celldetective 1.4.2__py3-none-any.whl → 1.5.0b1__py3-none-any.whl

celldetective/gui/settings/_settings_tracking.py

@@ -2,1122 +2,1332 @@
 Copyright © 2023 Laboratoire Adhesion et Inflammation, Authored by Remy Torro.
 """
 
-
-from PyQt5.QtWidgets import QRadioButton, QButtonGroup, QMessageBox, QComboBox, QFrame, QCheckBox, QFileDialog, QGridLayout, QTextEdit, QLineEdit, QVBoxLayout, QLabel, QHBoxLayout, QPushButton
+from PyQt5.QtWidgets import (
+    QRadioButton,
+    QButtonGroup,
+    QMessageBox,
+    QComboBox,
+    QFrame,
+    QCheckBox,
+    QFileDialog,
+    QGridLayout,
+    QTextEdit,
+    QLineEdit,
+    QVBoxLayout,
+    QLabel,
+    QHBoxLayout,
+    QPushButton,
+)
 from PyQt5.QtCore import Qt, QSize
+from matplotlib import pyplot as plt
+from mpl_toolkits.axes_grid1 import make_axes_locatable
 
-from celldetective.gui.gui_utils import FeatureChoice, ListWidget, QHSeperationLine, FigureCanvas, help_generic
+from celldetective.gui.gui_utils import (
+    help_generic,
+)
+from celldetective.gui.base.figure_canvas import FigureCanvas
+from celldetective.gui.base.list_widget import ListWidget
+from celldetective.gui.base.feature_choice import FeatureChoice
+from celldetective.gui.base.components import QHSeperationLine
 from superqt import QLabeledDoubleSlider, QLabeledSlider
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
-from celldetective.utils import extract_experiment_channels, get_software_location
-from celldetective.io import interpret_tracking_configuration, load_frames
+from celldetective import get_software_location
 from celldetective.measure import compute_haralick_features
+from celldetective.utils.experiment import extract_experiment_channels
+from celldetective.utils.data_loaders import interpret_tracking_configuration
 import numpy as np
 import json
 from shutil import copyfile
 import os
-import matplotlib.pyplot as plt
-from mpl_toolkits.axes_grid1 import make_axes_locatable
+
 from glob import glob
 from celldetective.gui.settings._settings_base import CelldetectiveSettingsPanel
+from celldetective.utils.image_loaders import load_frames
+from celldetective import get_logger
+
+logger = get_logger()
 
 
 class SettingsTracking(CelldetectiveSettingsPanel):
-	
-	"""
-	UI to set tracking parameters for bTrack.
-
-	"""
-
-	def __init__(self, parent_window=None):
-		
-		self.parent_window = parent_window
-		self.mode = self.parent_window.mode
-		self.exp_dir = self.parent_window.exp_dir
-
-		self.config_name = os.sep.join(["configs", f"btrack_config_{self.mode}.json"])
-		self.track_instructions_write_path = self.parent_window.exp_dir + os.sep.join(["configs", f"tracking_instructions_{self.mode}.json"])
-		
-		self.config_path = self.exp_dir + self.config_name
-		self.channel_names, self.channels = extract_experiment_channels(self.exp_dir)
-		self.channel_names = np.array(self.channel_names)
-		self.channels = np.array(self.channels)
-		self.minimum_height = 300
-
-		super().__init__(title="Configure tracking")
-		
-		self._add_to_layout()
-		self._load_previous_instructions()
-		
-		self._widget.setMinimumWidth(500)
-		self._adjustSize()
-		self.resize(int(self.width()*1.5), int(self._screen_height * 0.8))
-	
-	def _add_to_layout(self):
-		
-		tracker_hbox = QHBoxLayout()
-		tracker_hbox.setContentsMargins(15, 15, 15, 15)
-		tracker_hbox.addWidget(self.btrack_option, 50, alignment=Qt.AlignCenter)
-		tracker_hbox.addWidget(self.trackpy_option, 50, alignment=Qt.AlignCenter)
-		
-		self._layout.addLayout(tracker_hbox)
-		self._layout.addWidget(self.config_frame)
-		self._layout.addWidget(self.features_frame)
-		self._layout.addWidget(self.config_trackpy_frame)
-		self._layout.addWidget(self.post_proc_frame)
-		self._layout.addWidget(self.submit_btn)
-
-
-	def _create_widgets(self):
-
-		"""
-		Create the multibox design with collapsable frames.
-
-		"""
-		
-		super()._create_widgets()
-
-		self.btrack_option = QRadioButton('bTrack')
-		self.btrack_option.setChecked(True)
-
-		self.trackpy_option = QRadioButton('trackpy')
-		self.tracker_option_group = QButtonGroup()
-		self.tracker_option_group.addButton(self.btrack_option)
-		self.tracker_option_group.addButton(self.trackpy_option)
-
-		self.config_frame = QFrame()
-		self.config_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
-		self.populate_config_frame()
-
-		# Second collapsable frame FEATURES
-		self.features_frame = QFrame()
-		self.features_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
-		self.populate_features_frame()
-
-		self.config_trackpy_frame = QFrame()
-		self.config_trackpy_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
-		self.populate_config_trackpy_frame()
-		self.config_trackpy_frame.hide()
-
-		# Third collapsable frame POST-PROCESSING
-		self.post_proc_frame = QFrame()
-		self.post_proc_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
-		self.populate_post_proc_frame()
-
-		self.btrack_option.toggled.connect(self.show_tracking_options)
-		self.trackpy_option.toggled.connect(self.show_tracking_options)
-
-	def show_tracking_options(self):
-
-		if self.btrack_option.isChecked():
-			self.config_frame.show()
-			self.features_frame.show()
-			self.config_trackpy_frame.hide()
-			#self._adjustSize()
-		else:
-			self.config_frame.hide()
-			self.features_frame.hide()
-			self.config_trackpy_frame.show()
-			#self._adjustSize()
-	
-
-	def populate_post_proc_frame(self):
-
-		"""
-		Add widgets and layout in the POST-PROCESSING frame.
-		"""
-
-		grid = QGridLayout(self.post_proc_frame)
-
-		self.select_post_proc_btn = QPushButton()
-		self.select_post_proc_btn.clicked.connect(self.activate_post_proc_options)
-		self.select_post_proc_btn.setStyleSheet(self.button_select_all)
-
-		self.post_proc_lbl = QLabel("POST-PROCESSING")
-		self.post_proc_lbl.setStyleSheet("""
-			font-weight: bold;
-			padding: 0px;
-			""")
-		grid.addWidget(self.post_proc_lbl, 0, 0, 1, 4, alignment=Qt.AlignCenter)
-
-		title_hbox = QHBoxLayout()
-
-		self.collapse_post_proc_btn = QPushButton()
-		self.collapse_post_proc_btn.setIcon(icon(MDI6.chevron_down, color="black"))
-		self.collapse_post_proc_btn.setIconSize(QSize(20, 20))
-		self.collapse_post_proc_btn.setStyleSheet(self.button_select_all)
-		#grid.addWidget(self.collapse_post_proc_btn, 0, 0, 1, 4, alignment=Qt.AlignRight)
-
-		self.help_post_btn = QPushButton()
-		self.help_post_btn.setIcon(icon(MDI6.help_circle, color=self.help_color))
-		self.help_post_btn.setIconSize(QSize(20, 20))
-		self.help_post_btn.clicked.connect(self.help_post)
-		self.help_post_btn.setStyleSheet(self.button_select_all)
-		self.help_post_btn.setToolTip("Help.")
-
-		title_hbox.addWidget(self.select_post_proc_btn, 5)
-		title_hbox.addWidget(QLabel(), 85, alignment=Qt.AlignCenter)
-		title_hbox.addWidget(self.help_post_btn, 5)
-		title_hbox.addWidget(self.collapse_post_proc_btn, 5)
-		grid.addLayout(title_hbox, 0, 0, 1, 4)
-
-		self.generate_post_proc_panel_contents()
-		grid.addWidget(self.ContentsPostProc, 1, 0, 1, 4, alignment=Qt.AlignTop)
-		self.collapse_post_proc_btn.clicked.connect(lambda: self.ContentsPostProc.setHidden(not self.ContentsPostProc.isHidden()))
-		self.collapse_post_proc_btn.clicked.connect(self.collapse_post_advanced)
-		self.ContentsPostProc.hide()
-		self.uncheck_post_proc()
-
-	def collapse_post_advanced(self):
-
-		features_open = not self.ContentsFeatures.isHidden()
-		config_open = not self.ContentsConfig.isHidden()
-		post_open = not self.ContentsPostProc.isHidden()
-		is_open = np.array([features_open, config_open, post_open])
-
-		if self.ContentsPostProc.isHidden():
-			self.collapse_post_proc_btn.setIcon(icon(MDI6.chevron_down, color="black"))
-			self.collapse_post_proc_btn.setIconSize(QSize(20, 20))
-			if len(is_open[is_open])==0:
-				pass
-				#self._scroll_area.setMinimumHeight(int(self.minimum_height))
-				#self._adjustSize()
-		else:
-			self.collapse_post_proc_btn.setIcon(icon(MDI6.chevron_up, color="black"))
-			self.collapse_post_proc_btn.setIconSize(QSize(20, 20))
-
-
-	def help_post(self):
-		
-		"""
-		Helper for track post-processing strategy.
-		"""
-
-		dict_path = os.sep.join([get_software_location(), 'celldetective', 'gui', 'help', 'track-postprocessing.json'])
-
-		with open(dict_path) as f:
-			d = json.load(f)
-
-		suggestion = help_generic(d)
-		if isinstance(suggestion, str):
-			print(f"{suggestion=}")
-			msgBox = QMessageBox()
-			msgBox.setIcon(QMessageBox.Information)
-			msgBox.setTextFormat(Qt.RichText)
-			msgBox.setText(rf"{suggestion}")
-			msgBox.setWindowTitle("Info")
-			msgBox.setStandardButtons(QMessageBox.Ok)
-			returnValue = msgBox.exec()
-			if returnValue == QMessageBox.Ok:
-				return None		
-
-	def help_feature(self):
-		
-		"""
-		Helper for track post-processing strategy.
-		"""
-
-		dict_path = os.sep.join([get_software_location(), 'celldetective', 'gui', 'help', 'feature-btrack.json'])
-
-		with open(dict_path) as f:
-			d = json.load(f)
-
-		suggestion = help_generic(d)
-		if isinstance(suggestion, str):
-			print(f"{suggestion=}")
-			msgBox = QMessageBox()
-			msgBox.setIcon(QMessageBox.Information)
-			msgBox.setTextFormat(Qt.RichText)
-			msgBox.setText(rf"{suggestion}")
-			msgBox.setWindowTitle("Info")
-			msgBox.setStandardButtons(QMessageBox.Ok)
-			returnValue = msgBox.exec()
-			if returnValue == QMessageBox.Ok:
-				return None
-
-	def populate_features_frame(self):
-
-		"""
-		Add widgets and layout in the FEATURES frame.
-		"""
-
-		grid = QGridLayout(self.features_frame)
-		title_hbox = QHBoxLayout()
-		
-		self.select_features_btn = QPushButton()
-		self.select_features_btn.clicked.connect(self.activate_feature_options)
-		self.select_features_btn.setStyleSheet(self.button_select_all)
-
-		self.feature_lbl = QLabel("FEATURES")
-		self.feature_lbl.setStyleSheet("""
-			font-weight: bold;
-			padding: 0px;
-			""")
-		grid.addWidget(self.feature_lbl, 0, 0, 1, 4, alignment=Qt.AlignCenter)
-
-		self.collapse_features_btn = QPushButton()
-		self.collapse_features_btn.setIcon(icon(MDI6.chevron_down,color="black"))
-		self.collapse_features_btn.setIconSize(QSize(20, 20))
-		self.collapse_features_btn.setStyleSheet(self.button_select_all)
-
-		self.help_feature_btn = QPushButton()
-		self.help_feature_btn.setIcon(icon(MDI6.help_circle,color=self.help_color))
-		self.help_feature_btn.setIconSize(QSize(20, 20))
-		self.help_feature_btn.clicked.connect(self.help_feature)
-		self.help_feature_btn.setStyleSheet(self.button_select_all)
-		self.help_feature_btn.setToolTip("Help.")
-
-		title_hbox.addWidget(self.select_features_btn, 5)
-		title_hbox.addWidget(QLabel(), 85, alignment=Qt.AlignCenter)
-		title_hbox.addWidget(self.help_feature_btn, 5)
-		title_hbox.addWidget(self.collapse_features_btn, 5)
-		grid.addLayout(title_hbox, 0, 0, 1, 4)
-
-		self.generate_feature_panel_contents()
-		grid.addWidget(self.ContentsFeatures, 1, 0, 1, 4, alignment=Qt.AlignTop)
-		self.collapse_features_btn.clicked.connect(lambda: self.ContentsFeatures.setHidden(not self.ContentsFeatures.isHidden()))
-		self.collapse_features_btn.clicked.connect(self.collapse_features_advanced)
-		#self.ContentsFeatures.hide()
-		self.check_features()
-
-	def collapse_features_advanced(self):
-
-		"""
-		Switch the chevron icon and adjust the size for the FEATURES frame.
-		"""
-
-		features_open = not self.ContentsFeatures.isHidden()
-		config_open = not self.ContentsConfig.isHidden()
-		post_open = not self.ContentsPostProc.isHidden()
-		is_open = np.array([features_open, config_open, post_open])
-
-		if self.ContentsFeatures.isHidden():
-			self.collapse_features_btn.setIcon(icon(MDI6.chevron_down, color="black"))
-			self.collapse_features_btn.setIconSize(QSize(20, 20))
-			if len(is_open[is_open])==0:
-				pass
-				#self._scroll_area.setMinimumHeight(int(self.minimum_height))
-				#self._adjustSize()
-		else:
-			self.collapse_features_btn.setIcon(icon(MDI6.chevron_up, color="black"))
-			self.collapse_features_btn.setIconSize(QSize(20, 20))
-
-
-	def generate_post_proc_panel_contents(self):
-
-		self.ContentsPostProc = QFrame()
-		layout = QVBoxLayout(self.ContentsPostProc)
-		layout.setContentsMargins(0,0,0,0)
-
-		post_proc_layout  = QHBoxLayout()
-		self.post_proc_lbl = QLabel("Post processing on the tracks:")
-		post_proc_layout.addWidget(self.post_proc_lbl, 90)
-		layout.addLayout(post_proc_layout)
-
-		clean_traj_sublayout = QVBoxLayout()
-		clean_traj_sublayout.setContentsMargins(15,15,15,15)
-
-		tracklength_layout = QHBoxLayout()
-		self.min_tracklength_slider = QLabeledSlider()
-		self.min_tracklength_slider.setSingleStep(1)
-		self.min_tracklength_slider.setTickInterval(1)
-		self.min_tracklength_slider.setSingleStep(1)
-		self.min_tracklength_slider.setOrientation(Qt.Horizontal)
-		self.min_tracklength_slider.setRange(0,self.parent_window.parent_window.len_movie)
-		self.min_tracklength_slider.setValue(0)
-		tracklength_layout.addWidget(QLabel('Min. tracklength: '),40)
-		tracklength_layout.addWidget(self.min_tracklength_slider, 60)
-		clean_traj_sublayout.addLayout(tracklength_layout)
-
-		self.remove_not_in_first_checkbox = QCheckBox('Remove tracks that do not start at the beginning')
-		self.remove_not_in_first_checkbox.setIcon(icon(MDI6.arrow_expand_right,color="k"))
-		clean_traj_sublayout.addWidget(self.remove_not_in_first_checkbox)
-
-		self.remove_not_in_last_checkbox = QCheckBox('Remove tracks that do not end at the end')
-		self.remove_not_in_last_checkbox.setIcon(icon(MDI6.arrow_expand_left,color="k"))
-		clean_traj_sublayout.addWidget(self.remove_not_in_last_checkbox)
-
-		self.interpolate_gaps_checkbox = QCheckBox('Interpolate missed detections within tracks')
-		self.interpolate_gaps_checkbox.setIcon(icon(MDI6.chart_timeline_variant_shimmer,color="k"))
-		clean_traj_sublayout.addWidget(self.interpolate_gaps_checkbox)
-
-		self.extrapolate_post_checkbox = QCheckBox('Sustain last position until the end of the movie')
-		self.extrapolate_post_checkbox.setIcon(icon(MDI6.repeat,color="k"))
-
-		self.extrapolate_pre_checkbox = QCheckBox('Sustain first position from the beginning of the movie')
-		self.extrapolate_pre_checkbox.setIcon(icon(MDI6.repeat,color="k"))
-
-		clean_traj_sublayout.addWidget(self.extrapolate_post_checkbox)
-		clean_traj_sublayout.addWidget(self.extrapolate_pre_checkbox)
-
-		# self.interpolate_na_features_checkbox = QCheckBox('Interpolate features of missed detections')
-		# self.interpolate_na_features_checkbox.setIcon(icon(MDI6.format_color_fill,color="k"))
-
-		# clean_traj_sublayout.addWidget(self.interpolate_na_features_checkbox)
-		clean_traj_sublayout.addStretch()
-
-		self.post_proc_options_to_disable = [self.post_proc_lbl, self.min_tracklength_slider, self.remove_not_in_first_checkbox,
-											self.remove_not_in_last_checkbox, self.interpolate_gaps_checkbox, self.extrapolate_post_checkbox,
-											self.extrapolate_pre_checkbox] #, self.interpolate_na_features_checkbox
-
-		layout.addLayout(clean_traj_sublayout)
-
-	def generate_feature_panel_contents(self):
-		
-		self.ContentsFeatures = QFrame()
-		layout = QVBoxLayout(self.ContentsFeatures)
-		layout.setContentsMargins(0,0,0,0)
-
-		feature_layout = QHBoxLayout()
-		feature_layout.setContentsMargins(0,0,0,0)
-
-
-		self.feature_lbl = QLabel("Add features:")
-		self.del_feature_btn = QPushButton("")
-		self.del_feature_btn.setStyleSheet(self.button_select_all)
-		self.del_feature_btn.setIcon(icon(MDI6.trash_can,color="black"))
-		self.del_feature_btn.setToolTip("Remove feature")
-		self.del_feature_btn.setIconSize(QSize(20, 20))
-
-		self.add_feature_btn = QPushButton("")
-		self.add_feature_btn.setStyleSheet(self.button_select_all)
-		self.add_feature_btn.setIcon(icon(MDI6.filter_plus,color="black"))
-		self.add_feature_btn.setToolTip("Add feature")
-		self.add_feature_btn.setIconSize(QSize(20, 20))		
-
-		self.features_list = ListWidget(FeatureChoice, initial_features=['area','intensity_mean',])
-
-		self.del_feature_btn.clicked.connect(self.features_list.removeSel)
-		self.add_feature_btn.clicked.connect(self.features_list.addItem)
-
-		feature_layout.addWidget(self.feature_lbl, 90)
-		feature_layout.addWidget(self.del_feature_btn, 5)
-		feature_layout.addWidget(self.add_feature_btn, 5)
-		layout.addLayout(feature_layout)
-		layout.addWidget(self.features_list)
-
-		self.feat_sep2 = QHSeperationLine()
-		layout.addWidget(self.feat_sep2)
-
-		self.use_channel_lbl = QLabel('Use channel:')
-		layout.addWidget(self.use_channel_lbl)
-		self.mask_channels_cb = [QCheckBox() for i in range(len(self.channels))]
-		for cb,chn in zip(self.mask_channels_cb,self.channel_names):
-			cb.setText(chn)
-			cb.setChecked(True)
-			layout.addWidget(cb)
-
-		self.feat_sep1 = QHSeperationLine()
-		layout.addWidget(self.feat_sep1)
-
-		self.activate_haralick_btn = QCheckBox('activate Haralick texture features')
-		self.activate_haralick_btn.toggled.connect(self.show_haralick_options)
-		# Haralick features parameters
-
-		self.haralick_channel_choice = QComboBox()
-		self.haralick_channel_choice.addItems(self.channel_names)
-		self.haralick_channel_lbl = QLabel('Target channel: ')
-
-		self.haralick_distance_le = QLineEdit("1")
-		self.haralick_distance_lbl = QLabel('Distance: ')
-
-		self.haralick_n_gray_levels_le = QLineEdit("256")
-		self.haralick_n_gray_levels_lbl = QLabel('# gray levels: ')
-
-		# Slider to set vmin & vmax
-		self.haralick_scale_slider = QLabeledDoubleSlider()
-		self.haralick_scale_slider.setTickInterval(0.05)
-		self.haralick_scale_slider.setSingleStep(1)
-		self.haralick_scale_slider.setOrientation(Qt.Horizontal)
-		self.haralick_scale_slider.setRange(0,1)
-		self.haralick_scale_slider.setValue(0.5)
-		self.haralick_scale_lbl = QLabel('Scale: ')
-
-		self.haralick_percentile_min_le = QLineEdit('0.01')
-		self.haralick_percentile_max_le = QLineEdit('99.9')
-		self.haralick_normalization_mode_btn = QPushButton()
-		self.haralick_normalization_mode_btn.setStyleSheet(self.button_select_all)
-		self.haralick_normalization_mode_btn.setIcon(icon(MDI6.percent_circle,color="black"))
-		self.haralick_normalization_mode_btn.setIconSize(QSize(20, 20))		
-		self.haralick_normalization_mode_btn.setToolTip("Switch to absolute normalization values.")
-		self.percentile_mode = True
-
-		self.haralick_percentile_min_lbl = QLabel('Min percentile: ')
-		self.haralick_percentile_max_lbl = QLabel('Max percentile: ')
-
-		self.haralick_hist_btn = QPushButton()
-		self.haralick_hist_btn.clicked.connect(self.control_haralick_intensity_histogram)
-		self.haralick_hist_btn.setIcon(icon(MDI6.poll,color="k"))
-		self.haralick_hist_btn.setStyleSheet(self.button_select_all)
-
-		self.haralick_digit_btn = QPushButton()
-		self.haralick_digit_btn.clicked.connect(self.control_haralick_digitalization)
-		self.haralick_digit_btn.setIcon(icon(MDI6.image_check,color="k"))
-		self.haralick_digit_btn.setStyleSheet(self.button_select_all)
-
-		self.haralick_layout = QVBoxLayout()
-		self.haralick_layout.setContentsMargins(20,20,20,20)
-
-		activate_layout = QHBoxLayout()
-		activate_layout.addWidget(self.activate_haralick_btn, 80)
-		activate_layout.addWidget(self.haralick_hist_btn, 10)
-		activate_layout.addWidget(self.haralick_digit_btn, 10)
-		self.haralick_layout.addLayout(activate_layout)
-
-		channel_layout = QHBoxLayout()
-		channel_layout.addWidget(self.haralick_channel_lbl, 40)
-		channel_layout.addWidget(self.haralick_channel_choice, 60)
-		self.haralick_layout.addLayout(channel_layout)
-
-		distance_layout = QHBoxLayout()
-		distance_layout.addWidget(self.haralick_distance_lbl,40)
-		distance_layout.addWidget(self.haralick_distance_le, 60)
-		self.haralick_layout.addLayout(distance_layout)
-
-		gl_layout = QHBoxLayout()
-		gl_layout.addWidget(self.haralick_n_gray_levels_lbl,40)
-		gl_layout.addWidget(self.haralick_n_gray_levels_le,60)
-		self.haralick_layout.addLayout(gl_layout)
-
-		slider_layout = QHBoxLayout()
-		slider_layout.addWidget(self.haralick_scale_lbl,40)
-		slider_layout.addWidget(self.haralick_scale_slider,60)
-		self.haralick_layout.addLayout(slider_layout)
-
-		slider_min_percentile_layout = QHBoxLayout()
-		slider_min_percentile_layout.addWidget(self.haralick_percentile_min_lbl,40)
-		slider_min_percentile_layout.addWidget(self.haralick_percentile_min_le,55)
-		slider_min_percentile_layout.addWidget(self.haralick_normalization_mode_btn, 5)
-		self.haralick_layout.addLayout(slider_min_percentile_layout)
-
-		slider_max_percentile_layout = QHBoxLayout()
-		slider_max_percentile_layout.addWidget(self.haralick_percentile_max_lbl,40)
-		slider_max_percentile_layout.addWidget(self.haralick_percentile_max_le,60)
-		self.haralick_layout.addLayout(slider_max_percentile_layout)
-
-		self.haralick_to_hide = [self.haralick_hist_btn, self.haralick_digit_btn, self.haralick_channel_lbl, self.haralick_channel_choice,
-								self.haralick_distance_le, self.haralick_distance_lbl, self.haralick_n_gray_levels_le, self.haralick_n_gray_levels_lbl,
-								self.haralick_scale_lbl, self.haralick_scale_slider, self.haralick_percentile_min_lbl, self.haralick_percentile_min_le,
-								self.haralick_percentile_max_lbl, self.haralick_percentile_max_le, self.haralick_normalization_mode_btn]
-		for element in self.haralick_to_hide:
-			element.hide()
-
-		self.features_to_disable = [self.feature_lbl, self.del_feature_btn, self.add_feature_btn, self.features_list, 
-									self.use_channel_lbl, *self.mask_channels_cb, self.activate_haralick_btn]
-
-		self.haralick_normalization_mode_btn.clicked.connect(self.switch_to_absolute_normalization_mode)
-		layout.addLayout(self.haralick_layout)
-
-	def switch_to_absolute_normalization_mode(self):
-		if self.percentile_mode:
-			self.percentile_mode = False
-			self.haralick_normalization_mode_btn.setIcon(icon(MDI6.percent_circle_outline,color="black"))
-			self.haralick_normalization_mode_btn.setIconSize(QSize(20, 20))		
-			self.haralick_normalization_mode_btn.setToolTip("Switch to percentile normalization values.")			
-			self.haralick_percentile_min_lbl.setText('Min value: ')
-			self.haralick_percentile_max_lbl.setText('Max value: ')
-			self.haralick_percentile_min_le.setText('0')
-			self.haralick_percentile_max_le.setText('10000')
-
-		else:
-			self.percentile_mode = True
-			self.haralick_normalization_mode_btn.setIcon(icon(MDI6.percent_circle,color="black"))
-			self.haralick_normalization_mode_btn.setIconSize(QSize(20, 20))
-			self.haralick_normalization_mode_btn.setToolTip("Switch to absolute normalization values.")			
-			self.haralick_percentile_min_lbl.setText('Min percentile: ')
-			self.haralick_percentile_max_lbl.setText('Max percentile: ')			
-			self.haralick_percentile_min_le.setText('0.01')
-			self.haralick_percentile_max_le.setText('99.99')
-
-	def populate_config_frame(self):
-
-		grid = QGridLayout(self.config_frame)
-		panel_title = QLabel(f"CONFIGURATION")
-		panel_title.setStyleSheet("""
-			font-weight: bold;
-			padding: 0px;
-			""")
+    """
+    UI to set tracking parameters for bTrack.
 
-		grid.addWidget(panel_title, 0, 0, 1, 4, alignment=Qt.AlignCenter)
+    """
 
-		self.collapse_config_btn = QPushButton()
-		self.collapse_config_btn.setIcon(icon(MDI6.chevron_down,color="black"))
-		self.collapse_config_btn.setIconSize(QSize(20, 20))
-		self.collapse_config_btn.setStyleSheet(self.button_select_all)
-		grid.addWidget(self.collapse_config_btn, 0, 0, 1, 4, alignment=Qt.AlignRight)
+    def __init__(self, parent_window=None):
 
-		self.generate_config_panel_contents()
-		grid.addWidget(self.ContentsConfig, 1, 0, 1, 4, alignment=Qt.AlignTop)
-		self.collapse_config_btn.clicked.connect(lambda: self.ContentsConfig.setHidden(not self.ContentsConfig.isHidden()))
-		self.collapse_config_btn.clicked.connect(self.collapse_config_advanced)
-		#self.ContentsConfig.hide()
+        self.parent_window = parent_window
+        self.mode = self.parent_window.mode
+        self.exp_dir = self.parent_window.exp_dir
 
-	def populate_config_trackpy_frame(self):
+        self.config_name = os.sep.join(["configs", f"btrack_config_{self.mode}.json"])
+        self.track_instructions_write_path = self.parent_window.exp_dir + os.sep.join(
+            ["configs", f"tracking_instructions_{self.mode}.json"]
+        )
 
-		grid = QGridLayout(self.config_trackpy_frame)
-		panel_title = QLabel(f"CONFIGURATION")
-		panel_title.setStyleSheet("""
-			font-weight: bold;
-			padding: 0px;
-			""")
-
-		grid.addWidget(panel_title, 0, 0, 1, 4, alignment=Qt.AlignCenter)
-
-		self.collapse_config_trackpy_btn = QPushButton()
-		self.collapse_config_trackpy_btn.setIcon(icon(MDI6.chevron_down,color="black"))
-		self.collapse_config_trackpy_btn.setIconSize(QSize(20, 20))
-		self.collapse_config_trackpy_btn.setStyleSheet(self.button_select_all)
-		grid.addWidget(self.collapse_config_trackpy_btn, 0, 0, 1, 4, alignment=Qt.AlignRight)
-		self.generate_config_trackpy_panel_contents()
-		grid.addWidget(self.ContentsConfigTrackpy, 1, 0, 1, 4, alignment=Qt.AlignTop)
-		self.collapse_config_trackpy_btn.clicked.connect(lambda: self.ContentsConfigTrackpy.setHidden(not self.ContentsConfigTrackpy.isHidden()))
-		self.collapse_config_trackpy_btn.clicked.connect(self.collapse_config_trackpy_advanced)
-		#self.ContentsConfig.hide()
-
-
-	def collapse_config_advanced(self):
-
-		"""
-		Switch the chevron icon and adjust the size for the CONFIG frame.
-		"""
-
-		features_open = not self.ContentsFeatures.isHidden()
-		config_open = not self.ContentsConfig.isHidden()
-		post_open = not self.ContentsPostProc.isHidden()
-		is_open = np.array([features_open, config_open, post_open])
-
-		if self.ContentsConfig.isHidden():
-			self.collapse_config_btn.setIcon(icon(MDI6.chevron_down,color="black"))
-			self.collapse_config_btn.setIconSize(QSize(20, 20))
-			if len(is_open[is_open])==0:
-				pass
-				#self._scroll_area.setMinimumHeight(int(self.minimum_height))
-				#self._adjustSize()
-		else:
-			self.collapse_config_btn.setIcon(icon(MDI6.chevron_up,color="black"))
-			self.collapse_config_btn.setIconSize(QSize(20, 20))
-
-	def collapse_config_trackpy_advanced(self):
-
-		"""
-		Switch the chevron icon and adjust the size for the CONFIG frame.
-		"""
-
-
-		post_open = not self.ContentsPostProc.isHidden()
-		is_open = np.array([post_open])
-
-		if self.ContentsConfigTrackpy.isHidden():
-			self.collapse_config_trackpy_btn.setIcon(icon(MDI6.chevron_down,color="black"))
-			self.collapse_config_trackpy_btn.setIconSize(QSize(20, 20))
-			if len(is_open[is_open])==0:
-				pass
-				#self._scroll_area.setMinimumHeight(int(self.minimum_height))
-				#self._adjustSize()
-		else:
-			self.collapse_config_trackpy_btn.setIcon(icon(MDI6.chevron_up,color="black"))
-			self.collapse_config_trackpy_btn.setIconSize(QSize(20, 20))
-
-
-	def generate_config_trackpy_panel_contents(self):
-
-		self.ContentsConfigTrackpy = QFrame()
-		layout = QVBoxLayout(self.ContentsConfigTrackpy)
-		layout.setContentsMargins(0,0,0,0)
-
-		sr_layout = QHBoxLayout()
-		self.search_range_lbl = QLabel("search range [px]: ")
-		self.search_range_le = QLineEdit('30')
-		self.search_range_le.setPlaceholderText('search distance in pixels')
-		self.search_range_le.setValidator(self._floatValidator)
-		sr_layout.addWidget(self.search_range_lbl, 30)
-		sr_layout.addWidget(self.search_range_le, 70)
-		layout.addLayout(sr_layout)
-
-		memory_layout = QHBoxLayout()
-		self.memory_lbl = QLabel("memory [# frames]: ")
-		self.memory_slider = QLabeledSlider()
-		self.memory_slider.setSingleStep(1)
-		self.memory_slider.setTickInterval(1)
-		self.memory_slider.setSingleStep(1)
-		self.memory_slider.setOrientation(Qt.Horizontal)
-		self.memory_slider.setRange(0,self.parent_window.parent_window.len_movie)
-		self.memory_slider.setValue(0)
-		memory_layout.addWidget(self.memory_lbl, 30)
-		memory_layout.addWidget(self.memory_slider, 70)
-		layout.addLayout(memory_layout)
-
-
-	def generate_config_panel_contents(self):
-		
-		self.ContentsConfig = QFrame()
-		layout = QVBoxLayout(self.ContentsConfig)
-		layout.setContentsMargins(0,0,0,0)
-
-		btrack_config_layout = QHBoxLayout()
-		self.config_lbl = QLabel("bTrack configuration: ")
-		btrack_config_layout.addWidget(self.config_lbl, 90)
-
-		self.upload_btrack_config_btn = QPushButton()
-		self.upload_btrack_config_btn.setIcon(icon(MDI6.plus,color="black"))
-		self.upload_btrack_config_btn.setIconSize(QSize(20, 20))
-		self.upload_btrack_config_btn.setToolTip("Upload a new bTrack configuration.")
-		self.upload_btrack_config_btn.setStyleSheet(self.button_select_all)
-		self.upload_btrack_config_btn.clicked.connect(self.upload_btrack_config)
-		btrack_config_layout.addWidget(self.upload_btrack_config_btn, 5)  #4,3,1,1, alignment=Qt.AlignLeft
-
-		self.reset_config_btn = QPushButton()
-		self.reset_config_btn.setIcon(icon(MDI6.arrow_u_right_top,color="black"))
-		self.reset_config_btn.setIconSize(QSize(20, 20))
-		self.reset_config_btn.setToolTip("Reset the configuration to the default bTrack config.")
-		self.reset_config_btn.setStyleSheet(self.button_select_all)
-		self.reset_config_btn.clicked.connect(self.reset_btrack_config)
-		btrack_config_layout.addWidget(self.reset_config_btn, 5)  #4,3,1,1, alignment=Qt.AlignLeft
-
-		layout.addLayout(btrack_config_layout)
-
-		self.config_le = QTextEdit()
-		self.config_le.setMinimumHeight(150)
-		#self.config_le.setStyleSheet("""
-		#							background: #EEEDEB;
-		#							border: 2px solid black;
-		#							""")
-		layout.addWidget(self.config_le)
-		self.load_cell_config()
-
-
-	def show_haralick_options(self):
-
-		"""
-		Show the Haralick texture options.
-		"""
-
-		if self.activate_haralick_btn.isChecked():
-			for element in self.haralick_to_hide:
-				element.show()
-		else:
-			for element in self.haralick_to_hide:
-				element.hide()   		
-
-	def upload_btrack_config(self):
-
-		"""
-		Upload a specific bTrack config to the experiment folder for the cell population.
-		"""
-
-		self.file_dialog = QFileDialog()
-		try:
-			modelpath = os.sep.join([self._software_path, "celldetective","models","tracking_configs"]) + os.sep
-			print("Track config path: ", modelpath)
-			self.filename = self.file_dialog.getOpenFileName(None, "Load config", modelpath, "json files (*.json)")[0]
-			if self.filename!=self.config_path:
-				copyfile(self.filename, self.config_path)
-			self.load_cell_config()
-		except Exception as e:
-			print(e)
-			return None
-
-	def reset_btrack_config(self):
-
-		"""
-		Set the bTrack config to the default bTrack config.
-		"""
-
-		msgBox = QMessageBox()
-		msgBox.setIcon(QMessageBox.Question)
-		msgBox.setText("You are about to revert to the default bTrack configuration? Do you want to proceed?")
-		msgBox.setWindowTitle("Confirm")
-		msgBox.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
-		returnValue = msgBox.exec()
-		if returnValue == QMessageBox.Yes:
-			config = interpret_tracking_configuration(None)
-			if config!=self.config_path:
-				copyfile(config, self.config_path)
-			self.load_cell_config()
-		else:
-			return None
-
-	def activate_feature_options(self):
-
-		"""
-		Tick the features option.
-		"""
-
-		self.switch_feature_option()
-		if self.features_ticked:
-			for element in self.features_to_disable:
-				element.setEnabled(True)
-			self.select_features_btn.setIcon(icon(MDI6.checkbox_outline,color="black"))
-			self.select_features_btn.setIconSize(QSize(20, 20))
-		else:
-			for element in self.features_to_disable:
-				element.setEnabled(False)
-			self.select_features_btn.setIcon(icon(MDI6.checkbox_blank_outline,color="black"))
-			self.select_features_btn.setIconSize(QSize(20, 20))
-			self.features_list.list_widget.clearSelection()
-			self.activate_haralick_btn.setChecked(False)
-
-
-	def activate_post_proc_options(self):
-
-		"""
-		Tick the features option.
-		"""
-
-		self.switch_post_proc_option()
-		if self.post_proc_ticked:
-			for element in self.post_proc_options_to_disable:
-				element.setEnabled(True)
-			self.select_post_proc_btn.setIcon(icon(MDI6.checkbox_outline,color="black"))
-			self.select_post_proc_btn.setIconSize(QSize(20, 20))
-		else:
-			for element in self.post_proc_options_to_disable:
-				element.setEnabled(False)
-			self.select_post_proc_btn.setIcon(icon(MDI6.checkbox_blank_outline,color="black"))
-			self.select_post_proc_btn.setIconSize(QSize(20, 20))
-
-	def switch_feature_option(self):
-
-		"""
-		Switch the feature option.
-		"""
-
-		if self.features_ticked == True:
-			self.features_ticked = False
-		else:
-			self.features_ticked = True
-
-	def switch_post_proc_option(self):
-
-		"""
-		Switch the feature option.
-		"""
-
-		if self.post_proc_ticked == True:
-			self.post_proc_ticked = False
-		else:
-			self.post_proc_ticked = True	
-
-	# def adjustScrollArea(self):
-	#
-	# 	"""
-	# 	Auto-adjust scroll area to fill space
-	# 	(from https://stackoverflow.com/questions/66417576/make-qscrollarea-use-all-available-space-of-qmainwindow-height-axis)
-	# 	"""
-	#
-	# 	step = 5
-	# 	while self._scroll_area.verticalScrollBar().isVisible() and self.height() < self.maximumHeight():
-	# 		self.resize(self.width(), self.height() + step)
-
-	def load_cell_config(self):
-
-		"""
-		Load the cell configuration and write in the QLineEdit.
-		"""
-
-		file_name = interpret_tracking_configuration(self.config_path)
-		with open(file_name, 'r') as f:
-			json_data = json.load(f)
-			self.config_le.setText(json.dumps(json_data, indent=4))
-
-	def _write_instructions(self):
-
-		"""
-		Write the selected options in a json file for later reading by the software.
-		"""
-
-		print('Writing instructions...')
-		
-		if self.btrack_option.isChecked():
-			btrack_option = True
-		else:
-			btrack_option = False
-
-		# Fetch trackpky params
-		if not btrack_option:
-			search_range = int(self.search_range_le.text().replace(',','.'))
-			memory = self.memory_slider.value()
-		else:
-			search_range = None
-			memory = None	
-
-		tracking_options = {'btrack_config_path': self.config_path}
-		tracking_options.update({'btrack_option': btrack_option, 'search_range': search_range, 'memory': memory})
-
-		if not self.features_ticked:
-			features = None
-			masked_channels = None
-		else:
-			features = self.features_list.getItems()
-			masked_channels = self.channel_names[np.array([not cb.isChecked() for cb in self.mask_channels_cb])]
-			if len(masked_channels)==0:
-				masked_channels = None
-			else:
-				masked_channels = list(masked_channels)
-
-		tracking_options.update({'features': features, 'mask_channels': masked_channels})
-		
-		self.extract_haralick_options()
-		tracking_options.update({'haralick_options': self.haralick_options})
-
-		if self.post_proc_ticked:
-			post_processing_options = {"minimum_tracklength": int(self.min_tracklength_slider.value()),
-									   "remove_not_in_first": self.remove_not_in_first_checkbox.isChecked(), 
-									   "remove_not_in_last": self.remove_not_in_last_checkbox.isChecked(),
-									   "interpolate_position_gaps": self.interpolate_gaps_checkbox.isChecked(), 
-									   "extrapolate_tracks_pre": self.extrapolate_pre_checkbox.isChecked(),
-									   "extrapolate_tracks_post": self.extrapolate_post_checkbox.isChecked(),
-									   'interpolate_na': False, #self.interpolate_na_features_checkbox.isChecked()
-									   }
-		else:
-
-			post_processing_options = None
-
-		tracking_options.update({'post_processing_options': post_processing_options})
-		file_name = self.track_instructions_write_path
-		with open(file_name, 'w') as f:
-			json.dump(tracking_options, f, indent=4)
-
-		# Save the JSON data to the file
-		file_name = self.config_path
-		with open(file_name, 'w') as f:
-			f.write(self.config_le.toPlainText())
-		print('Done.')
-		self.close()
-
-	def uncheck_post_proc(self):
-		self.select_post_proc_btn.setIcon(icon(MDI6.checkbox_blank_outline,color="black"))
-		self.select_post_proc_btn.setIconSize(QSize(20, 20))
-		self.post_proc_ticked = False
-		for element in self.post_proc_options_to_disable:
-			element.setEnabled(False)
-
-	def check_post_proc(self):
-		self.select_post_proc_btn.setIcon(icon(MDI6.checkbox_outline,color="black"))
-		self.select_post_proc_btn.setIconSize(QSize(20, 20))
-		self.post_proc_ticked = True		
-		for element in self.post_proc_options_to_disable:
-			element.setEnabled(True)
-
-	def uncheck_features(self):
-		self.select_features_btn.setIcon(icon(MDI6.checkbox_blank_outline,color="black"))
-		self.select_features_btn.setIconSize(QSize(20, 20))
-		self.features_ticked = False
-		for element in self.features_to_disable:
-			element.setEnabled(False)
-
-	def check_features(self):
-		self.select_features_btn.setIcon(icon(MDI6.checkbox_outline,color="black"))
-		self.select_features_btn.setIconSize(QSize(20, 20))
-		self.features_ticked = True		
-		for element in self.features_to_disable:
-			element.setEnabled(True)
-
-	def extract_haralick_options(self):
-
-		if self.activate_haralick_btn.isChecked():
-			self.haralick_options = {"target_channel": self.haralick_channel_choice.currentIndex(),
-								"scale_factor": float(self.haralick_scale_slider.value()),
-								"n_intensity_bins": int(self.haralick_n_gray_levels_le.text()),
-								"distance" : int(self.haralick_distance_le.text()),
-								}
-			if self.percentile_mode:
-				self.haralick_options.update({"percentiles": (float(self.haralick_percentile_min_le.text()), float(self.haralick_percentile_max_le.text())), "clip_values": None})
-			else:
-				self.haralick_options.update({"percentiles": None, "clip_values": (float(self.haralick_percentile_min_le.text()), float(self.haralick_percentile_max_le.text()))})
-
-		else:
-			self.haralick_options = None		
-
-	def _load_previous_instructions(self):
-
-		"""
-		Read the tracking options from a previously written json file.
-		"""
-
-		print('Reading instructions..')
-		if os.path.exists(self.track_instructions_write_path):
-			with open(self.track_instructions_write_path, 'r') as f:
-				tracking_instructions = json.load(f)
-				print(tracking_instructions)
-				
-				# Features
-				features = tracking_instructions['features']
-				if (features is not None) and len(features)>0:
-					self.check_features()
-					self.ContentsFeatures.show()
-					self.features_list.list_widget.clear()
-					self.features_list.list_widget.addItems(features)
-				else:
-					self.ContentsFeatures.hide()
-					self.uncheck_features()
-
-				btrack_option = True
-				if 'btrack_option' in tracking_instructions:
-					btrack_option = tracking_instructions['btrack_option']
-				if btrack_option:
-					self.btrack_option.click()
-				else:
-					self.trackpy_option.click()
-
-				if 'search_range' in tracking_instructions:
-					search_range = tracking_instructions['search_range']
-					if search_range is not None:
-						self.search_range_le.setText(str(search_range).replace('.', ','))
-				if 'memory' in tracking_instructions:
-					memory = tracking_instructions['memory']
-					if memory is not None:
-						self.memory_slider.setValue(memory)
-
-				# Uncheck channels that are masked
-				mask_channels = tracking_instructions['mask_channels']
-				if (mask_channels is not None) and len(mask_channels)>0:
-					for ch in mask_channels:
-						for cb in self.mask_channels_cb:
-							if cb.text()==ch:
-								cb.setChecked(False)
-
-				haralick_options = tracking_instructions['haralick_options']
-				if haralick_options is None:
-					self.activate_haralick_btn.setChecked(False)
-					self.show_haralick_options()
-				else:
-					self.activate_haralick_btn.setChecked(True)
-					self.show_haralick_options()
-					if 'target_channel' in haralick_options:
-						idx = haralick_options['target_channel']
-						#idx = self.haralick_channel_choice.findText(text_to_find)
-						self.haralick_channel_choice.setCurrentIndex(idx)
-					if 'scale_factor' in haralick_options:
-						self.haralick_scale_slider.setValue(float(haralick_options['scale_factor']))
-					if ('percentiles' in haralick_options) and (haralick_options['percentiles'] is not None):
-						perc = list(haralick_options['percentiles'])
-						self.haralick_percentile_min_le.setText(str(perc[0]))
-						self.haralick_percentile_max_le.setText(str(perc[1]))
-					if ('clip_values' in haralick_options) and (haralick_options['clip_values'] is not None):
-						values = list(haralick_options['clip_values'])
-						self.haralick_percentile_min_le.setText(str(values[0]))
-						self.haralick_percentile_max_le.setText(str(values[1]))
-						self.percentile_mode=True
-						self.switch_to_absolute_normalization_mode()
-					if 'n_intensity_bins' in haralick_options:
-						self.haralick_n_gray_levels_le.setText(str(haralick_options['n_intensity_bins']))
-					if 'distance' in haralick_options:
-						self.haralick_distance_le.setText(str(haralick_options['distance']))
-		
-
-
-				# Post processing options
-				post_processing_options = tracking_instructions['post_processing_options']
-				if post_processing_options is None:
-					self.uncheck_post_proc()
-					self.ContentsPostProc.hide()
-					for element in [self.remove_not_in_last_checkbox, self.remove_not_in_first_checkbox, self.interpolate_gaps_checkbox, 
-									self.extrapolate_post_checkbox, self.extrapolate_pre_checkbox]: #self.interpolate_na_features_checkbox
-						element.setChecked(False)
-					self.min_tracklength_slider.setValue(0)
-
-				else:
-					self.check_post_proc()
-					self.ContentsPostProc.show()
-					if "minimum_tracklength" in post_processing_options:
-						self.min_tracklength_slider.setValue(int(post_processing_options["minimum_tracklength"]))
-					if "remove_not_in_first" in post_processing_options:
-						self.remove_not_in_first_checkbox.setChecked(post_processing_options["remove_not_in_first"])
-					if "remove_not_in_last" in post_processing_options:
-						self.remove_not_in_last_checkbox.setChecked(post_processing_options["remove_not_in_last"])
-					if "interpolate_position_gaps" in post_processing_options:
-						self.interpolate_gaps_checkbox.setChecked(post_processing_options["interpolate_position_gaps"])
-					if "extrapolate_tracks_pre" in post_processing_options:
-						self.extrapolate_pre_checkbox.setChecked(post_processing_options["extrapolate_tracks_pre"])
-					if "extrapolate_tracks_post" in post_processing_options:
-						self.extrapolate_post_checkbox.setChecked(post_processing_options["extrapolate_tracks_post"])
-					# if "interpolate_na" in post_processing_options:
-					# 	self.interpolate_na_features_checkbox.setChecked(post_processing_options["interpolate_na"])
-
-	def locate_image(self):
-		
-		"""
-		Load the first frame of the first movie found in the experiment folder as a sample.
-		"""
-
-		movies = glob(self.parent_window.parent_window.exp_dir + os.sep.join(["*", "*", "movie", self.parent_window.parent_window.movie_prefix+"*.tif"]))
-		if len(movies)==0:
-			msgBox = QMessageBox()
-			msgBox.setIcon(QMessageBox.Warning)
-			msgBox.setText("No movies are detected in the experiment folder. Cannot load an image to test Haralick.")
-			msgBox.setWindowTitle("Warning")
-			msgBox.setStandardButtons(QMessageBox.Ok)
-			returnValue = msgBox.exec()
-			if returnValue == QMessageBox.Yes:
-				self.test_frame = None
-				return None
-		else:
-			stack0 = movies[0]
-			n_channels = len(self.channels)
-			self.test_frame = load_frames(np.arange(n_channels), stack0, scale=None, normalize_input=False)
-
-	def control_haralick_digitalization(self):
-
-		"""
-		Load an image for the first experiment movie found. 
-		Apply the Haralick parameters and check the result of the digitization (normalization + binning of intensities).
-
-		"""
-
-		self.locate_image()
-		self.extract_haralick_options()
-		if self.test_frame is not None:
-			digitized_img = compute_haralick_features(self.test_frame, np.zeros(self.test_frame.shape[:2]), 
-													 channels=self.channel_names, return_digit_image_only=True,
-													 **self.haralick_options
-													 )
-
-			self.fig, self.ax = plt.subplots()
-			divider = make_axes_locatable(self.ax)
-			cax = divider.append_axes('right', size='5%', pad=0.05)
-
-			self.imshow_digit_window = FigureCanvas(self.fig, title="Haralick: control digitization")
-			self.ax.clear()
-			im = self.ax.imshow(digitized_img, cmap='gray')
-			self.fig.colorbar(im, cax=cax, orientation='vertical')
-			self.ax.set_xticks([])
-			self.ax.set_yticks([])
-			self.fig.set_facecolor('none')  # or 'None'
-			self.fig.canvas.setStyleSheet("background-color: transparent;")
-			self.imshow_digit_window.canvas.draw()
-			self.imshow_digit_window.show()
-
-	def control_haralick_intensity_histogram(self):
-
-		"""
-		Load an image for the first experiment movie found. 
-		Apply the Haralick normalization parameters and check the normalized intensity histogram.
-		
-		"""
-
-		self.locate_image()
-		self.extract_haralick_options()
-		if self.test_frame is not None:
-			norm_img = compute_haralick_features(self.test_frame, np.zeros(self.test_frame.shape[:2]), 
-													 channels=self.channel_names, return_norm_image_only=True,
-													 **self.haralick_options
-													 )
-			self.fig, self.ax = plt.subplots(1,1,figsize=(4,3))
-			self.hist_window = FigureCanvas(self.fig, title="Haralick: control digitized histogram")
-			self.ax.clear()
-			flat = norm_img.flatten()
-			self.ax.hist(flat[flat==flat], bins=self.haralick_options['n_intensity_bins'])
-			self.ax.set_xlabel('gray level value')
-			self.ax.set_ylabel('#')
-			plt.tight_layout()
-			self.fig.set_facecolor('none')  # or 'None'
-			self.fig.canvas.setStyleSheet("background-color: transparent;")
-			self.hist_window.canvas.draw()
-			self.hist_window.show()
+        self.config_path = self.exp_dir + self.config_name
+        self.channel_names, self.channels = extract_experiment_channels(self.exp_dir)
+        self.channel_names = np.array(self.channel_names)
+        self.channels = np.array(self.channels)
+        self.minimum_height = 300
+
+        super().__init__(title="Configure tracking")
+
+        self._add_to_layout()
+        self._load_previous_instructions()
+
+        self._widget.setMinimumWidth(500)
+        self._adjust_size()
+        self.resize(int(self.width() * 1.1), int(self._screen_height * 0.8))
+
+    def _add_to_layout(self):
+
+        tracker_hbox = QHBoxLayout()
+        tracker_hbox.setContentsMargins(15, 15, 15, 15)
+        tracker_hbox.addWidget(self.btrack_option, 50, alignment=Qt.AlignCenter)
+        tracker_hbox.addWidget(self.trackpy_option, 50, alignment=Qt.AlignCenter)
+
+        self._layout.addLayout(tracker_hbox)
+        self._layout.addWidget(self.config_frame)
+        self._layout.addWidget(self.features_frame)
+        self._layout.addWidget(self.config_trackpy_frame)
+        self._layout.addWidget(self.post_proc_frame)
+        self._layout.addWidget(self.submit_btn)
 
+    def _create_widgets(self):
+        """
+        Create the multibox design with collapsable frames.
 
+        """
 
+        super()._create_widgets()
 
+        self.btrack_option = QRadioButton("bTrack")
+        self.btrack_option.setChecked(True)
 
+        self.trackpy_option = QRadioButton("trackpy")
+        self.tracker_option_group = QButtonGroup()
+        self.tracker_option_group.addButton(self.btrack_option)
+        self.tracker_option_group.addButton(self.trackpy_option)
+
+        self.config_frame = QFrame()
+        self.config_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
+        self.populate_config_frame()
+
+        # Second collapsable frame FEATURES
+        self.features_frame = QFrame()
+        self.features_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
+        self.populate_features_frame()
+
+        self.config_trackpy_frame = QFrame()
+        self.config_trackpy_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
+        self.populate_config_trackpy_frame()
+        self.config_trackpy_frame.hide()
+
+        # Third collapsable frame POST-PROCESSING
+        self.post_proc_frame = QFrame()
+        self.post_proc_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
+        self.populate_post_proc_frame()
+
+        self.btrack_option.toggled.connect(self.show_tracking_options)
+        self.trackpy_option.toggled.connect(self.show_tracking_options)
+
+    def show_tracking_options(self):
+
+        if self.btrack_option.isChecked():
+            self.config_frame.show()
+            self.features_frame.show()
+            self.config_trackpy_frame.hide()
+            # self._adjustSize()
+        else:
+            self.config_frame.hide()
+            self.features_frame.hide()
+            self.config_trackpy_frame.show()
+            # self._adjustSize()
+
+    def populate_post_proc_frame(self):
+        """
+        Add widgets and layout in the POST-PROCESSING frame.
+        """
+
+        grid = QGridLayout(self.post_proc_frame)
+
+        self.select_post_proc_btn = QPushButton()
+        self.select_post_proc_btn.clicked.connect(self.activate_post_proc_options)
+        self.select_post_proc_btn.setStyleSheet(self.button_select_all)
+
+        self.post_proc_lbl = QLabel("POST-PROCESSING")
+        self.post_proc_lbl.setStyleSheet(
+            """
+			font-weight: bold;
+			padding: 0px;
+			"""
+        )
+        grid.addWidget(self.post_proc_lbl, 0, 0, 1, 4, alignment=Qt.AlignCenter)
+
+        title_hbox = QHBoxLayout()
+
+        self.collapse_post_proc_btn = QPushButton()
+        self.collapse_post_proc_btn.setIcon(icon(MDI6.chevron_down, color="black"))
+        self.collapse_post_proc_btn.setIconSize(QSize(20, 20))
+        self.collapse_post_proc_btn.setStyleSheet(self.button_select_all)
+        # grid.addWidget(self.collapse_post_proc_btn, 0, 0, 1, 4, alignment=Qt.AlignRight)
+
+        self.help_post_btn = QPushButton()
+        self.help_post_btn.setIcon(icon(MDI6.help_circle, color=self.help_color))
+        self.help_post_btn.setIconSize(QSize(20, 20))
+        self.help_post_btn.clicked.connect(self.help_post)
+        self.help_post_btn.setStyleSheet(self.button_select_all)
+        self.help_post_btn.setToolTip("Help.")
+
+        title_hbox.addWidget(self.select_post_proc_btn, 5)
+        title_hbox.addWidget(QLabel(), 85, alignment=Qt.AlignCenter)
+        title_hbox.addWidget(self.help_post_btn, 5)
+        title_hbox.addWidget(self.collapse_post_proc_btn, 5)
+        grid.addLayout(title_hbox, 0, 0, 1, 4)
+
+        self.generate_post_proc_panel_contents()
+        grid.addWidget(self.ContentsPostProc, 1, 0, 1, 4, alignment=Qt.AlignTop)
+        self.collapse_post_proc_btn.clicked.connect(
+            lambda: self.ContentsPostProc.setHidden(
+                not self.ContentsPostProc.isHidden()
+            )
+        )
+        self.collapse_post_proc_btn.clicked.connect(self.collapse_post_advanced)
+        self.ContentsPostProc.hide()
+        self.uncheck_post_proc()
+
+    def collapse_post_advanced(self):
+
+        features_open = not self.ContentsFeatures.isHidden()
+        config_open = not self.ContentsConfig.isHidden()
+        post_open = not self.ContentsPostProc.isHidden()
+        is_open = np.array([features_open, config_open, post_open])
+
+        if self.ContentsPostProc.isHidden():
+            self.collapse_post_proc_btn.setIcon(icon(MDI6.chevron_down, color="black"))
+            self.collapse_post_proc_btn.setIconSize(QSize(20, 20))
+            if len(is_open[is_open]) == 0:
+                pass
+                # self._scroll_area.setMinimumHeight(int(self.minimum_height))
+                # self._adjustSize()
+        else:
+            self.collapse_post_proc_btn.setIcon(icon(MDI6.chevron_up, color="black"))
+            self.collapse_post_proc_btn.setIconSize(QSize(20, 20))
+
+    def help_post(self):
+        """
+        Helper for track post-processing strategy.
+        """
+
+        dict_path = os.sep.join(
+            [
+                get_software_location(),
+                "celldetective",
+                "gui",
+                "help",
+                "track-postprocessing.json",
+            ]
+        )
+
+        with open(dict_path) as f:
+            d = json.load(f)
+
+        suggestion = help_generic(d)
+        if isinstance(suggestion, str):
+            logger.info(f"{suggestion=}")
+            msg_box = QMessageBox()
+            msg_box.setIcon(QMessageBox.Information)
+            msg_box.setTextFormat(Qt.RichText)
+            msg_box.setText(rf"{suggestion}")
+            msg_box.setWindowTitle("Info")
+            msg_box.setStandardButtons(QMessageBox.Ok)
+            return_value = msg_box.exec()
+            if return_value == QMessageBox.Ok:
+                return None
+
+    def help_feature(self):
+        """
+        Helper for track post-processing strategy.
+        """
+
+        dict_path = os.sep.join(
+            [
+                get_software_location(),
+                "celldetective",
+                "gui",
+                "help",
+                "feature-btrack.json",
+            ]
+        )
+
+        with open(dict_path) as f:
+            d = json.load(f)
+
+        suggestion = help_generic(d)
+        if isinstance(suggestion, str):
+            logger.info(f"{suggestion=}")
+            msg_box = QMessageBox()
+            msg_box.setIcon(QMessageBox.Information)
+            msg_box.setTextFormat(Qt.RichText)
+            msg_box.setText(rf"{suggestion}")
+            msg_box.setWindowTitle("Info")
+            msg_box.setStandardButtons(QMessageBox.Ok)
+            return_value = msg_box.exec()
+            if return_value == QMessageBox.Ok:
+                return None
+
+    def populate_features_frame(self):
+        """
+        Add widgets and layout in the FEATURES frame.
+        """
+
+        grid = QGridLayout(self.features_frame)
+        title_hbox = QHBoxLayout()
+
+        self.select_features_btn = QPushButton()
+        self.select_features_btn.clicked.connect(self.activate_feature_options)
+        self.select_features_btn.setStyleSheet(self.button_select_all)
+
+        self.feature_lbl = QLabel("FEATURES")
+        self.feature_lbl.setStyleSheet(
+            """
+			font-weight: bold;
+			padding: 0px;
+			"""
+        )
+        grid.addWidget(self.feature_lbl, 0, 0, 1, 4, alignment=Qt.AlignCenter)
+
+        self.collapse_features_btn = QPushButton()
+        self.collapse_features_btn.setIcon(icon(MDI6.chevron_down, color="black"))
+        self.collapse_features_btn.setIconSize(QSize(20, 20))
+        self.collapse_features_btn.setStyleSheet(self.button_select_all)
+
+        self.help_feature_btn = QPushButton()
+        self.help_feature_btn.setIcon(icon(MDI6.help_circle, color=self.help_color))
+        self.help_feature_btn.setIconSize(QSize(20, 20))
+        self.help_feature_btn.clicked.connect(self.help_feature)
+        self.help_feature_btn.setStyleSheet(self.button_select_all)
+        self.help_feature_btn.setToolTip("Help.")
+
+        title_hbox.addWidget(self.select_features_btn, 5)
+        title_hbox.addWidget(QLabel(), 85, alignment=Qt.AlignCenter)
+        title_hbox.addWidget(self.help_feature_btn, 5)
+        title_hbox.addWidget(self.collapse_features_btn, 5)
+        grid.addLayout(title_hbox, 0, 0, 1, 4)
+
+        self.generate_feature_panel_contents()
+        grid.addWidget(self.ContentsFeatures, 1, 0, 1, 4, alignment=Qt.AlignTop)
+        self.collapse_features_btn.clicked.connect(
+            lambda: self.ContentsFeatures.setHidden(
+                not self.ContentsFeatures.isHidden()
+            )
+        )
+        self.collapse_features_btn.clicked.connect(self.collapse_features_advanced)
+        # self.ContentsFeatures.hide()
+        self.check_features()
+
+    def collapse_features_advanced(self):
+        """
+        Switch the chevron icon and adjust the size for the FEATURES frame.
+        """
+
+        features_open = not self.ContentsFeatures.isHidden()
+        config_open = not self.ContentsConfig.isHidden()
+        post_open = not self.ContentsPostProc.isHidden()
+        is_open = np.array([features_open, config_open, post_open])
+
+        if self.ContentsFeatures.isHidden():
+            self.collapse_features_btn.setIcon(icon(MDI6.chevron_down, color="black"))
+            self.collapse_features_btn.setIconSize(QSize(20, 20))
+            if len(is_open[is_open]) == 0:
+                pass
+                # self._scroll_area.setMinimumHeight(int(self.minimum_height))
+                # self._adjustSize()
+        else:
+            self.collapse_features_btn.setIcon(icon(MDI6.chevron_up, color="black"))
+            self.collapse_features_btn.setIconSize(QSize(20, 20))
+
+    def generate_post_proc_panel_contents(self):
+
+        self.ContentsPostProc = QFrame()
+        layout = QVBoxLayout(self.ContentsPostProc)
+        layout.setContentsMargins(0, 0, 0, 0)
+
+        post_proc_layout = QHBoxLayout()
+        self.post_proc_lbl = QLabel("Post processing on the tracks:")
+        post_proc_layout.addWidget(self.post_proc_lbl, 90)
+        layout.addLayout(post_proc_layout)
+
+        clean_traj_sublayout = QVBoxLayout()
+        clean_traj_sublayout.setContentsMargins(15, 15, 15, 15)
+
+        tracklength_layout = QHBoxLayout()
+        self.min_tracklength_slider = QLabeledSlider()
+        self.min_tracklength_slider.setSingleStep(1)
+        self.min_tracklength_slider.setTickInterval(1)
+        self.min_tracklength_slider.setSingleStep(1)
+        self.min_tracklength_slider.setOrientation(Qt.Horizontal)
+        self.min_tracklength_slider.setRange(
+            0, self.parent_window.parent_window.len_movie
+        )
+        self.min_tracklength_slider.setValue(0)
+        tracklength_layout.addWidget(QLabel("Min. tracklength: "), 40)
+        tracklength_layout.addWidget(self.min_tracklength_slider, 60)
+        clean_traj_sublayout.addLayout(tracklength_layout)
+
+        self.remove_not_in_first_checkbox = QCheckBox(
+            "Remove tracks that do not start at the beginning"
+        )
+        self.remove_not_in_first_checkbox.setIcon(
+            icon(MDI6.arrow_expand_right, color="k")
+        )
+        clean_traj_sublayout.addWidget(self.remove_not_in_first_checkbox)
+
+        self.remove_not_in_last_checkbox = QCheckBox(
+            "Remove tracks that do not end at the end"
+        )
+        self.remove_not_in_last_checkbox.setIcon(
+            icon(MDI6.arrow_expand_left, color="k")
+        )
+        clean_traj_sublayout.addWidget(self.remove_not_in_last_checkbox)
+
+        self.interpolate_gaps_checkbox = QCheckBox(
+            "Interpolate missed detections within tracks"
+        )
+        self.interpolate_gaps_checkbox.setIcon(
+            icon(MDI6.chart_timeline_variant_shimmer, color="k")
+        )
+        clean_traj_sublayout.addWidget(self.interpolate_gaps_checkbox)
+
+        self.extrapolate_post_checkbox = QCheckBox(
+            "Sustain last position until the end of the movie"
+        )
+        self.extrapolate_post_checkbox.setIcon(icon(MDI6.repeat, color="k"))
+
+        self.extrapolate_pre_checkbox = QCheckBox(
+            "Sustain first position from the beginning of the movie"
+        )
+        self.extrapolate_pre_checkbox.setIcon(icon(MDI6.repeat, color="k"))
+
+        clean_traj_sublayout.addWidget(self.extrapolate_post_checkbox)
+        clean_traj_sublayout.addWidget(self.extrapolate_pre_checkbox)
+
+        # self.interpolate_na_features_checkbox = QCheckBox('Interpolate features of missed detections')
+        # self.interpolate_na_features_checkbox.setIcon(icon(MDI6.format_color_fill,color="k"))
+
+        # clean_traj_sublayout.addWidget(self.interpolate_na_features_checkbox)
+        clean_traj_sublayout.addStretch()
+
+        self.post_proc_options_to_disable = [
+            self.post_proc_lbl,
+            self.min_tracklength_slider,
+            self.remove_not_in_first_checkbox,
+            self.remove_not_in_last_checkbox,
+            self.interpolate_gaps_checkbox,
+            self.extrapolate_post_checkbox,
+            self.extrapolate_pre_checkbox,
+        ]  # , self.interpolate_na_features_checkbox
+
+        layout.addLayout(clean_traj_sublayout)
+
+    def generate_feature_panel_contents(self):
+
+        self.ContentsFeatures = QFrame()
+        layout = QVBoxLayout(self.ContentsFeatures)
+        layout.setContentsMargins(0, 0, 0, 0)
+
+        feature_layout = QHBoxLayout()
+        feature_layout.setContentsMargins(0, 0, 0, 0)
+
+        self.feature_lbl = QLabel("Add features:")
+        self.del_feature_btn = QPushButton("")
+        self.del_feature_btn.setStyleSheet(self.button_select_all)
+        self.del_feature_btn.setIcon(icon(MDI6.trash_can, color="black"))
+        self.del_feature_btn.setToolTip("Remove feature")
+        self.del_feature_btn.setIconSize(QSize(20, 20))
+
+        self.add_feature_btn = QPushButton("")
+        self.add_feature_btn.setStyleSheet(self.button_select_all)
+        self.add_feature_btn.setIcon(icon(MDI6.filter_plus, color="black"))
+        self.add_feature_btn.setToolTip("Add feature")
+        self.add_feature_btn.setIconSize(QSize(20, 20))
+
+        self.features_list = ListWidget(
+            FeatureChoice,
+            initial_features=[
+                "area",
+                "intensity_mean",
+            ],
+        )
+
+        self.del_feature_btn.clicked.connect(self.features_list.removeSel)
+        self.add_feature_btn.clicked.connect(self.features_list.addItem)
+
+        feature_layout.addWidget(self.feature_lbl, 90)
+        feature_layout.addWidget(self.del_feature_btn, 5)
+        feature_layout.addWidget(self.add_feature_btn, 5)
+        layout.addLayout(feature_layout)
+        layout.addWidget(self.features_list)
+
+        self.feat_sep2 = QHSeperationLine()
+        layout.addWidget(self.feat_sep2)
+
+        self.use_channel_lbl = QLabel("Use channel:")
+        layout.addWidget(self.use_channel_lbl)
+        self.mask_channels_cb = [QCheckBox() for i in range(len(self.channels))]
+        for cb, chn in zip(self.mask_channels_cb, self.channel_names):
+            cb.setText(chn)
+            cb.setChecked(True)
+            layout.addWidget(cb)
+
+        self.feat_sep1 = QHSeperationLine()
+        layout.addWidget(self.feat_sep1)
+
+        self.activate_haralick_btn = QCheckBox("activate Haralick texture features")
+        self.activate_haralick_btn.toggled.connect(self.show_haralick_options)
+        # Haralick features parameters
+
+        self.haralick_channel_choice = QComboBox()
+        self.haralick_channel_choice.addItems(self.channel_names)
+        self.haralick_channel_lbl = QLabel("Target channel: ")
+
+        self.haralick_distance_le = QLineEdit("1")
+        self.haralick_distance_lbl = QLabel("Distance: ")
+
+        self.haralick_n_gray_levels_le = QLineEdit("256")
+        self.haralick_n_gray_levels_lbl = QLabel("# gray levels: ")
+
+        # Slider to set vmin & vmax
+        self.haralick_scale_slider = QLabeledDoubleSlider()
+        self.haralick_scale_slider.setTickInterval(0.05)
+        self.haralick_scale_slider.setSingleStep(1)
+        self.haralick_scale_slider.setOrientation(Qt.Horizontal)
+        self.haralick_scale_slider.setRange(0, 1)
+        self.haralick_scale_slider.setValue(0.5)
+        self.haralick_scale_lbl = QLabel("Scale: ")
+
+        self.haralick_percentile_min_le = QLineEdit("0.01")
+        self.haralick_percentile_max_le = QLineEdit("99.9")
+        self.haralick_normalization_mode_btn = QPushButton()
+        self.haralick_normalization_mode_btn.setStyleSheet(self.button_select_all)
+        self.haralick_normalization_mode_btn.setIcon(
+            icon(MDI6.percent_circle, color="black")
+        )
+        self.haralick_normalization_mode_btn.setIconSize(QSize(20, 20))
+        self.haralick_normalization_mode_btn.setToolTip(
+            "Switch to absolute normalization values."
+        )
+        self.percentile_mode = True
+
+        self.haralick_percentile_min_lbl = QLabel("Min percentile: ")
+        self.haralick_percentile_max_lbl = QLabel("Max percentile: ")
+
+        self.haralick_hist_btn = QPushButton()
+        self.haralick_hist_btn.clicked.connect(
+            self.control_haralick_intensity_histogram
+        )
+        self.haralick_hist_btn.setIcon(icon(MDI6.poll, color="k"))
+        self.haralick_hist_btn.setStyleSheet(self.button_select_all)
+
+        self.haralick_digit_btn = QPushButton()
+        self.haralick_digit_btn.clicked.connect(self.control_haralick_digitalization)
+        self.haralick_digit_btn.setIcon(icon(MDI6.image_check, color="k"))
+        self.haralick_digit_btn.setStyleSheet(self.button_select_all)
+
+        self.haralick_layout = QVBoxLayout()
+        self.haralick_layout.setContentsMargins(20, 20, 20, 20)
+
+        activate_layout = QHBoxLayout()
+        activate_layout.addWidget(self.activate_haralick_btn, 80)
+        activate_layout.addWidget(self.haralick_hist_btn, 10)
+        activate_layout.addWidget(self.haralick_digit_btn, 10)
+        self.haralick_layout.addLayout(activate_layout)
+
+        channel_layout = QHBoxLayout()
+        channel_layout.addWidget(self.haralick_channel_lbl, 40)
+        channel_layout.addWidget(self.haralick_channel_choice, 60)
+        self.haralick_layout.addLayout(channel_layout)
+
+        distance_layout = QHBoxLayout()
+        distance_layout.addWidget(self.haralick_distance_lbl, 40)
+        distance_layout.addWidget(self.haralick_distance_le, 60)
+        self.haralick_layout.addLayout(distance_layout)
+
+        gl_layout = QHBoxLayout()
+        gl_layout.addWidget(self.haralick_n_gray_levels_lbl, 40)
+        gl_layout.addWidget(self.haralick_n_gray_levels_le, 60)
+        self.haralick_layout.addLayout(gl_layout)
+
+        slider_layout = QHBoxLayout()
+        slider_layout.addWidget(self.haralick_scale_lbl, 40)
+        slider_layout.addWidget(self.haralick_scale_slider, 60)
+        self.haralick_layout.addLayout(slider_layout)
+
+        slider_min_percentile_layout = QHBoxLayout()
+        slider_min_percentile_layout.addWidget(self.haralick_percentile_min_lbl, 40)
+        slider_min_percentile_layout.addWidget(self.haralick_percentile_min_le, 55)
+        slider_min_percentile_layout.addWidget(self.haralick_normalization_mode_btn, 5)
+        self.haralick_layout.addLayout(slider_min_percentile_layout)
+
+        slider_max_percentile_layout = QHBoxLayout()
+        slider_max_percentile_layout.addWidget(self.haralick_percentile_max_lbl, 40)
+        slider_max_percentile_layout.addWidget(self.haralick_percentile_max_le, 60)
+        self.haralick_layout.addLayout(slider_max_percentile_layout)
+
+        self.haralick_to_hide = [
+            self.haralick_hist_btn,
+            self.haralick_digit_btn,
+            self.haralick_channel_lbl,
+            self.haralick_channel_choice,
+            self.haralick_distance_le,
+            self.haralick_distance_lbl,
+            self.haralick_n_gray_levels_le,
+            self.haralick_n_gray_levels_lbl,
+            self.haralick_scale_lbl,
+            self.haralick_scale_slider,
+            self.haralick_percentile_min_lbl,
+            self.haralick_percentile_min_le,
+            self.haralick_percentile_max_lbl,
+            self.haralick_percentile_max_le,
+            self.haralick_normalization_mode_btn,
+        ]
+        for element in self.haralick_to_hide:
+            element.hide()
+
+        self.features_to_disable = [
+            self.feature_lbl,
+            self.del_feature_btn,
+            self.add_feature_btn,
+            self.features_list,
+            self.use_channel_lbl,
+            *self.mask_channels_cb,
+            self.activate_haralick_btn,
+        ]
+
+        self.haralick_normalization_mode_btn.clicked.connect(
+            self.switch_to_absolute_normalization_mode
+        )
+        layout.addLayout(self.haralick_layout)
+
+    def switch_to_absolute_normalization_mode(self):
+        if self.percentile_mode:
+            self.percentile_mode = False
+            self.haralick_normalization_mode_btn.setIcon(
+                icon(MDI6.percent_circle_outline, color="black")
+            )
+            self.haralick_normalization_mode_btn.setIconSize(QSize(20, 20))
+            self.haralick_normalization_mode_btn.setToolTip(
+                "Switch to percentile normalization values."
+            )
+            self.haralick_percentile_min_lbl.setText("Min value: ")
+            self.haralick_percentile_max_lbl.setText("Max value: ")
+            self.haralick_percentile_min_le.setText("0")
+            self.haralick_percentile_max_le.setText("10000")
+
+        else:
+            self.percentile_mode = True
+            self.haralick_normalization_mode_btn.setIcon(
+                icon(MDI6.percent_circle, color="black")
+            )
+            self.haralick_normalization_mode_btn.setIconSize(QSize(20, 20))
+            self.haralick_normalization_mode_btn.setToolTip(
+                "Switch to absolute normalization values."
+            )
+            self.haralick_percentile_min_lbl.setText("Min percentile: ")
+            self.haralick_percentile_max_lbl.setText("Max percentile: ")
+            self.haralick_percentile_min_le.setText("0.01")
+            self.haralick_percentile_max_le.setText("99.99")
+
+    def populate_config_frame(self):
+
+        grid = QGridLayout(self.config_frame)
+        panel_title = QLabel(f"CONFIGURATION")
+        panel_title.setStyleSheet(
+            """
+			font-weight: bold;
+			padding: 0px;
+			"""
+        )
+
+        grid.addWidget(panel_title, 0, 0, 1, 4, alignment=Qt.AlignCenter)
+
+        self.collapse_config_btn = QPushButton()
+        self.collapse_config_btn.setIcon(icon(MDI6.chevron_down, color="black"))
+        self.collapse_config_btn.setIconSize(QSize(20, 20))
+        self.collapse_config_btn.setStyleSheet(self.button_select_all)
+        grid.addWidget(self.collapse_config_btn, 0, 0, 1, 4, alignment=Qt.AlignRight)
+
+        self.generate_config_panel_contents()
+        grid.addWidget(self.ContentsConfig, 1, 0, 1, 4, alignment=Qt.AlignTop)
+        self.collapse_config_btn.clicked.connect(
+            lambda: self.ContentsConfig.setHidden(not self.ContentsConfig.isHidden())
+        )
+        self.collapse_config_btn.clicked.connect(self.collapse_config_advanced)
+        # self.ContentsConfig.hide()
+
+    def populate_config_trackpy_frame(self):
+
+        grid = QGridLayout(self.config_trackpy_frame)
+        panel_title = QLabel(f"CONFIGURATION")
+        panel_title.setStyleSheet(
+            """
+			font-weight: bold;
+			padding: 0px;
+			"""
+        )
+
+        grid.addWidget(panel_title, 0, 0, 1, 4, alignment=Qt.AlignCenter)
+
+        self.collapse_config_trackpy_btn = QPushButton()
+        self.collapse_config_trackpy_btn.setIcon(icon(MDI6.chevron_down, color="black"))
+        self.collapse_config_trackpy_btn.setIconSize(QSize(20, 20))
+        self.collapse_config_trackpy_btn.setStyleSheet(self.button_select_all)
+        grid.addWidget(
+            self.collapse_config_trackpy_btn, 0, 0, 1, 4, alignment=Qt.AlignRight
+        )
+        self.generate_config_trackpy_panel_contents()
+        grid.addWidget(self.ContentsConfigTrackpy, 1, 0, 1, 4, alignment=Qt.AlignTop)
+        self.collapse_config_trackpy_btn.clicked.connect(
+            lambda: self.ContentsConfigTrackpy.setHidden(
+                not self.ContentsConfigTrackpy.isHidden()
+            )
+        )
+        self.collapse_config_trackpy_btn.clicked.connect(
+            self.collapse_config_trackpy_advanced
+        )
+        # self.ContentsConfig.hide()
+
+    def collapse_config_advanced(self):
+        """
+        Switch the chevron icon and adjust the size for the CONFIG frame.
+        """
+
+        features_open = not self.ContentsFeatures.isHidden()
+        config_open = not self.ContentsConfig.isHidden()
+        post_open = not self.ContentsPostProc.isHidden()
+        is_open = np.array([features_open, config_open, post_open])
+
+        if self.ContentsConfig.isHidden():
+            self.collapse_config_btn.setIcon(icon(MDI6.chevron_down, color="black"))
+            self.collapse_config_btn.setIconSize(QSize(20, 20))
+            if len(is_open[is_open]) == 0:
+                pass
+                # self._scroll_area.setMinimumHeight(int(self.minimum_height))
+                # self._adjustSize()
+        else:
+            self.collapse_config_btn.setIcon(icon(MDI6.chevron_up, color="black"))
+            self.collapse_config_btn.setIconSize(QSize(20, 20))
+
+    def collapse_config_trackpy_advanced(self):
+        """
+        Switch the chevron icon and adjust the size for the CONFIG frame.
+        """
+
+        post_open = not self.ContentsPostProc.isHidden()
+        is_open = np.array([post_open])
+
+        if self.ContentsConfigTrackpy.isHidden():
+            self.collapse_config_trackpy_btn.setIcon(
+                icon(MDI6.chevron_down, color="black")
+            )
+            self.collapse_config_trackpy_btn.setIconSize(QSize(20, 20))
+            if len(is_open[is_open]) == 0:
+                pass
+                # self._scroll_area.setMinimumHeight(int(self.minimum_height))
+                # self._adjustSize()
+        else:
+            self.collapse_config_trackpy_btn.setIcon(
+                icon(MDI6.chevron_up, color="black")
+            )
+            self.collapse_config_trackpy_btn.setIconSize(QSize(20, 20))
+
+    def generate_config_trackpy_panel_contents(self):
+
+        self.ContentsConfigTrackpy = QFrame()
+        layout = QVBoxLayout(self.ContentsConfigTrackpy)
+        layout.setContentsMargins(0, 0, 0, 0)
+
+        sr_layout = QHBoxLayout()
+        self.search_range_lbl = QLabel("search range [px]: ")
+        self.search_range_le = QLineEdit("30")
+        self.search_range_le.setPlaceholderText("search distance in pixels")
+        self.search_range_le.setValidator(self._floatValidator)
+        sr_layout.addWidget(self.search_range_lbl, 30)
+        sr_layout.addWidget(self.search_range_le, 70)
+        layout.addLayout(sr_layout)
+
+        memory_layout = QHBoxLayout()
+        self.memory_lbl = QLabel("memory [# frames]: ")
+        self.memory_slider = QLabeledSlider()
+        self.memory_slider.setSingleStep(1)
+        self.memory_slider.setTickInterval(1)
+        self.memory_slider.setSingleStep(1)
+        self.memory_slider.setOrientation(Qt.Horizontal)
+        self.memory_slider.setRange(0, self.parent_window.parent_window.len_movie)
+        self.memory_slider.setValue(0)
+        memory_layout.addWidget(self.memory_lbl, 30)
+        memory_layout.addWidget(self.memory_slider, 70)
+        layout.addLayout(memory_layout)
+
+    def generate_config_panel_contents(self):
+
+        self.ContentsConfig = QFrame()
+        layout = QVBoxLayout(self.ContentsConfig)
+        layout.setContentsMargins(0, 0, 0, 0)
+
+        btrack_config_layout = QHBoxLayout()
+        self.config_lbl = QLabel("bTrack configuration: ")
+        btrack_config_layout.addWidget(self.config_lbl, 90)
+
+        self.upload_btrack_config_btn = QPushButton()
+        self.upload_btrack_config_btn.setIcon(icon(MDI6.plus, color="black"))
+        self.upload_btrack_config_btn.setIconSize(QSize(20, 20))
+        self.upload_btrack_config_btn.setToolTip("Upload a new bTrack configuration.")
+        self.upload_btrack_config_btn.setStyleSheet(self.button_select_all)
+        self.upload_btrack_config_btn.clicked.connect(self.upload_btrack_config)
+        btrack_config_layout.addWidget(
+            self.upload_btrack_config_btn, 5
+        )  # 4,3,1,1, alignment=Qt.AlignLeft
+
+        self.reset_config_btn = QPushButton()
+        self.reset_config_btn.setIcon(icon(MDI6.arrow_u_right_top, color="black"))
+        self.reset_config_btn.setIconSize(QSize(20, 20))
+        self.reset_config_btn.setToolTip(
+            "Reset the configuration to the default bTrack config."
+        )
+        self.reset_config_btn.setStyleSheet(self.button_select_all)
+        self.reset_config_btn.clicked.connect(self.reset_btrack_config)
+        btrack_config_layout.addWidget(
+            self.reset_config_btn, 5
+        )  # 4,3,1,1, alignment=Qt.AlignLeft
+
+        layout.addLayout(btrack_config_layout)
+
+        self.config_le = QTextEdit()
+        self.config_le.setMinimumHeight(150)
+        # self.config_le.setStyleSheet("""
+        # 							background: #EEEDEB;
+        # 							border: 2px solid black;
+        # 							""")
+        layout.addWidget(self.config_le)
+        self.load_cell_config()
+
+    def show_haralick_options(self):
+        """
+        Show the Haralick texture options.
+        """
+
+        if self.activate_haralick_btn.isChecked():
+            for element in self.haralick_to_hide:
+                element.show()
+        else:
+            for element in self.haralick_to_hide:
+                element.hide()
+
+    def upload_btrack_config(self):
+        """
+        Upload a specific bTrack config to the experiment folder for the cell population.
+        """
+
+        self.file_dialog = QFileDialog()
+        try:
+            modelpath = (
+                os.sep.join(
+                    [self._software_path, "celldetective", "models", "tracking_configs"]
+                )
+                + os.sep
+            )
+            print("Track config path: ", modelpath)
+            self.filename = self.file_dialog.getOpenFileName(
+                None, "Load config", modelpath, "json files (*.json)"
+            )[0]
+            if self.filename != self.config_path:
+                copyfile(self.filename, self.config_path)
+            self.load_cell_config()
+        except Exception as e:
+            print(e)
+            return None
+
+    def reset_btrack_config(self):
+        """
+        Set the bTrack config to the default bTrack config.
+        """
+
+        msgBox = QMessageBox()
+        msgBox.setIcon(QMessageBox.Question)
+        msgBox.setText(
+            "You are about to revert to the default bTrack configuration? Do you want to proceed?"
+        )
+        msgBox.setWindowTitle("Confirm")
+        msgBox.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
+        returnValue = msgBox.exec()
+        if returnValue == QMessageBox.Yes:
+            config = interpret_tracking_configuration(None)
+            if config != self.config_path:
+                copyfile(config, self.config_path)
+            self.load_cell_config()
+        else:
+            return None
+
+    def activate_feature_options(self):
+        """
+        Tick the features option.
+        """
+
+        self.switch_feature_option()
+        if self.features_ticked:
+            for element in self.features_to_disable:
+                element.setEnabled(True)
+            self.select_features_btn.setIcon(icon(MDI6.checkbox_outline, color="black"))
+            self.select_features_btn.setIconSize(QSize(20, 20))
+        else:
+            for element in self.features_to_disable:
+                element.setEnabled(False)
+            self.select_features_btn.setIcon(
+                icon(MDI6.checkbox_blank_outline, color="black")
+            )
+            self.select_features_btn.setIconSize(QSize(20, 20))
+            self.features_list.list_widget.clearSelection()
+            self.activate_haralick_btn.setChecked(False)
+
+    def activate_post_proc_options(self):
+        """
+        Tick the features option.
+        """
+
+        self.switch_post_proc_option()
+        if self.post_proc_ticked:
+            for element in self.post_proc_options_to_disable:
+                element.setEnabled(True)
+            self.select_post_proc_btn.setIcon(
+                icon(MDI6.checkbox_outline, color="black")
+            )
+            self.select_post_proc_btn.setIconSize(QSize(20, 20))
+        else:
+            for element in self.post_proc_options_to_disable:
+                element.setEnabled(False)
+            self.select_post_proc_btn.setIcon(
+                icon(MDI6.checkbox_blank_outline, color="black")
+            )
+            self.select_post_proc_btn.setIconSize(QSize(20, 20))
+
+    def switch_feature_option(self):
+        """
+        Switch the feature option.
+        """
+
+        if self.features_ticked == True:
+            self.features_ticked = False
+        else:
+            self.features_ticked = True
+
+    def switch_post_proc_option(self):
+        """
+        Switch the feature option.
+        """
+
+        if self.post_proc_ticked == True:
+            self.post_proc_ticked = False
+        else:
+            self.post_proc_ticked = True
+
+    # def adjustScrollArea(self):
+    #
+    # 	"""
+    # 	Auto-adjust scroll area to fill space
+    # 	(from https://stackoverflow.com/questions/66417576/make-qscrollarea-use-all-available-space-of-qmainwindow-height-axis)
+    # 	"""
+    #
+    # 	step = 5
+    # 	while self._scroll_area.verticalScrollBar().isVisible() and self.height() < self.maximumHeight():
+    # 		self.resize(self.width(), self.height() + step)
+
+    def load_cell_config(self):
+        """
+        Load the cell configuration and write in the QLineEdit.
+        """
+
+        file_name = interpret_tracking_configuration(self.config_path)
+        with open(file_name, "r") as f:
+            json_data = json.load(f)
+            self.config_le.setText(json.dumps(json_data, indent=4))
+
+    def _write_instructions(self):
+        """
+        Write the selected options in a json file for later reading by the software.
+        """
+
+        print("Writing instructions...")
+
+        if self.btrack_option.isChecked():
+            btrack_option = True
+        else:
+            btrack_option = False
+
+        # Fetch trackpky params
+        if not btrack_option:
+            search_range = int(self.search_range_le.text().replace(",", "."))
+            memory = self.memory_slider.value()
+        else:
+            search_range = None
+            memory = None
+
+        tracking_options = {"btrack_config_path": self.config_path}
+        tracking_options.update(
+            {
+                "btrack_option": btrack_option,
+                "search_range": search_range,
+                "memory": memory,
+            }
+        )
+
+        if not self.features_ticked:
+            features = None
+            masked_channels = None
+        else:
+            features = self.features_list.getItems()
+            masked_channels = self.channel_names[
+                np.array([not cb.isChecked() for cb in self.mask_channels_cb])
+            ]
+            if len(masked_channels) == 0:
+                masked_channels = None
+            else:
+                masked_channels = list(masked_channels)
+
+        tracking_options.update(
+            {"features": features, "mask_channels": masked_channels}
+        )
+
+        self.extract_haralick_options()
+        tracking_options.update({"haralick_options": self.haralick_options})
+
+        if self.post_proc_ticked:
+            post_processing_options = {
+                "minimum_tracklength": int(self.min_tracklength_slider.value()),
+                "remove_not_in_first": self.remove_not_in_first_checkbox.isChecked(),
+                "remove_not_in_last": self.remove_not_in_last_checkbox.isChecked(),
+                "interpolate_position_gaps": self.interpolate_gaps_checkbox.isChecked(),
+                "extrapolate_tracks_pre": self.extrapolate_pre_checkbox.isChecked(),
+                "extrapolate_tracks_post": self.extrapolate_post_checkbox.isChecked(),
+                "interpolate_na": False,  # self.interpolate_na_features_checkbox.isChecked()
+            }
+        else:
+
+            post_processing_options = None
+
+        tracking_options.update({"post_processing_options": post_processing_options})
+        file_name = self.track_instructions_write_path
+        with open(file_name, "w") as f:
+            json.dump(tracking_options, f, indent=4)
+
+        # Save the JSON data to the file
+        file_name = self.config_path
+        with open(file_name, "w") as f:
+            f.write(self.config_le.toPlainText())
+        print("Done.")
+        self.close()
+
+    def uncheck_post_proc(self):
+        self.select_post_proc_btn.setIcon(
+            icon(MDI6.checkbox_blank_outline, color="black")
+        )
+        self.select_post_proc_btn.setIconSize(QSize(20, 20))
+        self.post_proc_ticked = False
+        for element in self.post_proc_options_to_disable:
+            element.setEnabled(False)
+
+    def check_post_proc(self):
+        self.select_post_proc_btn.setIcon(icon(MDI6.checkbox_outline, color="black"))
+        self.select_post_proc_btn.setIconSize(QSize(20, 20))
+        self.post_proc_ticked = True
+        for element in self.post_proc_options_to_disable:
+            element.setEnabled(True)
+
+    def uncheck_features(self):
+        self.select_features_btn.setIcon(
+            icon(MDI6.checkbox_blank_outline, color="black")
+        )
+        self.select_features_btn.setIconSize(QSize(20, 20))
+        self.features_ticked = False
+        for element in self.features_to_disable:
+            element.setEnabled(False)
+
+    def check_features(self):
+        self.select_features_btn.setIcon(icon(MDI6.checkbox_outline, color="black"))
+        self.select_features_btn.setIconSize(QSize(20, 20))
+        self.features_ticked = True
+        for element in self.features_to_disable:
+            element.setEnabled(True)
+
+    def extract_haralick_options(self):
+
+        if self.activate_haralick_btn.isChecked():
+            self.haralick_options = {
+                "target_channel": self.haralick_channel_choice.currentIndex(),
+                "scale_factor": float(self.haralick_scale_slider.value()),
+                "n_intensity_bins": int(self.haralick_n_gray_levels_le.text()),
+                "distance": int(self.haralick_distance_le.text()),
+            }
+            if self.percentile_mode:
+                self.haralick_options.update(
+                    {
+                        "percentiles": (
+                            float(self.haralick_percentile_min_le.text()),
+                            float(self.haralick_percentile_max_le.text()),
+                        ),
+                        "clip_values": None,
+                    }
+                )
+            else:
+                self.haralick_options.update(
+                    {
+                        "percentiles": None,
+                        "clip_values": (
+                            float(self.haralick_percentile_min_le.text()),
+                            float(self.haralick_percentile_max_le.text()),
+                        ),
+                    }
+                )
+
+        else:
+            self.haralick_options = None
+
+    def _load_previous_instructions(self):
+        """
+        Read the tracking options from a previously written json file.
+        """
+
+        print("Reading instructions..")
+        if os.path.exists(self.track_instructions_write_path):
+            with open(self.track_instructions_write_path, "r") as f:
+                tracking_instructions = json.load(f)
+                print(tracking_instructions)
+
+                # Features
+                features = tracking_instructions["features"]
+                if (features is not None) and len(features) > 0:
+                    self.check_features()
+                    self.ContentsFeatures.show()
+                    self.features_list.list_widget.clear()
+                    self.features_list.list_widget.addItems(features)
+                else:
+                    self.ContentsFeatures.hide()
+                    self.uncheck_features()
+
+                btrack_option = True
+                if "btrack_option" in tracking_instructions:
+                    btrack_option = tracking_instructions["btrack_option"]
+                if btrack_option:
+                    self.btrack_option.click()
+                else:
+                    self.trackpy_option.click()
+
+                if "search_range" in tracking_instructions:
+                    search_range = tracking_instructions["search_range"]
+                    if search_range is not None:
+                        self.search_range_le.setText(
+                            str(search_range).replace(".", ",")
+                        )
+                if "memory" in tracking_instructions:
+                    memory = tracking_instructions["memory"]
+                    if memory is not None:
+                        self.memory_slider.setValue(memory)
+
+                # Uncheck channels that are masked
+                mask_channels = tracking_instructions["mask_channels"]
+                if (mask_channels is not None) and len(mask_channels) > 0:
+                    for ch in mask_channels:
+                        for cb in self.mask_channels_cb:
+                            if cb.text() == ch:
+                                cb.setChecked(False)
+
+                haralick_options = tracking_instructions["haralick_options"]
+                if haralick_options is None:
+                    self.activate_haralick_btn.setChecked(False)
+                    self.show_haralick_options()
+                else:
+                    self.activate_haralick_btn.setChecked(True)
+                    self.show_haralick_options()
+                    if "target_channel" in haralick_options:
+                        idx = haralick_options["target_channel"]
+                        # idx = self.haralick_channel_choice.findText(text_to_find)
+                        self.haralick_channel_choice.setCurrentIndex(idx)
+                    if "scale_factor" in haralick_options:
+                        self.haralick_scale_slider.setValue(
+                            float(haralick_options["scale_factor"])
+                        )
+                    if ("percentiles" in haralick_options) and (
+                        haralick_options["percentiles"] is not None
+                    ):
+                        perc = list(haralick_options["percentiles"])
+                        self.haralick_percentile_min_le.setText(str(perc[0]))
+                        self.haralick_percentile_max_le.setText(str(perc[1]))
+                    if ("clip_values" in haralick_options) and (
+                        haralick_options["clip_values"] is not None
+                    ):
+                        values = list(haralick_options["clip_values"])
+                        self.haralick_percentile_min_le.setText(str(values[0]))
+                        self.haralick_percentile_max_le.setText(str(values[1]))
+                        self.percentile_mode = True
+                        self.switch_to_absolute_normalization_mode()
+                    if "n_intensity_bins" in haralick_options:
+                        self.haralick_n_gray_levels_le.setText(
+                            str(haralick_options["n_intensity_bins"])
+                        )
+                    if "distance" in haralick_options:
+                        self.haralick_distance_le.setText(
+                            str(haralick_options["distance"])
+                        )
+
+                # Post processing options
+                post_processing_options = tracking_instructions[
+                    "post_processing_options"
+                ]
+                if post_processing_options is None:
+                    self.uncheck_post_proc()
+                    self.ContentsPostProc.hide()
+                    for element in [
+                        self.remove_not_in_last_checkbox,
+                        self.remove_not_in_first_checkbox,
+                        self.interpolate_gaps_checkbox,
+                        self.extrapolate_post_checkbox,
+                        self.extrapolate_pre_checkbox,
+                    ]:  # self.interpolate_na_features_checkbox
+                        element.setChecked(False)
+                    self.min_tracklength_slider.setValue(0)
+
+                else:
+                    self.check_post_proc()
+                    self.ContentsPostProc.show()
+                    if "minimum_tracklength" in post_processing_options:
+                        self.min_tracklength_slider.setValue(
+                            int(post_processing_options["minimum_tracklength"])
+                        )
+                    if "remove_not_in_first" in post_processing_options:
+                        self.remove_not_in_first_checkbox.setChecked(
+                            post_processing_options["remove_not_in_first"]
+                        )
+                    if "remove_not_in_last" in post_processing_options:
+                        self.remove_not_in_last_checkbox.setChecked(
+                            post_processing_options["remove_not_in_last"]
+                        )
+                    if "interpolate_position_gaps" in post_processing_options:
+                        self.interpolate_gaps_checkbox.setChecked(
+                            post_processing_options["interpolate_position_gaps"]
+                        )
+                    if "extrapolate_tracks_pre" in post_processing_options:
+                        self.extrapolate_pre_checkbox.setChecked(
+                            post_processing_options["extrapolate_tracks_pre"]
+                        )
+                    if "extrapolate_tracks_post" in post_processing_options:
+                        self.extrapolate_post_checkbox.setChecked(
+                            post_processing_options["extrapolate_tracks_post"]
+                        )
+                    # if "interpolate_na" in post_processing_options:
+                    # 	self.interpolate_na_features_checkbox.setChecked(post_processing_options["interpolate_na"])
+
+    def locate_image(self):
+        """
+        Load the first frame of the first movie found in the experiment folder as a sample.
+        """
+
+        movies = glob(
+            self.parent_window.parent_window.exp_dir
+            + os.sep.join(
+                [
+                    "*",
+                    "*",
+                    "movie",
+                    self.parent_window.parent_window.movie_prefix + "*.tif",
+                ]
+            )
+        )
+        if len(movies) == 0:
+            msgBox = QMessageBox()
+            msgBox.setIcon(QMessageBox.Warning)
+            msgBox.setText(
+                "No movies are detected in the experiment folder. Cannot load an image to test Haralick."
+            )
+            msgBox.setWindowTitle("Warning")
+            msgBox.setStandardButtons(QMessageBox.Ok)
+            returnValue = msgBox.exec()
+            if returnValue == QMessageBox.Yes:
+                self.test_frame = None
+                return None
+        else:
+            stack0 = movies[0]
+            n_channels = len(self.channels)
+            self.test_frame = load_frames(
+                np.arange(n_channels), stack0, scale=None, normalize_input=False
+            )
+
+    def control_haralick_digitalization(self):
+        """
+        Load an image for the first experiment movie found.
+        Apply the Haralick parameters and check the result of the digitization (normalization + binning of intensities).
+
+        """
+
+        self.locate_image()
+        self.extract_haralick_options()
+        if self.test_frame is not None:
+            digitized_img = compute_haralick_features(
+                self.test_frame,
+                np.zeros(self.test_frame.shape[:2]),
+                channels=self.channel_names,
+                return_digit_image_only=True,
+                **self.haralick_options,
+            )
+
+            self.fig, self.ax = plt.subplots()
+            divider = make_axes_locatable(self.ax)
+            cax = divider.append_axes("right", size="5%", pad=0.05)
+
+            self.imshow_digit_window = FigureCanvas(
+                self.fig, title="Haralick: control digitization"
+            )
+            self.ax.clear()
+            im = self.ax.imshow(digitized_img, cmap="gray")
+            self.fig.colorbar(im, cax=cax, orientation="vertical")
+            self.ax.set_xticks([])
+            self.ax.set_yticks([])
+            self.fig.set_facecolor("none")  # or 'None'
+            self.fig.canvas.setStyleSheet("background-color: transparent;")
+            self.imshow_digit_window.canvas.draw()
+            self.imshow_digit_window.show()
+
+    def control_haralick_intensity_histogram(self):
+        """
+        Load an image for the first experiment movie found.
+        Apply the Haralick normalization parameters and check the normalized intensity histogram.
+
+        """
+
+        self.locate_image()
+        self.extract_haralick_options()
+        if self.test_frame is not None:
+            norm_img = compute_haralick_features(
+                self.test_frame,
+                np.zeros(self.test_frame.shape[:2]),
+                channels=self.channel_names,
+                return_norm_image_only=True,
+                **self.haralick_options,
+            )
+            self.fig, self.ax = plt.subplots(1, 1, figsize=(4, 3))
+            self.hist_window = FigureCanvas(
+                self.fig, title="Haralick: control digitized histogram"
+            )
+            self.ax.clear()
+            flat = norm_img.flatten()
+            self.ax.hist(
+                flat[flat == flat], bins=self.haralick_options["n_intensity_bins"]
+            )
+            self.ax.set_xlabel("gray level value")
+            self.ax.set_ylabel("#")
+            plt.tight_layout()
+            self.fig.set_facecolor("none")  # or 'None'
+            self.fig.canvas.setStyleSheet("background-color: transparent;")
+            self.hist_window.canvas.draw()
+            self.hist_window.show()