celldetective 1.4.2__py3-none-any.whl → 1.5.0b0__py3-none-any.whl

celldetective/gui/configure_new_exp.py

@@ -1,7 +1,21 @@
-from PyQt5.QtWidgets import QApplication,QWidget, QMessageBox, QHBoxLayout, QFileDialog, QVBoxLayout, QScrollArea, QCheckBox, QGridLayout, QLabel, QLineEdit, QPushButton
+from PyQt5.QtWidgets import (
+    QApplication,
+    QWidget,
+    QMessageBox,
+    QHBoxLayout,
+    QFileDialog,
+    QVBoxLayout,
+    QScrollArea,
+    QCheckBox,
+    QGridLayout,
+    QLabel,
+    QLineEdit,
+    QPushButton,
+)
 from PyQt5.QtGui import QIntValidator, QDoubleValidator
-from celldetective.gui.gui_utils import center_window, help_generic
-from celldetective.utils import get_software_location
+from celldetective.gui.gui_utils import help_generic
+from celldetective.gui.base.utils import center_window
+from celldetective import get_software_location
 import json
 
 from superqt import QLabeledSlider
@@ -11,682 +25,774 @@ from fonticon_mdi6 import MDI6
 from configparser import ConfigParser
 import os
 from functools import partial
+import logging
 import numpy as np
-from celldetective.gui import CelldetectiveMainWindow, CelldetectiveWidget
+from celldetective.gui.base.components import (
+    CelldetectiveMainWindow,
+    CelldetectiveWidget,
+)
+
+logger = logging.getLogger(__name__)
 
 
 class ConfigNewExperiment(CelldetectiveMainWindow):
 
-	def __init__(self, parent_window=None):
-		
-		super().__init__()
-		self.parent_window = parent_window
-		self.setWindowTitle("New experiment")
-		center_window(self)
-		self.setFixedWidth(500)
-		self.setMaximumHeight(int(0.8*self.parent_window.screen_height))
-		self.onlyFloat = QDoubleValidator()
-		
-		self.newExpFolder = str(QFileDialog.getExistingDirectory(self, 'Select directory'))
-		self.populate_widget()
-
-	def populate_widget(self):
-		
-		# Create button widget and layout
-		self.scroll_area = QScrollArea(self)
-		button_widget = CelldetectiveWidget()
-		self.grid = QGridLayout()
-		button_widget.setLayout(self.grid)
-
-		self.grid.setContentsMargins(30, 30, 30, 30)
-		self.grid.addWidget(QLabel("Folder:"), 0, 0, 1, 3)
-		self.supFolder = QLineEdit()
-		self.supFolder.setAlignment(Qt.AlignLeft)	
-		self.supFolder.setEnabled(True)
-		self.supFolder.setText(self.newExpFolder)
-		self.grid.addWidget(self.supFolder, 1, 0, 1, 1)
-
-		self.browse_button = QPushButton("Browse...")
-		self.browse_button.clicked.connect(self.browse_experiment_folder)
-		self.browse_button.setIcon(icon(MDI6.folder, color="white"))
-		self.browse_button.setStyleSheet(self.button_style_sheet)
-		#self.browse_button.setIcon(QIcon_from_svg(abs_path+f"/icons/browse.svg", color='white'))
-		self.grid.addWidget(self.browse_button, 1, 1, 1, 1)
-
-		self.grid.addWidget(QLabel("Experiment name:"), 2, 0, 1, 3)
-		
-		self.expName = QLineEdit()
-		self.expName.setPlaceholderText('folder_name_for_the_experiment')
-		self.expName.setAlignment(Qt.AlignLeft)	
-		self.expName.setEnabled(True)
-		self.expName.setFixedWidth(400)
-		self.expName.setText("Untitled_Experiment")
-		self.grid.addWidget(self.expName, 3, 0, 1, 3)
-
-		self.generate_movie_settings()
-		self.grid.addLayout(self.ms_grid, 29, 0, 1, 3)
-
-		self.generate_channel_params_box()
-		self.grid.addLayout(self.channel_grid, 30, 0, 1, 3)
-
-		self.generate_population_params_box()
-		self.grid.addLayout(self.population_grid, 31, 0, 1, 3)
-
-		self.validate_button = QPushButton("Submit")
-		self.validate_button.clicked.connect(self.create_config)
-		self.validate_button.setStyleSheet(self.button_style_sheet)
-		#self.validate_button.setIcon(QIcon_from_svg(abs_path+f"/icons/process.svg", color='white'))
-
-		self.grid.addWidget(self.validate_button, 32, 0, 1, 3, alignment = Qt.AlignBottom)		
-		button_widget.adjustSize()
-
-		self.scroll_area.setAlignment(Qt.AlignCenter)
-		self.scroll_area.setWidget(button_widget)
-		self.scroll_area.setVerticalScrollBarPolicy(Qt.ScrollBarAsNeeded)
-		self.scroll_area.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
-		self.scroll_area.setWidgetResizable(True)
-		self.setCentralWidget(self.scroll_area)
-		self.show()
-
-		QApplication.processEvents()
-		self.adjustScrollArea()
-
-	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 generate_movie_settings(self):
-		
-		"""
-		Parameters related to the movie parameters
-		"""
-
-		onlyInt = QIntValidator()
-		onlyInt.setRange(0, 100000)
-
-		self.ms_grid = QGridLayout()
-		self.ms_grid.setContentsMargins(21,30,20,30)
-
-		ms_lbl = QLabel("MOVIE SETTINGS")
-		ms_lbl.setStyleSheet("""
-			font-weight: bold;
-			""")
-		self.ms_grid.addWidget(ms_lbl, 0,0,1,3, alignment=Qt.AlignCenter)
-
-		self.number_of_wells = QLabel("Number of wells:")
-		self.ms_grid.addWidget(self.number_of_wells, 1, 0, 1, 3)
-
-		self.help_btn = QPushButton()
-		self.help_btn.setIcon(icon(MDI6.help_circle,color=self.help_color))
-		self.help_btn.setIconSize(QSize(20, 20))
-		self.help_btn.clicked.connect(self.help_structure)
-		self.help_btn.setStyleSheet(self.button_select_all)
-		self.help_btn.setToolTip("Help.")
-		self.ms_grid.addWidget(self.help_btn, 1, 0, 1, 3, alignment=Qt.AlignRight)
-
-		self.SliderWells = QLabeledSlider(Qt.Horizontal, self)
-		self.SliderWells.setMinimum(1)
-		self.SliderWells.setMaximum(512)
-		self.ms_grid.addWidget(self.SliderWells, 2, 0, 1, 3, alignment=Qt.AlignTop)
-
-		self.number_of_positions = QLabel("Number of positions per well:")
-		self.ms_grid.addWidget(self.number_of_positions, 3, 0, 1, 3)
-
-		self.SliderPos = QLabeledSlider(Qt.Horizontal, self)
-		self.SliderPos.setMinimum(1)
-		self.SliderPos.setMaximum(512)
-
-		self.ms_grid.addWidget(self.SliderPos, 4, 0, 1, 3)
-
-		self.ms_grid.addWidget(QLabel("Calibration from pixel to µm:"), 5, 0, 1, 3)
-		self.PxToUm_field = QLineEdit()
-		self.PxToUm_field.setValidator(self.onlyFloat)
-		self.PxToUm_field.setPlaceholderText('1 px = XXX µm')
-		self.PxToUm_field.setAlignment(Qt.AlignLeft)	
-		self.PxToUm_field.setEnabled(True)
-		self.PxToUm_field.setFixedWidth(400)
-		self.PxToUm_field.setText("1,0")
-		self.ms_grid.addWidget(self.PxToUm_field, 6, 0, 1, 3)
-
-		self.ms_grid.addWidget(QLabel("Calibration from frame to minutes:"), 7, 0, 1, 3)
-		self.FrameToMin_field = QLineEdit()
-		self.FrameToMin_field.setAlignment(Qt.AlignLeft)	
-		self.FrameToMin_field.setEnabled(True)
-		self.FrameToMin_field.setFixedWidth(400)
-		self.FrameToMin_field.setValidator(self.onlyFloat)
-		self.FrameToMin_field.setPlaceholderText('1 frame = XXX min')
-		self.FrameToMin_field.setText("1,0")
-		self.ms_grid.addWidget(self.FrameToMin_field, 8, 0, 1, 3)
-
-		self.movie_length = QLabel("Number of frames:")
-		self.movie_length.setToolTip('Optional: depending on how the movies are encoded, the automatic extraction of the number of frames can be difficult.\nThe software will then rely on this value.')
-		self.ms_grid.addWidget(self.movie_length,9, 0, 1, 3)
-		self.MovieLengthSlider = QLabeledSlider(Qt.Horizontal, self)
-		self.MovieLengthSlider.setMinimum(1)
-		#self.MovieLengthSlider.setMaximum(128)
-		self.ms_grid.addWidget(self.MovieLengthSlider, 10, 0, 1, 3)
-
-		self.prefix_lbl = QLabel("Prefix for the movies:")
-		self.prefix_lbl.setToolTip('The stack file name must start with this prefix to be properly loaded.')
-		self.ms_grid.addWidget(self.prefix_lbl, 11, 0, 1, 3)
-		self.movie_prefix_field = QLineEdit()
-		self.movie_prefix_field.setAlignment(Qt.AlignLeft)	
-		self.movie_prefix_field.setEnabled(True)
-		self.movie_prefix_field.setFixedWidth(400)
-		self.movie_prefix_field.setText("")
-		self.ms_grid.addWidget(self.movie_prefix_field, 12, 0, 1, 3)
-
-		self.ms_grid.addWidget(QLabel("Image width:"), 13, 0, 1, 3)
-		self.shape_x_field = QLineEdit()
-		self.shape_x_field.setValidator(onlyInt)
-		self.shape_x_field.setAlignment(Qt.AlignLeft)	
-		self.shape_x_field.setEnabled(True)
-		self.shape_x_field.setFixedWidth(400)
-		self.shape_x_field.setText("2048")
-		self.ms_grid.addWidget(self.shape_x_field, 14, 0, 1, 3)
-
-		self.ms_grid.addWidget(QLabel("Image height:"), 15, 0, 1, 3)
-		self.shape_y_field = QLineEdit()
-		self.shape_y_field.setValidator(onlyInt)
-		self.shape_y_field.setAlignment(Qt.AlignLeft)	
-		self.shape_y_field.setEnabled(True)
-		self.shape_y_field.setFixedWidth(400)
-		self.shape_y_field.setText("2048")
-		self.ms_grid.addWidget(self.shape_y_field, 16, 0, 1, 3)
-
-	def help_structure(self):
-
-		"""
-		Helper to choose an experiment structure.
-		"""
-
-		dict_path = os.sep.join([get_software_location(),'celldetective','gui','help','exp-structure.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(suggestion+"\nSee <a href='https://celldetective.readthedocs.io/en/latest/get-started.html#data-organization'>the docs</a> for more information.")
-			msgBox.setWindowTitle("Info")
-			msgBox.setStandardButtons(QMessageBox.Ok)
-			returnValue = msgBox.exec()
-			if returnValue == QMessageBox.Ok:
-				return None		
-
-	def generate_channel_params_box(self):
-
-		"""
-		Parameters related to the movie channels
-		Rewrite all of it
-
-		"""
-
-		self.channel_grid = QGridLayout()
-		self.channel_grid.setContentsMargins(21,30,20,30)
-
-		channel_lbl = QLabel("CHANNELS")
-		channel_lbl.setStyleSheet("""
-			font-weight: bold;
-			""")
-		self.channel_grid.addWidget(channel_lbl, 0,0,1,3, alignment=Qt.AlignCenter)
-
-
-		self.channels = ['brightfield', "live nuclei channel\n(Hoechst, NucSpot®)", "dead nuclei channel\n(PI)", "effector fluorescence\n(CFSE)",
-						"adhesion\n(RICM, IRM)", "fluorescence miscellaneous 1\n(LAMP-1, Actin...)", "fluorescence miscellaneous 2\n(LAMP-1, Actin...)"]
-		self.channel_mapping = ['brightfield_channel', 'live_nuclei_channel', 'dead_nuclei_channel', 'effector_fluo_channel',
-								'adhesion_channel', 'fluo_channel_1', 'fluo_channel_2']
-		self.checkBoxes = [QCheckBox() for i in range(len(self.channels))]
-		self.sliders = [QLabeledSlider(Qt.Orientation.Horizontal) for i in range(len(self.channels))]
-
-		for i in range(len(self.channels)):
-
-			self.checkBoxes[i].setText(self.channels[i])
-			self.checkBoxes[i].toggled.connect(partial(self.show_slider, i))
-
-			self.channel_grid.addWidget(self.checkBoxes[i], i+1, 0, 1, 1)
-
-			self.sliders[i].setMinimum(0)
-			self.sliders[i].setMaximum(len(self.channels))
-			self.sliders[i].setEnabled(False)
-
-			self.channel_grid.addWidget(self.sliders[i], i+1, 1, 1, 2, alignment = Qt.AlignRight)
-
-		# Add channel button
-		self.addChannelBtn = QPushButton('Add channel')
-		self.addChannelBtn.setIcon(icon(MDI6.plus,color="white"))
-		self.addChannelBtn.setIconSize(QSize(25, 25))
-		self.addChannelBtn.setStyleSheet(self.button_style_sheet)
-		self.addChannelBtn.clicked.connect(self.add_custom_channel)
-		self.channel_grid.addWidget(self.addChannelBtn, 1000, 0, 1, 1)
-
-	def add_custom_channel(self):
-
-		self.CustomChannelWidget = CelldetectiveWidget()
-		self.CustomChannelWidget.setWindowTitle("Custom channel")
-		layout = QVBoxLayout()
-		self.CustomChannelWidget.setLayout(layout)
-
-		self.name_le = QLineEdit('custom_channel')
-		hbox = QHBoxLayout()
-		hbox.addWidget(QLabel('channel name: '), 33)
-		hbox.addWidget(self.name_le, 66)
-		layout.addLayout(hbox)
-
-		self.createBtn = QPushButton('create')
-		self.createBtn.setStyleSheet(self.button_style_sheet)
-		self.createBtn.clicked.connect(self.write_custom_channel)
-		layout.addWidget(self.createBtn)
-		center_window(self.CustomChannelWidget)
-		self.CustomChannelWidget.show()
-
-		print('new channel added')
-
-	def write_custom_channel(self):
-		
-		self.new_channel_name = self.name_le.text()
-		name_map = self.new_channel_name
-		name_map = name_map.replace('_channel','')
-		name_map = name_map.replace('channel','')
-		name_map = name_map.replace(' ','')
-		if not name_map.endswith('_channel'):
-			name_map += '_channel'
-
-		self.channels.append(self.new_channel_name)
-		self.channel_mapping.append(name_map)
-		self.checkBoxes.append(QCheckBox())
-		self.sliders.append(QLabeledSlider(Qt.Orientation.Horizontal))
-		self.CustomChannelWidget.close()
-
-		self.checkBoxes[-1].setText(self.channels[-1])
-		self.checkBoxes[-1].toggled.connect(partial(self.show_slider, len(self.channels)-1))
-		self.channel_grid.addWidget(self.checkBoxes[-1], len(self.channels)+1, 0, 1, 1)
-
-		self.sliders[-1].setMinimum(0)
-		for i in range(len(self.channels)):
-			self.sliders[i].setMaximum(len(self.channels))
-		self.sliders[-1].setEnabled(False)
-		self.channel_grid.addWidget(self.sliders[-1], len(self.channels)+1, 1, 1, 2, alignment = Qt.AlignRight)
-
-	def show_slider(self, index):
-		if self.checkBoxes[index].isChecked():
-			self.sliders[index].setEnabled(True)
-		else:
-			self.sliders[index].setEnabled(False)
-
-	def generate_population_params_box(self):
-
-		"""
-		Parameters related to the movie channels
-		Rewrite all of it
-
-		"""
-
-		self.population_grid = QGridLayout()
-		self.population_grid.setContentsMargins(21,30,20,30)
-
-		pop_lbl = QLabel("CELL POPULATIONS")
-		pop_lbl.setStyleSheet("""
-			font-weight: bold;
-			""")
-		self.population_grid.addWidget(pop_lbl, 0,0,1,3, alignment=Qt.AlignCenter)
-
-
-		self.populations = ['effectors','targets']
-		self.population_checkboxes = [QCheckBox() for i in range(len(self.populations))]
-
-		for i in range(len(self.populations)):
-
-			self.population_checkboxes[i].setText(self.populations[i])
-			self.population_checkboxes[i].setChecked(True)
-			self.population_grid.addWidget(self.population_checkboxes[i], i+1, 0, 1, 1)
-
-		# Add channel button
-		self.addPopBtn = QPushButton('Add a cell population')
-		self.addPopBtn.setIcon(icon(MDI6.plus,color="white"))
-		self.addPopBtn.setIconSize(QSize(25, 25))
-		self.addPopBtn.setStyleSheet(self.button_style_sheet)
-		self.addPopBtn.clicked.connect(self.add_custom_population)
-		self.population_grid.addWidget(self.addPopBtn, 1000, 0, 1, 1)
-
-
-	def add_custom_population(self):
-		self.CustomPopWidget = CelldetectiveWidget()
-		self.CustomPopWidget.setWindowTitle("Define custom population")
-		layout = QVBoxLayout()
-		self.CustomPopWidget.setLayout(layout)
-
-		self.name_le = QLineEdit()
-		self.name_le.setPlaceholderText('name')
-		self.name_le.textChanged.connect(self.check_population_name)
-		hbox = QHBoxLayout()
-		hbox.addWidget(QLabel('population name: '), 33)
-		hbox.addWidget(self.name_le, 66)
-		layout.addLayout(hbox)
-
-		self.addPopBtn = QPushButton('add')
-		self.addPopBtn.setStyleSheet(self.button_style_sheet)
-		self.addPopBtn.setEnabled(False)
-		self.addPopBtn.clicked.connect(self.write_custom_population)
-		layout.addWidget(self.addPopBtn)
-		center_window(self.CustomPopWidget)
-		self.CustomPopWidget.show()
-
-	def check_population_name(self, text):
-		# define all conditions for valid population name (like no space)
-		if len(text)>0 and ' ' not in text:
-			self.addPopBtn.setEnabled(True)
-		else:
-			self.addPopBtn.setEnabled(False)
-
-	def write_custom_population(self):
-
-		self.new_population_name = self.name_le.text()
-		name_map = self.new_population_name
-
-		self.populations.append(self.new_population_name)
-		self.population_checkboxes.append(QCheckBox())
-		self.CustomPopWidget.close()
-
-		self.population_checkboxes[-1].setText(self.populations[-1])
-		self.population_grid.addWidget(self.population_checkboxes[-1], len(self.populations)+1, 0, 1, 1)
-
-	def browse_experiment_folder(self):
-
-		"""
-		Set a new base directory.
-		"""
-
-		self.newExpFolder = str(QFileDialog.getExistingDirectory(self, 'Select directory'))
-		self.supFolder.setText(self.newExpFolder)
-
-	def create_config(self):
-
-		"""
-		Create the folder tree, the config, issue a warning if the experiment folder already exists.
-		"""
-
-		channel_indices = []
-		for i in range(len(self.channels)):
-			if self.checkBoxes[i].isChecked():
-				channel_indices.append(self.sliders[i].value())
-		if not channel_indices:
-			msgBox = QMessageBox()
-			msgBox.setIcon(QMessageBox.Warning)
-			msgBox.setText("Please set at least one channel before proceeding.")
-			msgBox.setWindowTitle("Warning")
-			msgBox.setStandardButtons(QMessageBox.Ok)
-			returnValue = msgBox.exec()
-			if returnValue == QMessageBox.Ok:
-				return None
-
-		if len(channel_indices) != len(set(channel_indices)):
-			msgBox = QMessageBox()
-			msgBox.setIcon(QMessageBox.Warning)
-			msgBox.setText("Some channel indices are repeated. Please check your configuration.")
-			msgBox.setWindowTitle("Warning")
-			msgBox.setStandardButtons(QMessageBox.Ok)
-			returnValue = msgBox.exec()
-			if returnValue == QMessageBox.Ok:
-				return None
-
-		populations_checked = [self.population_checkboxes[i].isChecked() for i in range(len(self.population_checkboxes))]
-		if not np.any(populations_checked):
-			msgBox = QMessageBox()
-			msgBox.setIcon(QMessageBox.Warning)
-			msgBox.setText("Please set at least one cell population before proceeding...")
-			msgBox.setWindowTitle("Warning")
-			msgBox.setStandardButtons(QMessageBox.Ok)
-			returnValue = msgBox.exec()
-			if returnValue == QMessageBox.Ok:
-				return None
-
-		sorted_list = set(channel_indices)
-		expected_list = set(np.arange(max(sorted_list)+1))
-		print(sorted_list, expected_list, sorted_list==expected_list)
-
-		if not sorted_list==expected_list:
-			msgBox = QMessageBox()
-			msgBox.setIcon(QMessageBox.Warning)
-			msgBox.setText("There is a gap in your channel indices. Please check your configuration.")
-			msgBox.setWindowTitle("Warning")
-			msgBox.setStandardButtons(QMessageBox.Ok)
-			returnValue = msgBox.exec()
-			if returnValue == QMessageBox.Ok:
-				return None			
-		
-		try:
-			
-			folder = self.supFolder.text()
-			folder = folder.replace('\\','/')
-			folder = rf"{folder}"
-
-			name = str(self.expName.text())
-			name = name.replace(' ','')
-
-			self.directory = os.sep.join([folder,name])
-			os.mkdir(self.directory)
-			os.chdir(self.directory)
-			self.create_subfolders()
-			self.annotate_wells()
-
-		except FileExistsError:
-			msgBox = QMessageBox()
-			msgBox.setIcon(QMessageBox.Warning)
-			msgBox.setText("This experiment already exists... Please select another name.")
-			msgBox.setWindowTitle("Warning")
-			msgBox.setStandardButtons(QMessageBox.Ok)
-			returnValue = msgBox.exec()
-			if returnValue == QMessageBox.Ok:
-				return None
-
-	def create_subfolders(self):
-
-		"""
-		Create the well folders and position folders within the wells.
-		"""
-		
-		self.nbr_wells = self.SliderWells.value()
-		self.nbr_positions = self.SliderPos.value()
-		for k in range(self.nbr_wells):
-			well_name = f"W{k+1}"+os.sep
-			os.mkdir(well_name)
-			for p in range(self.nbr_positions):
-				position_name = well_name+f"{k+1}0{p}"+os.sep
-				os.mkdir(position_name)
-				os.mkdir(position_name+os.sep+"movie"+os.sep)
-
-	def annotate_wells(self):
-		self.w = SetupConditionLabels(self, self.nbr_wells)
-		self.w.show()
-
-
-	def create_config_file(self):
-
-		"""
-
-		Write all user input parameters to a configuration file associated to an experiment.
-		"""
-
-
-		config = ConfigParser(interpolation=None)
-
-		config.add_section('Populations')
-		pops = ','.join([self.populations[i].lower() for i in range(len(self.population_checkboxes)) if self.population_checkboxes[i].isChecked()])
-		config.set('Populations','populations', pops)
-
-		# add a new section and some values
-		config.add_section('MovieSettings')
-		config.set('MovieSettings', 'PxToUm', self.PxToUm_field.text().replace(',','.'))
-		config.set('MovieSettings', 'FrameToMin', self.FrameToMin_field.text().replace(',','.'))
-		config.set('MovieSettings', 'len_movie', str(self.MovieLengthSlider.value()))
-		config.set('MovieSettings', 'shape_x', self.shape_x_field.text())
-		config.set('MovieSettings', 'shape_y', self.shape_y_field.text())
-		config.set('MovieSettings', 'movie_prefix', self.movie_prefix_field.text())
-
-		config.add_section('Channels')
-		for i in range(len(self.channels)):
-			if self.checkBoxes[i].isChecked():
-				config.set('Channels', self.channel_mapping[i], str(self.sliders[i].value()))
-			else:
-				config.set('Channels', self.channel_mapping[i], "nan")
-
-		config.add_section('Labels')
-		config.set('Labels', 'cell_types', self.cell_types)
-		config.set('Labels', 'antibodies', self.antibodies)
-		config.set('Labels', 'concentrations', self.concentrations)
-		config.set('Labels', 'pharmaceutical_agents', self.pharmaceutical_agents)
-
-		config.add_section('Metadata')
-		config.set('Metadata', 'concentration_units', self.concentration_units)
-
-
-		# save to a file
-		with open('config.ini', 'w') as configfile:
-			config.write(configfile)
-
-		self.parent_window.set_experiment_path(self.directory)
-		print(f'New experiment successfully configured in folder {self.directory}...')
-		self.close()
+    def __init__(self, parent_window=None):
 
-class SetupConditionLabels(CelldetectiveWidget):
-	def __init__(self, parent_window, n_wells):
-		super().__init__()
-		self.parent_window = parent_window
-		self.n_wells = n_wells
-		self.setWindowTitle("Well conditions")
-		
-		# --- Outer layout ---
-		self.outer_layout = QVBoxLayout(self)
-		self.outer_layout.setContentsMargins(10, 10, 10, 10)
-		
-		# --- Scroll area ---
-		self.scroll = QScrollArea(self)
-		self.scroll.setWidgetResizable(True)
-		self.outer_layout.addWidget(self.scroll, stretch=1)  # takes most space
-		
-		# Container inside scroll
-		self.container = QWidget()
-		self.scroll.setWidget(self.container)
-		
-		# Content layout (scrollable part)
-		self.layout = QVBoxLayout(self.container)
-		self.layout.setContentsMargins(30, 30, 30, 30)
-		
-		self.onlyFloat = QDoubleValidator()
-		self.populate()
-		
-		self.concentration_units_le = QLineEdit('pM')
-		self.concentration_units_le.setPlaceholderText('concentration units')
-		
-		concentration_units_layout = QHBoxLayout()
-		concentration_units_layout.addWidget(QLabel('concentration\nunits: '), 5, alignment=Qt.AlignLeft)
-		concentration_units_layout.addWidget(self.concentration_units_le, 10)
-		concentration_units_layout.addWidget(QLabel(''), 85)
-		self.outer_layout.addLayout(concentration_units_layout)
-		
-		# --- Fixed button row (not scrollable) ---
-		btn_hbox = QHBoxLayout()
-		btn_hbox.setContentsMargins(0, 15, 0, 0)
-		
-		self.skip_btn = QPushButton('Skip')
-		self.skip_btn.setStyleSheet(self.button_style_sheet_2)
-		self.skip_btn.clicked.connect(self.set_default_values)
-		btn_hbox.addWidget(self.skip_btn)
-		
-		self.submit_btn = QPushButton('Submit')
-		self.submit_btn.setStyleSheet(self.button_style_sheet)
-		self.submit_btn.clicked.connect(self.set_user_values)
-		btn_hbox.addWidget(self.submit_btn)
-		
-		self.outer_layout.addLayout(btn_hbox)  # outside scroll
-		self.setMinimumWidth(int(0.6 * self.parent_window.parent_window.screen_width))
-		
-		center_window(self)
-
-	def populate(self):
-		self.cell_type_cbs = [QLineEdit() for i in range(self.n_wells)]
-		self.antibodies_cbs = [QLineEdit() for i in range(self.n_wells)]
-		self.concentrations_cbs = [QLineEdit() for i in range(self.n_wells)]
-		self.pharmaceutical_agents_cbs = [QLineEdit() for i in range(self.n_wells)]
-
-		for i in range(self.n_wells):
-			hbox = QHBoxLayout()
-			hbox.setContentsMargins(15, 5, 15, 5)
-			hbox.addWidget(QLabel(f'well {i+1}'), 5, alignment=Qt.AlignLeft)
-			hbox.addWidget(QLabel('cell type: '), 5)
-			hbox.addWidget(self.cell_type_cbs[i], 10)
-			self.cell_type_cbs[i].setPlaceholderText('e.g. T-cell, NK')
-			
-			hbox.addWidget(QLabel('antibody: '), 5)
-			hbox.addWidget(self.antibodies_cbs[i], 10)
-			self.antibodies_cbs[i].setPlaceholderText('e.g. anti-CD4')
-			
-			hbox.addWidget(QLabel('concentration: '), 5)
-			hbox.addWidget(self.concentrations_cbs[i], 10)
-			self.concentrations_cbs[i].setPlaceholderText('e.g. 100 (pM)')
-			self.concentrations_cbs[i].setValidator(self.onlyFloat)
-			
-			hbox.addWidget(QLabel('pharmaceutical agents: '), 5)
-			hbox.addWidget(self.pharmaceutical_agents_cbs[i], 10)
-			self.pharmaceutical_agents_cbs[i].setPlaceholderText('e.g. dextran')
-			
-			self.layout.addLayout(hbox)
-		
-
-	def set_default_values(self):
-		
-		for i in range(self.n_wells):
-			self.cell_type_cbs[i].setText(str(i))
-			self.antibodies_cbs[i].setText(str(i))
-			self.concentrations_cbs[i].setText(str(i))
-			self.pharmaceutical_agents_cbs[i].setText(str(i))
-		self.set_attributes()
-		self.parent_window.create_config_file()
-		self.close()
-
-	def set_user_values(self):
-		for i in range(self.n_wells):
-			if self.cell_type_cbs[i].text()=='':
-				self.cell_type_cbs[i].setText(str(i))
-			if self.antibodies_cbs[i].text()=='':
-				self.antibodies_cbs[i].setText(str(i))
-			if self.concentrations_cbs[i].text()=='':
-				self.concentrations_cbs[i].setText(str(i))
-			if self.pharmaceutical_agents_cbs[i].text()=='':
-				self.pharmaceutical_agents_cbs[i].setText(str(i))
-		self.set_attributes()
-		self.parent_window.create_config_file()
-		self.close()
-
-	def set_attributes(self):
-
-		cell_type_text = [c.text() for c in self.cell_type_cbs]
-		self.parent_window.cell_types = ','.join(cell_type_text)
-
-		antibodies_text = [c.text() for c in self.antibodies_cbs]
-		self.parent_window.antibodies = ','.join(antibodies_text)
-
-		concentrations_text = [c.text() for c in self.concentrations_cbs]
-		self.parent_window.concentrations = ','.join(concentrations_text)
-
-		pharamaceutical_text = [c.text() for c in self.pharmaceutical_agents_cbs]
-		self.parent_window.pharmaceutical_agents = ','.join(pharamaceutical_text)
-
-		self.parent_window.concentration_units = self.concentration_units_le.text()
+        super().__init__()
+        self.parent_window = parent_window
+        self.setWindowTitle("New experiment")
+        self.setFixedWidth(500)
+        self.setMaximumHeight(int(0.8 * self.parent_window.screen_height))
+        self.onlyFloat = QDoubleValidator()
+        self.newExpFolder = str(
+            QFileDialog.getExistingDirectory(self, "Select directory")
+        )
+        self.init_widgets()
+        self.add_to_layout()
+        self.connect_signals()
+        QApplication.processEvents()
+        self.adjustScrollArea()
+
+    def init_widgets(self):
+        self.scroll_area = QScrollArea(self)
+        self.grid = QGridLayout()
+
+        self.supFolder = QLineEdit()
+        self.supFolder.setAlignment(Qt.AlignLeft)
+        self.supFolder.setEnabled(True)
+        self.supFolder.setText(self.newExpFolder)
+
+        self.browse_button = QPushButton("Browse...")
+        self.browse_button.setIcon(icon(MDI6.folder, color="white"))
+        self.browse_button.setStyleSheet(self.button_style_sheet)
+
+        self.expName = QLineEdit()
+        self.expName.setPlaceholderText("folder_name_for_the_experiment")
+        self.expName.setAlignment(Qt.AlignLeft)
+        self.expName.setEnabled(True)
+        self.expName.setFixedWidth(400)
+        self.expName.setText("Untitled_Experiment")
+
+        self.generate_movie_settings()
+
+        self.validate_button = QPushButton("Submit")
+        self.validate_button.setStyleSheet(self.button_style_sheet)
+
+    def connect_signals(self):
+        self.browse_button.clicked.connect(self.browse_experiment_folder)
+        self.validate_button.clicked.connect(self.create_config)
+
+    def add_to_layout(self):
+
+        button_widget = CelldetectiveWidget()
+        button_widget.setLayout(self.grid)
+
+        self.grid.setContentsMargins(30, 30, 30, 30)
+        self.grid.addWidget(QLabel("Folder:"), 0, 0, 1, 3)
 
+        self.grid.addWidget(self.supFolder, 1, 0, 1, 1)
 
+        self.grid.addWidget(self.browse_button, 1, 1, 1, 1)
 
+        self.grid.addWidget(QLabel("Experiment name:"), 2, 0, 1, 3)
 
+        self.grid.addWidget(self.expName, 3, 0, 1, 3)
 
+        self.grid.addLayout(self.ms_grid, 29, 0, 1, 3)
+
+        self.generate_channel_params_box()
+        self.grid.addLayout(self.channel_grid, 30, 0, 1, 3)
+
+        self.generate_population_params_box()
+        self.grid.addLayout(self.population_grid, 31, 0, 1, 3)
+
+        self.grid.addWidget(self.validate_button, 32, 0, 1, 3, alignment=Qt.AlignBottom)
+        button_widget.adjustSize()
+
+        self.scroll_area.setAlignment(Qt.AlignCenter)
+        self.scroll_area.setWidget(button_widget)
+        self.scroll_area.setVerticalScrollBarPolicy(Qt.ScrollBarAsNeeded)
+        self.scroll_area.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
+        self.scroll_area.setWidgetResizable(True)
+        self.setCentralWidget(self.scroll_area)
+        self.show()
+
+    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 generate_movie_settings(self):
+        """
+        Parameters related to the movie parameters
+        """
+
+        onlyInt = QIntValidator()
+        onlyInt.setRange(0, 100000)
+
+        self.ms_grid = QGridLayout()
+        self.ms_grid.setContentsMargins(21, 30, 20, 30)
+
+        ms_lbl = QLabel("SETTINGS")
+        ms_lbl.setStyleSheet(
+            """
+			font-weight: bold;
+			"""
+        )
+        self.ms_grid.addWidget(ms_lbl, 0, 0, 1, 3, alignment=Qt.AlignCenter)
+
+        self.number_of_wells = QLabel("Number of wells:")
+        self.ms_grid.addWidget(self.number_of_wells, 1, 0, 1, 3)
+
+        self.help_btn = QPushButton()
+        self.help_btn.setIcon(icon(MDI6.help_circle, color=self.help_color))
+        self.help_btn.setIconSize(QSize(20, 20))
+        self.help_btn.clicked.connect(self.help_structure)
+        self.help_btn.setStyleSheet(self.button_select_all)
+        self.help_btn.setToolTip("Help.")
+        self.ms_grid.addWidget(self.help_btn, 1, 0, 1, 3, alignment=Qt.AlignRight)
+
+        self.SliderWells = QLabeledSlider(Qt.Horizontal, self)
+        self.SliderWells.setMinimum(1)
+        self.SliderWells.setMaximum(512)
+        self.ms_grid.addWidget(self.SliderWells, 2, 0, 1, 3, alignment=Qt.AlignTop)
+
+        self.number_of_positions = QLabel("Number of positions per well:")
+        self.ms_grid.addWidget(self.number_of_positions, 3, 0, 1, 3)
+
+        self.SliderPos = QLabeledSlider(Qt.Horizontal, self)
+        self.SliderPos.setMinimum(1)
+        self.SliderPos.setMaximum(512)
+
+        self.ms_grid.addWidget(self.SliderPos, 4, 0, 1, 3)
+
+        self.ms_grid.addWidget(QLabel("Calibration from pixel to µm:"), 5, 0, 1, 3)
+        self.PxToUm_field = QLineEdit()
+        self.PxToUm_field.setValidator(self.onlyFloat)
+        self.PxToUm_field.setPlaceholderText("1 px = XXX µm")
+        self.PxToUm_field.setAlignment(Qt.AlignLeft)
+        self.PxToUm_field.setEnabled(True)
+        self.PxToUm_field.setFixedWidth(400)
+        self.PxToUm_field.setText("1,0")
+        self.ms_grid.addWidget(self.PxToUm_field, 6, 0, 1, 3)
+
+        self.ms_grid.addWidget(QLabel("Calibration from frame to minutes:"), 7, 0, 1, 3)
+        self.FrameToMin_field = QLineEdit()
+        self.FrameToMin_field.setAlignment(Qt.AlignLeft)
+        self.FrameToMin_field.setEnabled(True)
+        self.FrameToMin_field.setFixedWidth(400)
+        self.FrameToMin_field.setValidator(self.onlyFloat)
+        self.FrameToMin_field.setPlaceholderText("1 frame = XXX min")
+        self.FrameToMin_field.setText("1,0")
+        self.ms_grid.addWidget(self.FrameToMin_field, 8, 0, 1, 3)
+
+        self.movie_length = QLabel("Number of frames:")
+        self.movie_length.setToolTip(
+            "Optional: depending on how the movies are encoded, the automatic extraction of the number of frames can be difficult.\nThe software will then rely on this value."
+        )
+        self.ms_grid.addWidget(self.movie_length, 9, 0, 1, 3)
+        self.MovieLengthSlider = QLabeledSlider(Qt.Horizontal, self)
+        self.MovieLengthSlider.setMinimum(1)
+        # self.MovieLengthSlider.setMaximum(128)
+        self.ms_grid.addWidget(self.MovieLengthSlider, 10, 0, 1, 3)
+
+        self.prefix_lbl = QLabel("Prefix for the movies:")
+        self.prefix_lbl.setToolTip(
+            "The stack file name must start with this prefix to be properly loaded."
+        )
+        self.ms_grid.addWidget(self.prefix_lbl, 11, 0, 1, 3)
+        self.movie_prefix_field = QLineEdit()
+        self.movie_prefix_field.setAlignment(Qt.AlignLeft)
+        self.movie_prefix_field.setEnabled(True)
+        self.movie_prefix_field.setFixedWidth(400)
+        self.movie_prefix_field.setText("")
+        self.ms_grid.addWidget(self.movie_prefix_field, 12, 0, 1, 3)
+
+        self.ms_grid.addWidget(QLabel("Image width:"), 13, 0, 1, 3)
+        self.shape_x_field = QLineEdit()
+        self.shape_x_field.setValidator(onlyInt)
+        self.shape_x_field.setAlignment(Qt.AlignLeft)
+        self.shape_x_field.setEnabled(True)
+        self.shape_x_field.setFixedWidth(400)
+        self.shape_x_field.setText("2048")
+        self.ms_grid.addWidget(self.shape_x_field, 14, 0, 1, 3)
+
+        self.ms_grid.addWidget(QLabel("Image height:"), 15, 0, 1, 3)
+        self.shape_y_field = QLineEdit()
+        self.shape_y_field.setValidator(onlyInt)
+        self.shape_y_field.setAlignment(Qt.AlignLeft)
+        self.shape_y_field.setEnabled(True)
+        self.shape_y_field.setFixedWidth(400)
+        self.shape_y_field.setText("2048")
+        self.ms_grid.addWidget(self.shape_y_field, 16, 0, 1, 3)
+
+    def help_structure(self):
+        """
+        Helper to choose an experiment structure.
+        """
+
+        dict_path = os.sep.join(
+            [
+                get_software_location(),
+                "celldetective",
+                "gui",
+                "help",
+                "exp-structure.json",
+            ]
+        )
+
+        with open(dict_path) as f:
+            d = json.load(f)
+
+        suggestion = help_generic(d)
+        if isinstance(suggestion, str):
+            logger.info(f"{suggestion=}")
+            msgBox = QMessageBox()
+            msgBox = QMessageBox()
+            msgBox.setIcon(QMessageBox.Information)
+            msgBox.setTextFormat(Qt.RichText)
+            msgBox.setText(
+                suggestion
+                + "\nSee <a href='https://celldetective.readthedocs.io/en/latest/get-started.html#data-organization'>the docs</a> for more information."
+            )
+            msgBox.setWindowTitle("Info")
+            msgBox.setStandardButtons(QMessageBox.Ok)
+            returnValue = msgBox.exec()
+            if returnValue == QMessageBox.Ok:
+                return None
+
+    def generate_channel_params_box(self):
+        """
+        Parameters related to the movie channels
+        Rewrite all of it
+
+        """
+
+        self.channel_grid = QGridLayout()
+        self.channel_grid.setContentsMargins(21, 30, 20, 30)
+
+        channel_lbl = QLabel("CHANNELS")
+        channel_lbl.setStyleSheet(
+            """
+			font-weight: bold;
+			"""
+        )
+        self.channel_grid.addWidget(channel_lbl, 0, 0, 1, 3, alignment=Qt.AlignCenter)
+
+        self.channels = [
+            "brightfield",
+            "live nuclei channel\n(Hoechst, NucSpot®)",
+            "dead nuclei channel\n(PI)",
+            "effector fluorescence\n(CFSE)",
+            "adhesion\n(RICM, IRM)",
+            "fluorescence miscellaneous 1\n(LAMP-1, Actin...)",
+            "fluorescence miscellaneous 2\n(LAMP-1, Actin...)",
+        ]
+        self.channel_mapping = [
+            "brightfield_channel",
+            "live_nuclei_channel",
+            "dead_nuclei_channel",
+            "effector_fluo_channel",
+            "adhesion_channel",
+            "fluo_channel_1",
+            "fluo_channel_2",
+        ]
+        self.checkBoxes = [QCheckBox() for i in range(len(self.channels))]
+        self.sliders = [
+            QLabeledSlider(Qt.Orientation.Horizontal) for i in range(len(self.channels))
+        ]
+
+        for i in range(len(self.channels)):
+
+            self.checkBoxes[i].setText(self.channels[i])
+            self.checkBoxes[i].toggled.connect(partial(self.show_slider, i))
+
+            self.channel_grid.addWidget(self.checkBoxes[i], i + 1, 0, 1, 1)
+
+            self.sliders[i].setMinimum(0)
+            self.sliders[i].setMaximum(len(self.channels))
+            self.sliders[i].setEnabled(False)
+
+            self.channel_grid.addWidget(
+                self.sliders[i], i + 1, 1, 1, 2, alignment=Qt.AlignRight
+            )
+
+        # Add channel button
+        self.addChannelBtn = QPushButton("Add channel")
+        self.addChannelBtn.setIcon(icon(MDI6.plus, color="white"))
+        self.addChannelBtn.setIconSize(QSize(25, 25))
+        self.addChannelBtn.setStyleSheet(self.button_style_sheet)
+        self.addChannelBtn.clicked.connect(self.add_custom_channel)
+        self.channel_grid.addWidget(self.addChannelBtn, 1000, 0, 1, 1)
+
+    def add_custom_channel(self):
+
+        self.CustomChannelWidget = CelldetectiveWidget()
+        self.CustomChannelWidget.setWindowTitle("Custom channel")
+        layout = QVBoxLayout()
+        self.CustomChannelWidget.setLayout(layout)
+
+        self.name_le = QLineEdit("custom_channel")
+        hbox = QHBoxLayout()
+        hbox.addWidget(QLabel("channel name: "), 33)
+        hbox.addWidget(self.name_le, 66)
+        layout.addLayout(hbox)
+
+        self.createBtn = QPushButton("create")
+        self.createBtn.setStyleSheet(self.button_style_sheet)
+        self.createBtn.clicked.connect(self.write_custom_channel)
+        layout.addWidget(self.createBtn)
+        center_window(self.CustomChannelWidget)
+        self.CustomChannelWidget.show()
+        logger.info("new channel added")
+
+    def write_custom_channel(self):
+
+        self.new_channel_name = self.name_le.text()
+        name_map = self.new_channel_name
+        name_map = name_map.replace("_channel", "")
+        name_map = name_map.replace("channel", "")
+        name_map = name_map.replace(" ", "")
+        if not name_map.endswith("_channel"):
+            name_map += "_channel"
+
+        self.channels.append(self.new_channel_name)
+        self.channel_mapping.append(name_map)
+        self.checkBoxes.append(QCheckBox())
+        self.sliders.append(QLabeledSlider(Qt.Orientation.Horizontal))
+        self.CustomChannelWidget.close()
+
+        self.checkBoxes[-1].setText(self.channels[-1])
+        self.checkBoxes[-1].toggled.connect(
+            partial(self.show_slider, len(self.channels) - 1)
+        )
+        self.channel_grid.addWidget(
+            self.checkBoxes[-1], len(self.channels) + 1, 0, 1, 1
+        )
+
+        self.sliders[-1].setMinimum(0)
+        for i in range(len(self.channels)):
+            self.sliders[i].setMaximum(len(self.channels))
+        self.sliders[-1].setEnabled(False)
+        self.channel_grid.addWidget(
+            self.sliders[-1], len(self.channels) + 1, 1, 1, 2, alignment=Qt.AlignRight
+        )
+
+    def show_slider(self, index):
+        if self.checkBoxes[index].isChecked():
+            self.sliders[index].setEnabled(True)
+        else:
+            self.sliders[index].setEnabled(False)
+
+    def generate_population_params_box(self):
+        """
+        Parameters related to the movie channels
+        Rewrite all of it
+
+        """
+
+        self.population_grid = QGridLayout()
+        self.population_grid.setContentsMargins(21, 30, 20, 30)
+
+        pop_lbl = QLabel("CELL POPULATIONS")
+        pop_lbl.setStyleSheet(
+            """
+			font-weight: bold;
+			"""
+        )
+        self.population_grid.addWidget(pop_lbl, 0, 0, 1, 3, alignment=Qt.AlignCenter)
+
+        self.populations = ["effectors", "targets"]
+        self.population_checkboxes = [QCheckBox() for i in range(len(self.populations))]
+
+        for i in range(len(self.populations)):
+
+            self.population_checkboxes[i].setText(self.populations[i])
+            self.population_checkboxes[i].setChecked(True)
+            self.population_grid.addWidget(
+                self.population_checkboxes[i], i + 1, 0, 1, 1
+            )
+
+        # Add channel button
+        self.addPopBtn = QPushButton("Add a cell population")
+        self.addPopBtn.setIcon(icon(MDI6.plus, color="white"))
+        self.addPopBtn.setIconSize(QSize(25, 25))
+        self.addPopBtn.setStyleSheet(self.button_style_sheet)
+        self.addPopBtn.clicked.connect(self.add_custom_population)
+        self.population_grid.addWidget(self.addPopBtn, 1000, 0, 1, 1)
+
+    def add_custom_population(self):
+        self.CustomPopWidget = CelldetectiveWidget()
+        self.CustomPopWidget.setWindowTitle("Define custom population")
+        layout = QVBoxLayout()
+        self.CustomPopWidget.setLayout(layout)
+
+        self.name_le = QLineEdit()
+        self.name_le.setPlaceholderText("name")
+        self.name_le.textChanged.connect(self.check_population_name)
+        hbox = QHBoxLayout()
+        hbox.addWidget(QLabel("population name: "), 33)
+        hbox.addWidget(self.name_le, 66)
+        layout.addLayout(hbox)
+
+        self.addPopBtn = QPushButton("add")
+        self.addPopBtn.setStyleSheet(self.button_style_sheet)
+        self.addPopBtn.setEnabled(False)
+        self.addPopBtn.clicked.connect(self.write_custom_population)
+        layout.addWidget(self.addPopBtn)
+        center_window(self.CustomPopWidget)
+        self.CustomPopWidget.show()
+
+    def check_population_name(self, text):
+        # define all conditions for valid population name (like no space)
+        if len(text) > 0 and " " not in text:
+            self.addPopBtn.setEnabled(True)
+        else:
+            self.addPopBtn.setEnabled(False)
+
+    def write_custom_population(self):
+
+        self.new_population_name = self.name_le.text()
+        name_map = self.new_population_name
+
+        self.populations.append(self.new_population_name)
+        self.population_checkboxes.append(QCheckBox())
+        self.CustomPopWidget.close()
+
+        self.population_checkboxes[-1].setText(self.populations[-1])
+        self.population_grid.addWidget(
+            self.population_checkboxes[-1], len(self.populations) + 1, 0, 1, 1
+        )
+
+    def browse_experiment_folder(self):
+        """
+        Set a new base directory.
+        """
+
+        self.newExpFolder = str(
+            QFileDialog.getExistingDirectory(self, "Select directory")
+        )
+        self.supFolder.setText(self.newExpFolder)
+
+    def create_config(self):
+        """
+        Create the folder tree, the config, issue a warning if the experiment folder already exists.
+        """
+
+        if not os.path.exists(self.supFolder.text()):
+            msgBox = QMessageBox()
+            msgBox.setIcon(QMessageBox.Critical)
+            msgBox.setText(
+                "The target path for the experiment project does not exist... Abort."
+            )
+            msgBox.setWindowTitle("Error")
+            msgBox.setStandardButtons(QMessageBox.Ok)
+            msgBox.exec()
+            return None
+
+        channel_indices = []
+        for i in range(len(self.channels)):
+            if self.checkBoxes[i].isChecked():
+                channel_indices.append(self.sliders[i].value())
+        if not channel_indices:
+            msgBox = QMessageBox()
+            msgBox.setIcon(QMessageBox.Warning)
+            msgBox.setText("Please set at least one channel before proceeding.")
+            msgBox.setWindowTitle("Warning")
+            msgBox.setStandardButtons(QMessageBox.Ok)
+            returnValue = msgBox.exec()
+            if returnValue == QMessageBox.Ok:
+                return None
+
+        if len(channel_indices) != len(set(channel_indices)):
+            msgBox = QMessageBox()
+            msgBox.setIcon(QMessageBox.Warning)
+            msgBox.setText(
+                "Some channel indices are repeated. Please check your configuration."
+            )
+            msgBox.setWindowTitle("Warning")
+            msgBox.setStandardButtons(QMessageBox.Ok)
+            returnValue = msgBox.exec()
+            if returnValue == QMessageBox.Ok:
+                return None
+
+        populations_checked = [
+            self.population_checkboxes[i].isChecked()
+            for i in range(len(self.population_checkboxes))
+        ]
+        if not np.any(populations_checked):
+            msgBox = QMessageBox()
+            msgBox.setIcon(QMessageBox.Warning)
+            msgBox.setText(
+                "Please set at least one cell population before proceeding..."
+            )
+            msgBox.setWindowTitle("Warning")
+            msgBox.setStandardButtons(QMessageBox.Ok)
+            returnValue = msgBox.exec()
+            if returnValue == QMessageBox.Ok:
+                return None
+
+        sorted_list = set(channel_indices)
+        expected_list = set(np.arange(max(sorted_list) + 1))
+        logger.debug(f"{sorted_list} {expected_list} {sorted_list==expected_list}")
+
+        if not sorted_list == expected_list:
+            msgBox = QMessageBox()
+            msgBox.setIcon(QMessageBox.Warning)
+            msgBox.setText(
+                "There is a gap in your channel indices. Please check your configuration."
+            )
+            msgBox.setWindowTitle("Warning")
+            msgBox.setStandardButtons(QMessageBox.Ok)
+            returnValue = msgBox.exec()
+            if returnValue == QMessageBox.Ok:
+                return None
+
+        try:
+
+            folder = self.supFolder.text()
+            folder = folder.replace("\\", "/")
+            folder = rf"{folder}"
+
+            name = str(self.expName.text())
+            name = name.replace(" ", "")
+
+            self.directory = "/".join([folder, name])
+            os.mkdir(self.directory)
+            os.chdir(self.directory)
+            self.create_subfolders()
+            self.annotate_wells()
+
+        except FileExistsError:
+            msgBox = QMessageBox()
+            msgBox.setIcon(QMessageBox.Warning)
+            msgBox.setText(
+                "This experiment already exists... Please select another name."
+            )
+            msgBox.setWindowTitle("Warning")
+            msgBox.setStandardButtons(QMessageBox.Ok)
+            returnValue = msgBox.exec()
+            if returnValue == QMessageBox.Ok:
+                return None
+
+    def create_subfolders(self):
+        """
+        Create the well folders and position folders within the wells.
+        """
+
+        self.nbr_wells = self.SliderWells.value()
+        self.nbr_positions = self.SliderPos.value()
+        for k in range(self.nbr_wells):
+            well_name = f"W{k+1}" + os.sep
+            os.mkdir(well_name)
+            for p in range(self.nbr_positions):
+                position_name = well_name + f"{k+1}0{p}" + os.sep
+                os.mkdir(position_name)
+                os.mkdir(position_name + os.sep + "movie" + os.sep)
+
+    def annotate_wells(self):
+        self.w = SetupConditionLabels(self, self.nbr_wells)
+        self.w.show()
+
+    def create_config_file(self):
+        """
+
+        Write all user input parameters to a configuration file associated to an experiment.
+        """
+
+        config = ConfigParser(interpolation=None)
+
+        config.add_section("Populations")
+        pops = ",".join(
+            [
+                self.populations[i].lower()
+                for i in range(len(self.population_checkboxes))
+                if self.population_checkboxes[i].isChecked()
+            ]
+        )
+        config.set("Populations", "populations", pops)
+
+        # add a new section and some values
+        config.add_section("MovieSettings")
+        config.set(
+            "MovieSettings", "PxToUm", self.PxToUm_field.text().replace(",", ".")
+        )
+        config.set(
+            "MovieSettings",
+            "FrameToMin",
+            self.FrameToMin_field.text().replace(",", "."),
+        )
+        config.set("MovieSettings", "len_movie", str(self.MovieLengthSlider.value()))
+        config.set("MovieSettings", "shape_x", self.shape_x_field.text())
+        config.set("MovieSettings", "shape_y", self.shape_y_field.text())
+        config.set("MovieSettings", "movie_prefix", self.movie_prefix_field.text())
+
+        config.add_section("Channels")
+        for i in range(len(self.channels)):
+            if self.checkBoxes[i].isChecked():
+                config.set(
+                    "Channels", self.channel_mapping[i], str(self.sliders[i].value())
+                )
+            else:
+                config.set("Channels", self.channel_mapping[i], "nan")
+
+        config.add_section("Labels")
+        config.set("Labels", "cell_types", self.cell_types)
+        config.set("Labels", "antibodies", self.antibodies)
+        config.set("Labels", "concentrations", self.concentrations)
+        config.set("Labels", "pharmaceutical_agents", self.pharmaceutical_agents)
+
+        config.add_section("Metadata")
+        config.set("Metadata", "concentration_units", self.concentration_units)
+
+        # save to a file
+        with open("config.ini", "w") as configfile:
+            config.write(configfile)
+
+        self.parent_window.set_experiment_path(self.directory)
+        logger.info(
+            f"New experiment successfully configured in folder {self.directory}..."
+        )
+        self.close()
+
+
+class SetupConditionLabels(CelldetectiveWidget):
+    def __init__(self, parent_window, n_wells):
+        super().__init__()
+        self.parent_window = parent_window
+        self.n_wells = n_wells
+        self.setWindowTitle("Well conditions")
+
+        # --- Outer layout ---
+        self.outer_layout = QVBoxLayout(self)
+        self.outer_layout.setContentsMargins(10, 10, 10, 10)
+
+        # --- Scroll area ---
+        self.scroll = QScrollArea(self)
+        self.scroll.setWidgetResizable(True)
+        self.outer_layout.addWidget(self.scroll, stretch=1)  # takes most space
+
+        # Container inside scroll
+        self.container = QWidget()
+        self.scroll.setWidget(self.container)
+
+        # Content layout (scrollable part)
+        self.layout = QVBoxLayout(self.container)
+        self.layout.setContentsMargins(30, 30, 30, 30)
+
+        self.onlyFloat = QDoubleValidator()
+        self.populate()
+
+        self.concentration_units_le = QLineEdit("pM")
+        self.concentration_units_le.setPlaceholderText("concentration units")
+        self.concentration_units_le.textChanged.connect(self.update_placeholders)
+
+        concentration_units_layout = QHBoxLayout()
+        concentration_units_layout.addWidget(
+            QLabel("concentration\nunits: "), 5, alignment=Qt.AlignLeft
+        )
+        concentration_units_layout.addWidget(self.concentration_units_le, 10)
+        concentration_units_layout.addWidget(QLabel(""), 85)
+        self.outer_layout.addLayout(concentration_units_layout)
+
+        # --- Fixed button row (not scrollable) ---
+        btn_hbox = QHBoxLayout()
+        btn_hbox.setContentsMargins(0, 15, 0, 0)
+
+        self.skip_btn = QPushButton("Skip")
+        self.skip_btn.setStyleSheet(self.button_style_sheet_2)
+        self.skip_btn.clicked.connect(self.set_default_values)
+        btn_hbox.addWidget(self.skip_btn)
+
+        self.submit_btn = QPushButton("Submit")
+        self.submit_btn.setStyleSheet(self.button_style_sheet)
+        self.submit_btn.clicked.connect(self.set_user_values)
+        btn_hbox.addWidget(self.submit_btn)
+
+        self.outer_layout.addLayout(btn_hbox)  # outside scroll
+        self.setMinimumWidth(int(0.6 * self.parent_window.parent_window.screen_width))
+
+        center_window(self)
+
+    def populate(self):
+        self.cell_type_cbs = [QLineEdit() for i in range(self.n_wells)]
+        self.antibodies_cbs = [QLineEdit() for i in range(self.n_wells)]
+        self.concentrations_cbs = [QLineEdit() for i in range(self.n_wells)]
+        self.pharmaceutical_agents_cbs = [QLineEdit() for i in range(self.n_wells)]
+
+        for i in range(self.n_wells):
+            hbox = QHBoxLayout()
+            hbox.setContentsMargins(15, 5, 15, 5)
+            hbox.addWidget(QLabel(f"well {i+1}"), 5, alignment=Qt.AlignLeft)
+            hbox.addWidget(QLabel("cell type: "), 5)
+            hbox.addWidget(self.cell_type_cbs[i], 10)
+            self.cell_type_cbs[i].setPlaceholderText("e.g. T-cell, NK")
+
+            hbox.addWidget(QLabel("antibody: "), 5)
+            hbox.addWidget(self.antibodies_cbs[i], 10)
+            self.antibodies_cbs[i].setPlaceholderText("e.g. anti-CD4")
+
+            hbox.addWidget(QLabel("concentration: "), 5)
+            hbox.addWidget(self.concentrations_cbs[i], 10)
+            self.concentrations_cbs[i].setPlaceholderText("e.g. 100 (pM)")
+            self.concentrations_cbs[i].setValidator(self.onlyFloat)
+
+            hbox.addWidget(QLabel("pharmaceutical agents: "), 5)
+            hbox.addWidget(self.pharmaceutical_agents_cbs[i], 10)
+            self.pharmaceutical_agents_cbs[i].setPlaceholderText("e.g. dextran")
+
+            self.layout.addLayout(hbox)
+
+    def update_placeholders(self, new_unit):
+        for le in self.concentrations_cbs:
+            le.setPlaceholderText(f"e.g. 100 ({new_unit})")
+
+    def set_default_values(self):
+
+        for i in range(self.n_wells):
+            self.cell_type_cbs[i].setText(str(i))
+            self.antibodies_cbs[i].setText(str(i))
+            self.concentrations_cbs[i].setText(str(i))
+            self.pharmaceutical_agents_cbs[i].setText(str(i))
+        self.set_attributes()
+        self.parent_window.create_config_file()
+        self.close()
+
+    def set_user_values(self):
+        for i in range(self.n_wells):
+            if self.cell_type_cbs[i].text() == "":
+                self.cell_type_cbs[i].setText(str(i))
+            if self.antibodies_cbs[i].text() == "":
+                self.antibodies_cbs[i].setText(str(i))
+            if self.concentrations_cbs[i].text() == "":
+                self.concentrations_cbs[i].setText(str(i))
+            if self.pharmaceutical_agents_cbs[i].text() == "":
+                self.pharmaceutical_agents_cbs[i].setText(str(i))
+        self.set_attributes()
+        self.parent_window.create_config_file()
+        self.close()
+
+    def set_attributes(self):
+
+        cell_type_text = [c.text() for c in self.cell_type_cbs]
+        self.parent_window.cell_types = ",".join(cell_type_text)
+
+        antibodies_text = [c.text() for c in self.antibodies_cbs]
+        self.parent_window.antibodies = ",".join(antibodies_text)
+
+        concentrations_text = [c.text() for c in self.concentrations_cbs]
+        self.parent_window.concentrations = ",".join(concentrations_text)
+
+        pharamaceutical_text = [c.text() for c in self.pharmaceutical_agents_cbs]
+        self.parent_window.pharmaceutical_agents = ",".join(pharamaceutical_text)
+
+        self.parent_window.concentration_units = self.concentration_units_le.text()