celldetective 1.3.9.post4__py3-none-any.whl → 1.4.0__py3-none-any.whl

celldetective/gui/processes/segment_cells.py

@@ -47,11 +47,7 @@ class BaseSegmentProcess(Process):
 	def write_folders(self):
 
 		self.mode = self.mode.lower()
-
-		if self.mode=="target" or self.mode=="targets":
-			self.label_folder = "labels_targets"
-		elif self.mode=="effector" or self.mode=="effectors":
-			self.label_folder = "labels_effectors"
+		self.label_folder = f"labels_{self.mode}"
 
 		if os.path.exists(self.pos+self.label_folder):
 			print('Erasing the previous labels folder...')
@@ -123,6 +119,14 @@ class SegmentCellDLProcess(BaseSegmentProcess):
 	def extract_model_input_parameters(self):
 
 		self.required_channels = self.input_config["channels"]
+		if 'selected_channels' in self.input_config:
+			self.required_channels = self.input_config['selected_channels']
+		
+		self.target_cell_size = None
+		if 'target_cell_size_um' in self.input_config and 'cell_size_um' in self.input_config:
+			self.target_cell_size = self.input_config['target_cell_size_um']
+			self.cell_size = self.input_config['cell_size_um']
+
 		self.normalize_kwargs = _get_normalize_kwargs_from_config(self.input_config)
 
 		self.model_type = self.input_config['model_type']
@@ -152,6 +156,14 @@ class SegmentCellDLProcess(BaseSegmentProcess):
 		self.scale = _estimate_scale_factor(self.spatial_calibration, self.required_spatial_calibration)
 		print(f"Scale: {self.scale}...")
 
+		if self.target_cell_size is not None and self.scale is not None:
+			self.scale *= self.cell_size / self.target_cell_size
+		elif self.target_cell_size is not None:
+			if self.target_cell_size != self.cell_size:
+				self.scale = self.cell_size / self.target_cell_size
+
+		print(f"Scale accounting for expected cell size: {self.scale}...")
+
 	def locate_model_path(self):
 
 		self.model_complete_path = locate_segmentation_model(self.model_name)
@@ -183,7 +195,11 @@ class SegmentCellDLProcess(BaseSegmentProcess):
 			elif self.model_type=='cellpose':
 				model, scale_model = _prep_cellpose_model(self.model_name, self.model_complete_path, use_gpu=self.use_gpu, n_channels=len(self.required_channels), scale=self.scale)
 
-			for t in tqdm(range(self.len_movie),desc="frame"):
+			list_indices = range(self.len_movie)
+			if self.flip:
+				list_indices = reversed(list_indices)
+
+			for t in tqdm(list_indices,desc="frame"):
 				
 				f = _load_frames_to_segment(self.file, self.img_num_channels[:,t], scale_model=scale_model, normalize_kwargs=self.normalize_kwargs)
 
@@ -219,6 +235,7 @@ class SegmentCellDLProcess(BaseSegmentProcess):
 			pass		
 		
 		gc.collect()
+		print("Done.")
 
 		# Send end signal
 		self.queue.put("finished")
@@ -339,6 +356,9 @@ class SegmentCellThresholdProcess(BaseSegmentProcess):
 	def run(self):
 
 		self.indices = list(range(self.img_num_channels.shape[1]))
+		if self.flip:
+			self.indices = reversed(self.indices)
+		
 		chunks = np.array_split(self.indices, self.n_threads)
 
 		with concurrent.futures.ThreadPoolExecutor(max_workers=self.n_threads) as executor:
@@ -349,6 +369,7 @@ class SegmentCellThresholdProcess(BaseSegmentProcess):
 			except Exception as e:
 				print("Exception: ", e)
 
+		print('Done.')
 		# Send end signal
 		self.queue.put("finished")
 		self.queue.close()

celldetective/gui/processes/track_cells.py

@@ -147,6 +147,12 @@ class TrackingProcess(Process):
 			self.napari_name = "napari_effector_trajectories.npy"
 			self.table_name = "trajectories_effectors.csv"
 
+		else:
+			self.label_folder = f"labels_{self.mode}"
+			self.instruction_file = os.sep.join(["configs",f"tracking_instructions_{self.mode}.json"])
+			self.napari_name = f"napari_{self.mode}_trajectories.npy"
+			self.table_name = f"trajectories_{self.mode}.csv"			
+
 	def extract_experiment_parameters(self):
 
 		self.movie_prefix = ConfigSectionMap(self.config,"MovieSettings")["movie_prefix"]

celldetective/gui/retrain_segmentation_model_options.py

@@ -1,7 +1,7 @@
-from PyQt5.QtWidgets import QDialog, QMainWindow, QApplication,QRadioButton, QMessageBox, QScrollArea, QComboBox, QFrame, QFileDialog, QGridLayout, QLineEdit, QVBoxLayout, QWidget, QLabel, QHBoxLayout, QPushButton
+from PyQt5.QtWidgets import QApplication,QRadioButton, QScrollArea, QComboBox, QFrame, QFileDialog, QGridLayout, QLineEdit, QVBoxLayout, QLabel, QHBoxLayout, QPushButton
 from PyQt5.QtCore import Qt, QSize
-from PyQt5.QtGui import QDoubleValidator, QIntValidator, QIcon
-from celldetective.gui.gui_utils import center_window
+from PyQt5.QtGui import QDoubleValidator, QIntValidator
+from celldetective.gui.gui_utils import center_window, generic_message
 from celldetective.gui.layouts import ChannelNormGenerator
 
 from superqt import QLabeledDoubleSlider,QLabeledSlider
@@ -16,11 +16,10 @@ import json
 import os
 from glob import glob
 from datetime import datetime
-from celldetective.gui import Styles
-from celldetective.gui.processes.train_segmentation_model import TrainSegModelProcess
-from celldetective.gui.workers import ProgressWindow
+from celldetective.gui import CelldetectiveMainWindow, CelldetectiveWidget
 
-class ConfigSegmentationModelTraining(QMainWindow, Styles):
+
+class ConfigSegmentationModelTraining(CelldetectiveMainWindow):
 	
 	"""
 	UI to set segmentation model training instructions.
@@ -33,7 +32,6 @@ class ConfigSegmentationModelTraining(QMainWindow, Styles):
 		self.parent_window = parent_window
 		self.use_gpu = self.parent_window.use_gpu
 		self.setWindowTitle("Train segmentation model")
-		self.setWindowIcon(QIcon(os.sep.join(['celldetective','icons','mexican-hat.png'])))
 		self.mode = self.parent_window.mode
 		self.exp_dir = self.parent_window.exp_dir
 		self.soft_path = get_software_location()
@@ -62,7 +60,7 @@ class ConfigSegmentationModelTraining(QMainWindow, Styles):
 		
 		# Create button widget and layout
 		self.scroll_area = QScrollArea(self)
-		self.button_widget = QWidget()
+		self.button_widget = CelldetectiveWidget()
 		self.main_layout = QVBoxLayout()
 		self.button_widget.setLayout(self.main_layout)
 		self.main_layout.setContentsMargins(30,30,30,30)
@@ -154,7 +152,7 @@ class ConfigSegmentationModelTraining(QMainWindow, Styles):
 		self.epochs_slider.setRange(1,300)
 		self.epochs_slider.setSingleStep(1)
 		self.epochs_slider.setTickInterval(1)		
-		self.epochs_slider.setOrientation(1)
+		self.epochs_slider.setOrientation(Qt.Horizontal)
 		self.epochs_slider.setValue(100)
 		epochs_layout.addWidget(self.epochs_slider, 70)
 		layout.addLayout(epochs_layout)
@@ -241,7 +239,7 @@ class ConfigSegmentationModelTraining(QMainWindow, Styles):
 		self.augmentation_slider = QLabeledDoubleSlider()
 		self.augmentation_slider.setSingleStep(0.01)
 		self.augmentation_slider.setTickInterval(0.01)		
-		self.augmentation_slider.setOrientation(1)
+		self.augmentation_slider.setOrientation(Qt.Horizontal)
 		self.augmentation_slider.setRange(0.01, 3)
 		self.augmentation_slider.setValue(2.0)
 
@@ -253,7 +251,7 @@ class ConfigSegmentationModelTraining(QMainWindow, Styles):
 		self.validation_slider = QLabeledDoubleSlider()
 		self.validation_slider.setSingleStep(0.01)
 		self.validation_slider.setTickInterval(0.01)		
-		self.validation_slider.setOrientation(1)
+		self.validation_slider.setOrientation(Qt.Horizontal)
 		self.validation_slider.setRange(0,0.9)
 		self.validation_slider.setValue(0.2)		
 		validation_split_layout.addWidget(self.validation_slider, 70)
@@ -587,14 +585,8 @@ class ConfigSegmentationModelTraining(QMainWindow, Styles):
 		try:
 			lr = float(self.lr_le.text().replace(',','.'))
 		except:
-			msgBox = QMessageBox()
-			msgBox.setIcon(QMessageBox.Warning)
-			msgBox.setText("Invalid value encountered for the learning rate.")
-			msgBox.setWindowTitle("Warning")
-			msgBox.setStandardButtons(QMessageBox.Ok)
-			returnValue = msgBox.exec()
-			if returnValue == QMessageBox.Ok:
-				return None			
+			generic_message('Invalid value encountered for the learning rate.')
+			return None
 		
 		bs = int(self.bs_le.text())
 		epochs = self.epochs_slider.value()

celldetective/gui/retrain_signal_model_options.py

@@ -1,4 +1,4 @@
-from PyQt5.QtWidgets import QMainWindow, QApplication, QDialog, QMessageBox, QScrollArea, QComboBox, QFrame, QCheckBox, QFileDialog, QGridLayout, QLineEdit, QVBoxLayout, QWidget, QLabel, QHBoxLayout, QPushButton
+from PyQt5.QtWidgets import QApplication, QDialog, QMessageBox, QScrollArea, QComboBox, QFrame, QCheckBox, QFileDialog, QGridLayout, QLineEdit, QVBoxLayout, QLabel, QHBoxLayout, QPushButton
 from PyQt5.QtCore import Qt, QSize
 from PyQt5.QtGui import QDoubleValidator, QIntValidator, QIcon
 from celldetective.gui.gui_utils import center_window
@@ -14,12 +14,12 @@ import json
 import os
 from glob import glob
 from datetime import datetime
-from celldetective.gui import Styles
+from celldetective.gui import CelldetectiveMainWindow, CelldetectiveWidget
 from pandas.api.types import is_numeric_dtype
 from celldetective.gui.processes.train_signal_model import TrainSignalModelProcess
 from celldetective.gui.workers import ProgressWindow
 
-class ConfigSignalModelTraining(QMainWindow, Styles):
+class ConfigSignalModelTraining(CelldetectiveMainWindow):
 	
 	"""
 	UI to set measurement instructions.
@@ -31,7 +31,6 @@ class ConfigSignalModelTraining(QMainWindow, Styles):
 		super().__init__()
 		self.parent_window = parent_window
 		self.setWindowTitle("Train signal model")
-		self.setWindowIcon(QIcon(os.sep.join(['celldetective','icons','mexican-hat.png'])))
 		self.mode = self.parent_window.mode
 		self.exp_dir = self.parent_window.exp_dir
 		self.soft_path = get_software_location()
@@ -69,7 +68,7 @@ class ConfigSignalModelTraining(QMainWindow, Styles):
 		
 		# Create button widget and layout
 		self.scroll_area = QScrollArea(self)
-		self.button_widget = QWidget()
+		self.button_widget = CelldetectiveWidget()
 		self.main_layout = QVBoxLayout()
 		self.button_widget.setLayout(self.main_layout)
 		self.main_layout.setContentsMargins(30,30,30,30)
@@ -156,7 +155,7 @@ class ConfigSignalModelTraining(QMainWindow, Styles):
 		self.epochs_slider.setRange(1,3000)
 		self.epochs_slider.setSingleStep(1)
 		self.epochs_slider.setTickInterval(1)		
-		self.epochs_slider.setOrientation(1)
+		self.epochs_slider.setOrientation(Qt.Horizontal)
 		self.epochs_slider.setValue(300)
 		epochs_layout.addWidget(self.epochs_slider, 70)
 		layout.addLayout(epochs_layout)
@@ -243,7 +242,7 @@ class ConfigSignalModelTraining(QMainWindow, Styles):
 		self.augmentation_slider = QLabeledDoubleSlider()
 		self.augmentation_slider.setSingleStep(0.01)
 		self.augmentation_slider.setTickInterval(0.01)		
-		self.augmentation_slider.setOrientation(1)
+		self.augmentation_slider.setOrientation(Qt.Horizontal)
 		self.augmentation_slider.setRange(1, 5)
 		self.augmentation_slider.setValue(2)
 
@@ -255,7 +254,7 @@ class ConfigSignalModelTraining(QMainWindow, Styles):
 		self.validation_slider = QLabeledDoubleSlider()
 		self.validation_slider.setSingleStep(0.01)
 		self.validation_slider.setTickInterval(0.01)		
-		self.validation_slider.setOrientation(1)
+		self.validation_slider.setOrientation(Qt.Horizontal)
 		self.validation_slider.setRange(0,0.9)
 		self.validation_slider.setValue(0.25)		
 		validation_split_layout.addWidget(self.validation_slider, 70)
@@ -332,7 +331,7 @@ class ConfigSignalModelTraining(QMainWindow, Styles):
 		self.model_length_slider.setSingleStep(1)
 		self.model_length_slider.setTickInterval(1)
 		self.model_length_slider.setSingleStep(1)
-		self.model_length_slider.setOrientation(1)
+		self.model_length_slider.setOrientation(Qt.Horizontal)
 		self.model_length_slider.setRange(0,1024)
 		self.model_length_slider.setValue(128)		
 		model_length_layout.addWidget(self.model_length_slider, 70)
@@ -341,25 +340,22 @@ class ConfigSignalModelTraining(QMainWindow, Styles):
 	def neighborhood_changed(self):
 
 		neigh = self.neighborhood_choice_cb.currentText()
-		self.current_neighborhood = neigh.replace('target_ref_','').replace('effector_ref_','')
-		self.reference_population = ['targets' if 'target' in neigh else 'effectors'][0]
-		if 'target' in neigh:
-			if 'self' in neigh:
-				self.neighbor_population = 'targets'
-			else:
-				self.neighbor_population = 'effectors'
+		self.current_neighborhood = neigh
+		for pop in self.dataframes.keys():
+			self.current_neighborhood = self.current_neighborhood.replace(f'{pop}_ref_', '')
+
+		self.reference_population = self.neighborhood_choice_cb.currentText().split('_')[0]
+		if '_(' in self.current_neighborhood and ')_' in self.current_neighborhood:
+			self.neighbor_population = self.current_neighborhood.split('_(')[-1].split(')_')[0].split('-')[-1]
+			self.reference_population = self.current_neighborhood.split('_(')[-1].split(')_')[0].split('-')[0]
 		else:
-			if 'self' in neigh:
-				self.neighbor_population = 'effectors'
-			else:
-				self.neighbor_population = 'targets'
-		
+			if 'self' in self.current_neighborhood:
+				self.neighbor_population = self.reference_population
+
 		print(f'Current neighborhood: {self.current_neighborhood}')
 		print(f'New reference population: {self.reference_population}')
 		print(f'New neighbor population: {self.neighbor_population}')
 
-		# reload reference signals / neighbor signals / pair signals
-		# fill the channel cbs
 		self.df_reference = self.dataframes[self.reference_population]
 		self.df_neighbor = self.dataframes[self.neighbor_population]
 		self.df_pairs = load_experiment_tables(self.parent_window.exp_dir, population='pairs', load_pickle=False)
@@ -374,45 +370,50 @@ class ConfigSignalModelTraining(QMainWindow, Styles):
 		self.signals = ['--'] + num_cols_pairs + num_cols_reference + num_cols_neighbor
 
 		for cb in self.ch_norm.channel_cbs:
-			# try:
-			# 	cb.disconnect()
-			# except:
-			# 	pass
 			cb.clear()
 			cb.addItems(self.signals)
 
 	def fill_available_neighborhoods(self):
-		
-		df_targets = load_experiment_tables(self.parent_window.exp_dir, population='targets', load_pickle=True)
-		df_effectors = load_experiment_tables(self.parent_window.exp_dir, population='effectors', load_pickle=True)
-
-		self.dataframes = {
-			'targets': df_targets,
-			'effectors': df_effectors,
-		}
 
+		self.dataframes = {}
 		self.neighborhood_cols = []
-		self.reference_populations = []
-		self.neighbor_populations = []
-		if df_targets is not None:
-			self.neighborhood_cols.extend(['target_ref_'+c for c in list(df_targets.columns) if c.startswith('neighborhood')])
-			self.reference_populations.extend(['targets' for c in list(df_targets.columns) if c.startswith('neighborhood')])
-			for c in list(df_targets.columns):
-				if c.startswith('neighborhood') and '_2_' in c:
-					self.neighbor_populations.append('effectors')
-				elif c.startswith('neighborhood') and 'self' in c:
-					self.neighbor_populations.append('targets')
-		
-		if df_effectors is not None:
-			self.neighborhood_cols.extend(['effector_ref_'+c for c in list(df_effectors.columns) if c.startswith('neighborhood')])
-			self.reference_populations.extend(['effectors' for c in list(df_effectors.columns) if c.startswith('neighborhood')])
-			for c in list(df_effectors.columns):
-				if c.startswith('neighborhood') and '_2_' in c:
-					self.neighbor_populations.append('targets')
-				elif c.startswith('neighborhood') and 'self' in c:
-					self.neighbor_populations.append('effectors')
-
-		print(f"The following neighborhoods were detected: {self.neighborhood_cols=} {self.reference_populations=} {self.neighbor_populations=}")
+		for population in self.parent_window.parent_window.populations:
+			df_pop = load_experiment_tables(self.parent_window.exp_dir, population=pop, load_pickle=True)
+			self.dataframes.update({pop: df_pop})
+			if df_pop is not None:
+				self.neighborhood_cols.extend(
+					[f'{pop}_ref_' + c for c in list(df_pop.columns) if c.startswith('neighborhood')])
+
+		# df_targets = load_experiment_tables(self.parent_window.exp_dir, population='targets', load_pickle=True)
+		# df_effectors = load_experiment_tables(self.parent_window.exp_dir, population='effectors', load_pickle=True)
+		#
+		# self.dataframes = {
+		# 	'targets': df_targets,
+		# 	'effectors': df_effectors,
+		# }
+		#
+		# self.neighborhood_cols = []
+		# self.reference_populations = []
+		# self.neighbor_populations = []
+		# if df_targets is not None:
+		# 	self.neighborhood_cols.extend(['target_ref_'+c for c in list(df_targets.columns) if c.startswith('neighborhood')])
+		# 	self.reference_populations.extend(['targets' for c in list(df_targets.columns) if c.startswith('neighborhood')])
+		# 	for c in list(df_targets.columns):
+		# 		if c.startswith('neighborhood') and '_2_' in c:
+		# 			self.neighbor_populations.append('effectors')
+		# 		elif c.startswith('neighborhood') and 'self' in c:
+		# 			self.neighbor_populations.append('targets')
+		#
+		# if df_effectors is not None:
+		# 	self.neighborhood_cols.extend(['effector_ref_'+c for c in list(df_effectors.columns) if c.startswith('neighborhood')])
+		# 	self.reference_populations.extend(['effectors' for c in list(df_effectors.columns) if c.startswith('neighborhood')])
+		# 	for c in list(df_effectors.columns):
+		# 		if c.startswith('neighborhood') and '_2_' in c:
+		# 			self.neighbor_populations.append('targets')
+		# 		elif c.startswith('neighborhood') and 'self' in c:
+		# 			self.neighbor_populations.append('effectors')
+		#
+		# print(f"The following neighborhoods were detected: {self.neighborhood_cols=} {self.reference_populations=} {self.neighbor_populations=}")
 
 		self.neighborhood_choice_cb.addItems(self.neighborhood_cols)
 

celldetective/gui/seg_model_loader.py

@@ -1,8 +1,8 @@
-from PyQt5.QtWidgets import QWidget, QGridLayout, QComboBox, QVBoxLayout, QLabel, QLineEdit, QHBoxLayout, QRadioButton, QFileDialog, QPushButton, QMessageBox
+from PyQt5.QtWidgets import QGridLayout, QComboBox, QVBoxLayout, QLabel, QLineEdit, QHBoxLayout, QRadioButton, QFileDialog, QPushButton, QMessageBox
 from PyQt5.QtCore import Qt, QSize
-from celldetective.gui.gui_utils import center_window
+from celldetective.gui.gui_utils import center_window, generic_message
 from celldetective.gui.layouts import ChannelNormGenerator
-from celldetective.gui import ThresholdConfigWizard
+from celldetective.gui import ThresholdConfigWizard, CelldetectiveWidget
 from PyQt5.QtGui import QDoubleValidator
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
@@ -16,7 +16,7 @@ import gc
 from cellpose.models import CellposeModel
 
 
-class SegmentationModelLoader(QWidget, Styles):
+class SegmentationModelLoader(CelldetectiveWidget):
 	
 	"""
 	Upload a segmentation model or define a Threshold pipeline.
@@ -27,15 +27,10 @@ class SegmentationModelLoader(QWidget, Styles):
 		super().__init__()
 		self.parent_window = parent_window
 		self.mode = self.parent_window.mode
-		if self.mode=="targets":
-			self.target_folder = "segmentation_targets"
-		elif self.mode=="effectors":
-			self.target_folder = "segmentation_effectors"
+		self.target_folder = f"segmentation_{self.mode}"
 		self.setWindowTitle('Upload model')
 		self.generate_content()
-		self.setWindowIcon(self.celldetective_icon)
 		center_window(self)
-		self.setAttribute(Qt.WA_DeleteOnClose)
 
 	def generate_content(self):
 
@@ -230,14 +225,9 @@ class SegmentationModelLoader(QWidget, Styles):
 						self.destination = os.path.split(os.path.dirname(os.path.realpath(__file__)))[0]+f"/models/{self.target_folder}/"+self.modelname
 						self.folder_dest = self.destination
 					else:
-						msgBox = QMessageBox()
-						msgBox.setIcon(QMessageBox.Warning)
-						msgBox.setText("StarDist model not recognized... Please ensure that it contains a thresholds.json file or that it is a valid StarDist model...")
-						msgBox.setWindowTitle("Warning")
-						msgBox.setStandardButtons(QMessageBox.Ok)
-						returnValue = msgBox.exec()
-						if returnValue == QMessageBox.Ok:
-							return None					
+						generic_message(
+							"StarDist model not recognized... Please ensure that it contains a thresholds.json file or that it is a valid StarDist model...")
+						return None
 				
 				if self.seg_mode=="cellpose":
 					self.file_label.setText(self.filename.split("/")[-1])
@@ -264,15 +254,8 @@ class SegmentationModelLoader(QWidget, Styles):
 					self.merge_lbl.hide()
 					self.file_label.setText(self.filename[0].split("/")[-1])
 				else:
-					msgBox = QMessageBox()
-					msgBox.setIcon(QMessageBox.Warning)
-					msgBox.setText("You selected more than one pipeline. Please set a merging procedure for the resulting masks...")
-					msgBox.setWindowTitle("Warning")
-					msgBox.setStandardButtons(QMessageBox.Ok)
-					returnValue = msgBox.exec()
-					if returnValue == QMessageBox.Ok:
-						pass
-
+					generic_message(
+						"You selected more than one pipeline. Please set a merging procedure for the resulting masks...")
 					self.merge_cb.show()
 					self.merge_lbl.show()
 					self.file_label.setText(f"{n_files} configs loaded...")
@@ -327,14 +310,8 @@ class SegmentationModelLoader(QWidget, Styles):
 			channels.append(self.channel_layout.channel_cbs[i].currentText())
 
 		if self.file_label.text()=='No file chosen':
-			msgBox = QMessageBox()
-			msgBox.setIcon(QMessageBox.Warning)
-			msgBox.setText("Please select a model first.")
-			msgBox.setWindowTitle("Warning")
-			msgBox.setStandardButtons(QMessageBox.Ok)
-			returnValue = msgBox.exec()
-			if returnValue == QMessageBox.Ok:
-				return None
+			generic_message('Please select a model first...')
+			return None
 
 		if not self.threshold_button.isChecked():
 			
@@ -343,14 +320,8 @@ class SegmentationModelLoader(QWidget, Styles):
 				try:
 					shutil.copytree(self.filename, self.destination)
 				except FileExistsError:
-					msgBox = QMessageBox()
-					msgBox.setIcon(QMessageBox.Warning)
-					msgBox.setText("A model with the same name already exists in the models folder. Please rename it.")
-					msgBox.setWindowTitle("Warning")
-					msgBox.setStandardButtons(QMessageBox.Ok)
-					returnValue = msgBox.exec()
-					if returnValue == QMessageBox.Ok:
-						return None
+					generic_message("A model with the same name already exists in the models folder. Please rename it.")
+					return None
 
 			elif self.cellpose_button.isChecked():
 
@@ -359,15 +330,8 @@ class SegmentationModelLoader(QWidget, Styles):
 						os.mkdir(self.folder_dest)
 					shutil.copy(self.filename, self.destination)
 				except FileExistsError:
-					msgBox = QMessageBox()
-					msgBox.setIcon(QMessageBox.Warning)
-					msgBox.setText("A model with the same name already exists in the models folder. Please rename it.")
-					msgBox.setWindowTitle("Warning")
-					msgBox.setStandardButtons(QMessageBox.Ok)
-					returnValue = msgBox.exec()
-					if returnValue == QMessageBox.Ok:
-						return None
-				
+					generic_message("A model with the same name already exists in the models folder. Please rename it.")
+					return None
 				try:
 					model = CellposeModel(pretrained_model=self.destination, model_type=None, nchan=len(channels))
 					self.scale_model = model.diam_mean
@@ -392,16 +356,11 @@ class SegmentationModelLoader(QWidget, Styles):
 			if not isinstance(self.filename, list):
 				if not self.filename is None:
 					self.filename = [self.filename]
-			if self.mode=="targets":
-				self.parent_window.threshold_config_targets = self.filename
-				self.parent_window.seg_model_list.setCurrentText('Threshold')
-				print('Path to the traditional segmentation pipeline successfully set in celldetective...')
-				self.close()
-			elif self.mode=="effectors":
-				self.parent_window.threshold_config_effectors = self.filename
-				self.parent_window.seg_model_list.setCurrentText('Threshold')
-				print('Path to the traditional segmentation pipeline successfully set in celldetective...')
-				self.close()
+
+			idx = self.parent_window.parent_window.populations.index(self.mode)
+			self.parent_window.threshold_configs[idx] = self.filename
+			self.parent_window.seg_model_list.setCurrentText('Threshold')
+			self.close()
 
 	def generate_input_config(self):