+
+        if not self.vars['several_blob_per_arena'] and self.vars['save_graph']:
+            if self.coord_network is None:
+                self.coord_network = np.array(np.nonzero(self.binary))
+            if self.vars['origin_state'] == "constant":
+                extract_graph_dynamics(self.converted_video, self.coord_network, self.one_descriptor_per_arena['arena'],
+                                       0, self.origin, coord_pseudopods)
+            else:
+                extract_graph_dynamics(self.converted_video, self.coord_network, self.one_descriptor_per_arena['arena'],
+                                       0, None, coord_pseudopods)
+
+    def study_cytoscillations(self, show_seg: bool=False):
+        """
+
+            Study the cytoskeletal oscillations within a video frame by frame.
+
+            This method performs an analysis of cytoskeletal oscillations in the video,
+            identifying regions of influx and efflux based on pixel connectivity.
+            It also handles memory allocation for the oscillations video, computes
+            connected components, and optionally displays the segmented regions.
+
+            Args:
+                show_seg (bool): If True, display the segmentation results.
+        """
+        if self.vars['save_coord_thickening_slimming'] or self.vars['oscilacyto_analysis']:
+            oscillations_video = detect_oscillations_dynamics(self.converted_video, self.binary,
+                                                              self.one_descriptor_per_arena['arena'], self.start,
+                                                              self.vars['expected_oscillation_period'],
+                                                              self.time_interval,
+                                                              self.vars['minimal_oscillating_cluster_size'],
+                                                              self.vars['min_ram_free'],
+                                                              self.vars['lose_accuracy_to_save_memory'],
+                                                              self.vars['save_coord_thickening_slimming'])
+            del oscillations_video
+
+
+    def fractal_descriptions(self):
+        """
+
+        Method for analyzing fractal patterns in binary data.
+
+        Fractal analysis is performed on the binary representation of the data,
+        optionally considering network dynamics if specified. The results
+        include fractal dimensions, R-values, and box counts for the data.
+
+        If network analysis is enabled, additional fractal dimensions,
+        R-values, and box counts are calculated for the inner network.
+        If 'output_in_mm' is True, then values in mm can be obtained.
+
+        """
+        if self.vars['fractal_analysis']:
+            logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Starting fractal analysis.")
+
+            if self.vars['save_coord_network']:
+                box_counting_dimensions = np.zeros((self.dims[0], 7), dtype=np.float64)
+            else:
+                box_counting_dimensions = np.zeros((self.dims[0], 3), dtype=np.float64)
+
+            for t in np.arange(self.dims[0]):
+                if self.vars['save_coord_network']:
+                    current_network = np.zeros(self.dims[1:], dtype=np.uint8)
+                    net_t = self.coord_network[1:, self.coord_network[0, :] == t]
+                    current_network[net_t[0], net_t[1]] = 1
+                    box_counting_dimensions[t, 0] = current_network.sum()
+                    zoomed_binary, side_lengths = prepare_box_counting(self.binary[t, ...], min_mesh_side=self.vars[
+                        'fractal_box_side_threshold'], zoom_step=self.vars['fractal_zoom_step'], contours=True)
+                    box_counting_dimensions[t, 1], box_counting_dimensions[t, 2], box_counting_dimensions[
+                        t, 3] = box_counting_dimension(zoomed_binary, side_lengths)
+                    zoomed_binary, side_lengths = prepare_box_counting(current_network,
+                                                                       min_mesh_side=self.vars[
+                                                                           'fractal_box_side_threshold'],
+                                                                       zoom_step=self.vars['fractal_zoom_step'],
+                                                                       contours=False)
+                    box_counting_dimensions[t, 4], box_counting_dimensions[t, 5], box_counting_dimensions[
+                        t, 6] = box_counting_dimension(zoomed_binary, side_lengths)
+                else:
+                    zoomed_binary, side_lengths = prepare_box_counting(self.binary[t, ...],
+                                                                       min_mesh_side=self.vars['fractal_box_side_threshold'],
+                                                                       zoom_step=self.vars['fractal_zoom_step'], contours=True)
+                    box_counting_dimensions[t, :] = box_counting_dimension(zoomed_binary, side_lengths)
+
+            if self.vars['save_coord_network']:
+                self.one_row_per_frame["inner_network_size"] = box_counting_dimensions[:, 0]
+                self.one_row_per_frame["fractal_dimension"] = box_counting_dimensions[:, 1]
+                self.one_row_per_frame["fractal_r_value"] = box_counting_dimensions[:, 2]
+                self.one_row_per_frame["fractal_box_nb"] = box_counting_dimensions[:, 3]
+                self.one_row_per_frame["inner_network_fractal_dimension"] = box_counting_dimensions[:, 4]
+                self.one_row_per_frame["inner_network_fractal_r_value"] = box_counting_dimensions[:, 5]
+                self.one_row_per_frame["inner_network_fractal_box_nb"] = box_counting_dimensions[:, 6]
+                if self.vars['output_in_mm']:
+                    self.one_row_per_frame["inner_network_size"] *= self.vars['average_pixel_size']
+            else:
+                self.one_row_per_frame["fractal_dimension"] = box_counting_dimensions[:, 0]
+                self.one_row_per_frame["fractal_box_nb"] = box_counting_dimensions[:, 1]
+                self.one_row_per_frame["fractal_r_value"] = box_counting_dimensions[:, 2]
+
+            if self.vars['save_coord_network']:
+                del self.coord_network
+
+    def save_efficiency_tests(self):
+        """
+        Provide images allowing to assess the analysis efficiency
+
+        This method generates two test images used for assessing
+        the efficiency of the analysis. It performs various operations on
+        video frames to create these images, including copying and manipulating
+        frames from the video, detecting contours on binary images,
+        and drawing the arena label on the left of the frames.
+        """
+        # Provide images allowing to assess the analysis efficiency
+        if self.dims[0] > 1:
+            after_one_tenth_of_time = np.ceil(self.dims[0] / 10).astype(np.uint64)
+        else:
+            after_one_tenth_of_time = 0
+
+        last_good_detection = self.dims[0] - 1
+        if self.dims[0] > self.lost_frames:
+            if self.vars['do_threshold_segmentation']:
+                last_good_detection -= self.lost_frames
+        else:
+            last_good_detection = 0
+        if self.visu is None:
+            if len(self.converted_video.shape) == 3:
+                self.converted_video = np.stack((self.converted_video, self.converted_video, self.converted_video),
+                                             axis=3)
+            self.efficiency_test_1 = deepcopy(self.converted_video[after_one_tenth_of_time, ...])
+            self.efficiency_test_2 = deepcopy(self.converted_video[last_good_detection, ...])
+        else:
+            self.efficiency_test_1 = deepcopy(self.visu[after_one_tenth_of_time, :, :, :])
+            self.efficiency_test_2 = deepcopy(self.visu[last_good_detection, :, :, :])
+
+        position = (25, self.dims[1] // 2)
+        text = str(self.one_descriptor_per_arena['arena'])
+        contours = np.nonzero(get_contours(self.binary[after_one_tenth_of_time, :, :]))
+        self.efficiency_test_1[contours[0], contours[1], :] = self.vars['contour_color']
+        self.efficiency_test_1 = cv2.putText(self.efficiency_test_1, text, position, cv2.FONT_HERSHEY_SIMPLEX, 1,
+                                        (self.vars["contour_color"], self.vars["contour_color"],
+                                         self.vars["contour_color"], 255), 3)
+
+        eroded_binary = cv2.erode(self.binary[last_good_detection, :, :], cross_33)
+        contours = np.nonzero(self.binary[last_good_detection, :, :] - eroded_binary)
+        self.efficiency_test_2[contours[0], contours[1], :] = self.vars['contour_color']
+        self.efficiency_test_2 = cv2.putText(self.efficiency_test_2, text, position, cv2.FONT_HERSHEY_SIMPLEX, 1,
+                                         (self.vars["contour_color"], self.vars["contour_color"],
+                                          self.vars["contour_color"], 255), 3)
+
+    def save_video(self):
+        """
+        Save processed video with contours and other annotations.
+
+        This method processes the binary image to extract contours, overlay them
+        on a video, and save the resulting video file.
+
+        Notes:
+            - This method uses OpenCV for image processing and contour extraction.
+            - The processed video includes contours colored according to the
+              `contour_color` specified in the variables.
+            - Additional annotations such as time in minutes are added to each
+              frame if applicable.
+
+        """
+        if self.vars['save_processed_videos']:
+            self.check_converted_video_type()
+            if len(self.converted_video.shape) == 3:
+                self.converted_video = np.stack((self.converted_video, self.converted_video, self.converted_video),
+                                                axis=3)
+            for t in np.arange(self.dims[0]):
+
+                eroded_binary = cv2.erode(self.binary[t, :, :], cross_33)
+                contours = np.nonzero(self.binary[t, :, :] - eroded_binary)
+                self.converted_video[t, contours[0], contours[1], :] = self.vars['contour_color']
+                if "iso_digi_transi" in self.one_descriptor_per_arena.keys():
+                    if self.vars['iso_digi_analysis']  and not self.vars['several_blob_per_arena'] and not pd.isna(self.one_descriptor_per_arena["iso_digi_transi"]):
+                        if self.one_descriptor_per_arena['is_growth_isotropic'] == 1:
+                            if t < self.one_descriptor_per_arena["iso_digi_transi"]:
+                                self.converted_video[t, contours[0], contours[1], :] = 0, 0, 255
+            del self.binary
+            del self.surfarea
+            del self.borders
+            del self.origin
+            del self.origin_idx
+            del self.mean_intensity_per_frame
+            del self.erodila_disk
+            collect()
+            if self.visu is None:
+                true_frame_width = self.dims[2]
+                if len(self.vars['background_list']) == 0:
+                    self.background = None
+                else:
+                    self.background = self.vars['background_list'][self.one_descriptor_per_arena['arena'] - 1]
+                if os.path.isfile(f"ind_{self.one_descriptor_per_arena['arena']}.npy"):
+                    self.visu = video2numpy(f"ind_{self.one_descriptor_per_arena['arena']}.npy",
+                              None, true_frame_width=true_frame_width)
+                else:
+                    self.visu = self.converted_video
+                if len(self.visu.shape) == 3:
+                    self.visu = np.stack((self.visu, self.visu, self.visu), axis=3)
+            self.converted_video = np.concatenate((self.visu, self.converted_video), axis=2)
+
+            if np.any(self.one_row_per_frame['time'] > 0):
+                position = (5, self.dims[1] - 5)
+                print(self.vars['time_step_is_arbitrary'])
+                if self.vars['time_step_is_arbitrary']:
+                    time_unit = ""
+                else:
+                    time_unit = " min"
+                for t in np.arange(self.dims[0]):
+                    image = self.converted_video[t, ...]
+                    text = str(self.one_row_per_frame['time'][t]) + time_unit
+                    image = cv2.putText(image,  # numpy array on which text is written
+                                    text,  # text
+                                    position,  # position at which writing has to start
+                                    cv2.FONT_HERSHEY_SIMPLEX,  # font family
+                                    1,  # font size
+                                    (self.vars["contour_color"], self.vars["contour_color"], self.vars["contour_color"], 255),  #(209, 80, 0, 255),  
+                                    2)  # font stroke
+                    self.converted_video[t, ...] = image
+            vid_name = f"ind_{self.one_descriptor_per_arena['arena']}{self.vars['videos_extension']}"
+            write_video(self.converted_video, vid_name, is_color=True, fps=self.vars['video_fps'])
+
+    def save_results(self):
+        """
+        Save the results of testing and video processing.
+
+        This method handles the saving of efficiency tests, video files,
+        and CSV data related to test results. It checks for existing files before writing new data.
+        Additionally, it cleans up temporary files if configured to do so.
+        """
+        self.save_efficiency_tests()
+        self.save_video()
+        if self.vars['several_blob_per_arena']:
+            try:
+                with open(f"one_row_per_frame_arena{self.one_descriptor_per_arena['arena']}.csv", 'w') as file:
+                    self.one_row_per_frame.to_csv(file, sep=';', index=False, lineterminator='\n')
+            except PermissionError:
+                logging.error(f"Never let one_row_per_frame_arena{self.one_descriptor_per_arena['arena']}.csv open when Cellects runs")
+
+            create_new_csv: bool = False
+            if os.path.isfile("one_row_per_arena.csv"):
+                try:
+                    with open(f"one_row_per_arena.csv", 'r') as file:
+                        stats = pd.read_csv(file, header=0, sep=";")
+                except PermissionError:
+                    logging.error("Never let one_row_per_arena.csv open when Cellects runs")
+
+                if len(self.one_descriptor_per_arena) == len(stats.columns) - 1:
+                    try:
+                        with open(f"one_row_per_arena.csv", 'w') as file:
+                            stats.iloc[(self.one_descriptor_per_arena['arena'] - 1), 1:] = self.one_descriptor_per_arena.values()
+                            stats.to_csv(file, sep=';', index=False, lineterminator='\n')
+                    except PermissionError:
+                        logging.error("Never let one_row_per_arena.csv open when Cellects runs")
+                else:
+                    create_new_csv = True
+            else:
+                create_new_csv = True
+            if create_new_csv:
+                with open(f"one_row_per_arena.csv", 'w') as file:
+                    stats = pd.DataFrame(np.zeros((len(self.vars['analyzed_individuals']), len(self.one_descriptor_per_arena))),
+                               columns=list(self.one_descriptor_per_arena.keys()))
+                    stats.iloc[(self.one_descriptor_per_arena['arena'] - 1), :] = self.one_descriptor_per_arena.values()
+                    stats.to_csv(file, sep=';', index=False, lineterminator='\n')
+        if not self.vars['keep_unaltered_videos'] and os.path.isfile(f"ind_{self.one_descriptor_per_arena['arena']}.npy"):
+            os.remove(f"ind_{self.one_descriptor_per_arena['arena']}.npy")
+
+    def change_results_of_one_arena(self, save_video: bool = True):
+        """
+        Manages the saving and updating of CSV files based on data extracted from analyzed
+        one arena. Specifically handles three CSV files: "one_row_per_arena.csv",
+        "one_row_per_frame.csv", and "one_row_per_oscillating_cluster.csv".
+        Each file is updated or created based on the presence of existing data.
+        The method ensures that each CSV file contains the relevant information for
+        the given arena, frame, and oscillator cluster data.
+        """
+        if save_video:
+            self.save_video()
+        # I/ Update/Create one_row_per_arena.csv
+        create_new_csv: bool = False
+        if os.path.isfile("one_row_per_arena.csv"):
+            try:
+                with open(f"one_row_per_arena.csv", 'r') as file:
+                    stats = pd.read_csv(file, header=0, sep=";")
+                for stat_name, stat_value in self.one_descriptor_per_arena.items():
+                    if stat_name in stats.columns:
+                        stats.loc[(self.one_descriptor_per_arena['arena'] - 1), stat_name] = np.uint32(self.one_descriptor_per_arena[stat_name])
+                with open(f"one_row_per_arena.csv", 'w') as file:
+                    stats.to_csv(file, sep=';', index=False, lineterminator='\n')
+            except PermissionError:
+                logging.error("Never let one_row_per_arena.csv open when Cellects runs")
+            except Exception as e:
+                logging.error(f"{e}")
+                create_new_csv = True
+        else:
+            create_new_csv = True
+        if create_new_csv:
+            logging.info("Create a new one_row_per_arena.csv file")
+            try:
+                with open(f"one_row_per_arena.csv", 'w') as file:
+                    stats = pd.DataFrame(np.zeros((len(self.vars['analyzed_individuals']), len(self.one_descriptor_per_arena))),
+                               columns=list(self.one_descriptor_per_arena.keys()))
+                    stats.iloc[(self.one_descriptor_per_arena['arena'] - 1), :] = self.one_descriptor_per_arena.values() #  np.array(list(self.one_descriptor_per_arena.values()), dtype=np.uint32)
+                    stats.to_csv(file, sep=';', index=False, lineterminator='\n')
+            except PermissionError:
+                logging.error("Never let one_row_per_arena.csv open when Cellects runs")
+
+        # II/ Update/Create one_row_per_frame.csv
+        create_new_csv = False
+        if os.path.isfile("one_row_per_frame.csv"):
+            try:
+                with open(f"one_row_per_frame.csv", 'r') as file:
+                    descriptors = pd.read_csv(file, header=0, sep=";")
+                for stat_name, stat_value in self.one_row_per_frame.items():
+                    if stat_name in descriptors.columns:
+                        descriptors.loc[((self.one_descriptor_per_arena['arena'] - 1) * self.dims[0]):((self.one_descriptor_per_arena['arena']) * self.dims[0] - 1), stat_name] = self.one_row_per_frame.loc[:, stat_name].values[:]
+                with open(f"one_row_per_frame.csv", 'w') as file:
+                    descriptors.to_csv(file, sep=';', index=False, lineterminator='\n')
+            except PermissionError:
+                logging.error("Never let one_row_per_frame.csv open when Cellects runs")
+            except Exception as e:
+                logging.error(f"{e}")
+                create_new_csv = True
+        else:
+            create_new_csv = True
+        if create_new_csv:
+            logging.info("Create a new one_row_per_frame.csv file")
+            try:
+                with open(f"one_row_per_frame.csv", 'w') as file:
+                    descriptors = pd.DataFrame(np.zeros((len(self.vars['analyzed_individuals']) * self.dims[0], len(self.one_row_per_frame.columns))),
+                               columns=list(self.one_row_per_frame.keys()))
+                    descriptors.iloc[((self.one_descriptor_per_arena['arena'] - 1) * self.dims[0]):((self.one_descriptor_per_arena['arena']) * self.dims[0]), :] = self.one_row_per_frame
+                    descriptors.to_csv(file, sep=';', index=False, lineterminator='\n')
+            except PermissionError:
+                logging.error("Never let one_row_per_frame.csv open when Cellects runs")
+