celldetective 1.3.3.post1__tar.gz → 1.3.4__tar.gz

{celldetective-1.3.3.post1 → celldetective-1.3.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: celldetective
-Version: 1.3.3.post1
+Version: 1.3.4
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro
@@ -41,6 +41,7 @@ Requires-Dist: pytest
 Requires-Dist: pytest-qt
 Requires-Dist: h5py
 Requires-Dist: cliffs_delta
+Requires-Dist: requests
 
 # Celldetective
 

celldetective-1.3.4/celldetective/__main__.py

@@ -0,0 +1,66 @@
+#!/usr/bin/env python3
+import sys
+from PyQt5.QtWidgets import QApplication, QSplashScreen
+from PyQt5.QtGui import QPixmap
+from os import sep
+from celldetective.utils import get_software_location
+from time import time, sleep
+
+#os.environ['QT_DEBUG_PLUGINS'] = '1'
+
+if __name__ == "__main__":
+
+	splash=True
+	print('Loading the libraries...')
+
+	App = QApplication(sys.argv)
+	App.setStyle("Fusion")
+
+	software_location = get_software_location()
+
+	if splash:
+		start = time()
+		splash_pix = QPixmap(sep.join([software_location,'celldetective','icons','splash.png']))
+		splash = QSplashScreen(splash_pix)
+		splash.setMask(splash_pix.mask())
+		splash.show()
+		#App.processEvents(QEventLoop.AllEvents, 300)
+		while time() - start < 1:
+			sleep(0.001)
+			App.processEvents()
+
+	try:
+		
+		import requests
+		import re
+		from celldetective import __version__
+
+		package = 'celldetective'
+		response = requests.get(f'https://pypi.org/pypi/{package}/json')
+		latest_version = response.json()['info']['version']
+
+		latest_version_num = re.sub('[^0-9]','', latest_version)
+		current_version_num = re.sub('[^0-9]','',__version__)
+
+		if len(latest_version_num)!=len(current_version_num):
+			max_length = max([len(latest_version_num),len(current_version_num)])
+			latest_version_num = int(latest_version_num.zfill(max_length - len(latest_version_num)))
+			current_version_num = int(current_version_num.zfill(max_length - len(current_version_num)))
+
+		if latest_version_num > current_version_num:
+			print('Update is available...\nPlease update using `pip install --upgrade celldetective`...')
+	
+	except Exception as e:
+
+		print(f"{e=}")
+
+	from celldetective.gui.InitWindow import AppInitWindow
+
+	print('Libraries successfully loaded...')
+
+	window = AppInitWindow(App, software_location=software_location)
+
+	if splash:
+		splash.finish(window)
+
+	sys.exit(App.exec())

celldetective-1.3.4/celldetective/_version.py

@@ -0,0 +1 @@
+__version__ = "1.3.4"

{celldetective-1.3.3.post1 → celldetective-1.3.4}/celldetective/extra_properties.py

@@ -29,6 +29,27 @@ from celldetective.utils import interpolate_nan, contour_of_instance_segmentatio
 
 # Percentiles
 
+def custom_area(regionmask):
+	return np.sum(regionmask)
+
+def intensity_area_under_one(regionmask, intensity_image):
+	
+	subregion = regionmask[intensity_image<1]
+	if len(subregion)>0:
+		return np.sum(subregion)
+	else:
+		return 0.0
+
+def intensity_fraction_of_area_under_one(regionmask, intensity_image):
+
+	subregion = regionmask[intensity_image<1]
+	area = np.sum(regionmask)
+
+	if len(subregion) > 0:
+		return float(np.sum(subregion)) / float(area)
+	else:
+		return 0.0
+
 def intensity_percentile_ninety_nine(regionmask, intensity_image):
 	return np.nanpercentile(intensity_image[regionmask],99)
 

{celldetective-1.3.3.post1 → celldetective-1.3.4}/celldetective/filters.py

@@ -4,15 +4,19 @@ import scipy.ndimage as snd
 import numpy as np
 
 def gauss_filter(img, sigma, interpolate=True, *kwargs):
+
 	if interpolate:
 		img = interpolate_nan(img.astype(float))
+
 	return snd.gaussian_filter(img.astype(float), sigma, *kwargs)
 
 def median_filter(img, size, interpolate=True, *kwargs):
+
 	if interpolate:
 		img = interpolate_nan(img.astype(float))
 
 	size = int(size)
+	
 	return snd.median_filter(img, size, *kwargs)
 
 def maximum_filter(img, size, interpolate=True, *kwargs):
@@ -65,13 +69,17 @@ def std_filter(img, size, interpolate=True):
 
 	if interpolate:
 		img = interpolate_nan(img.astype(float))
+	
 	size = int(size)
 	img = img.astype(float)
+	
 	win_mean = snd.uniform_filter(img, (size,size), mode='wrap')
 	win_sqr_mean = snd.uniform_filter(img**2, (size, size), mode='wrap')
-	win_sqr_mean[win_sqr_mean!=win_sqr_mean] = 0.
 	win_sqr_mean[win_sqr_mean<=0.] = 0. # add this to prevent sqrt from breaking
-	img = np.sqrt(win_sqr_mean - win_mean**2)
+	
+	sub = np.subtract(win_sqr_mean,win_mean**2)
+	sub[sub<=0.] = 0.
+	img = np.sqrt(sub)
 
 	return img
 
@@ -96,16 +104,21 @@ def local_filter(img, *kwargs):
 	return binary.astype(float)
 
 def niblack_filter(img, *kwargs):
+
 	thresh = threshold_niblack(img, *kwargs)
 	binary = img >= thresh
 	return binary.astype(float)
 
 def sauvola_filter(img, *kwargs):
+
 	thresh = threshold_sauvola(img, *kwargs)
 	binary = img >= thresh
 	return binary.astype(float)
 
 def log_filter(img, sigma, *kwargs):
+
+	if interpolate:
+		img = interpolate_nan(img.astype(float))
 	return snd.gaussian_laplace(img.astype(float), sigma, *kwargs)
 
 def tophat_filter(img, size, connectivity=4, interpolate=True, *kwargs):

{celldetective-1.3.3.post1 → celldetective-1.3.4}/celldetective/gui/InitWindow.py

@@ -1,48 +1,49 @@
-from PyQt5.QtWidgets import QApplication, QMainWindow
-from celldetective.utils import get_software_location, download_zenodo_file
 import os
+
+from PyQt5.QtWidgets import QApplication, QMainWindow
 from PyQt5.QtWidgets import QFileDialog, QWidget, QVBoxLayout, QCheckBox, QHBoxLayout, QLabel, QLineEdit, QPushButton, QMessageBox, QMenu, QAction
 from PyQt5.QtCore import Qt, QUrl
 from PyQt5.QtGui import QIcon, QDesktopServices, QIntValidator
+
 from glob import glob
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
-import gc
-from celldetective.gui import Styles, ControlPanel, ConfigNewExperiment
-from celldetective.gui.gui_utils import center_window
-import subprocess
-import os
+
 from celldetective.gui.about import AboutWidget
 from celldetective.io import correct_annotation
-import psutil
-import subprocess
+from celldetective.utils import download_zenodo_file
+from celldetective.gui.gui_utils import center_window
+from celldetective.gui import Styles, ControlPanel, ConfigNewExperiment
+
+import gc
+from subprocess import check_output, Popen
+from psutil import cpu_count
 import json
 
-class AppInitWindow(QMainWindow):
+class AppInitWindow(QMainWindow, Styles):
 
 	"""
 	Initial window to set the experiment folder or create a new one.
 	"""
 
-	def __init__(self, parent_window=None):
+	def __init__(self, parent_window=None, software_location=None):
+
 		super().__init__()
 
 		self.parent_window = parent_window
-		self.Styles = Styles()
-		self.init_styles()
 		self.setWindowTitle("celldetective")
 
-		self.n_threads = min([1,psutil.cpu_count()])
+		self.n_threads = min([1,cpu_count()])
 
 		try:
-			subprocess.check_output('nvidia-smi')
+			check_output('nvidia-smi')
 			print('NVIDIA GPU detected (activate or disable in Memory & Threads)...')
 			self.use_gpu = True
 		except Exception: # this command not being found can raise quite a few different errors depending on the configuration
 			print('No NVIDIA GPU detected...')
 			self.use_gpu = False
-			
-		self.soft_path = get_software_location()
+		
+		self.soft_path = software_location
 		self.onlyInt = QIntValidator()
 		self.setWindowIcon(QIcon(os.sep.join([self.soft_path,'celldetective','icons','logo.png'])))
 		center_window(self)
@@ -65,6 +66,7 @@ class AppInitWindow(QMainWindow):
 		self.show()
 	
 	def closeEvent(self, event):
+
 		QApplication.closeAllWindows()
 		event.accept()
 		gc.collect()
@@ -188,6 +190,9 @@ class AppInitWindow(QMainWindow):
 	def download_spreading_assay_demo(self):
 		
 		self.target_dir = str(QFileDialog.getExistingDirectory(self, 'Select Folder for Download'))
+		if self.target_dir=='':
+			return None
+		
 		if not os.path.exists(os.sep.join([self.target_dir,'demo_ricm'])):
 			download_zenodo_file('demo_ricm', self.target_dir)
 		self.experiment_path_selection.setText(os.sep.join([self.target_dir, 'demo_ricm']))
@@ -196,6 +201,9 @@ class AppInitWindow(QMainWindow):
 	def download_cytotoxicity_assay_demo(self):
 		
 		self.target_dir = str(QFileDialog.getExistingDirectory(self, 'Select Folder for Download'))
+		if self.target_dir=='':
+			return None
+
 		if not os.path.exists(os.sep.join([self.target_dir,'demo_adcc'])):
 			download_zenodo_file('demo_adcc', self.target_dir)
 		self.experiment_path_selection.setText(os.sep.join([self.target_dir, 'demo_adcc']))
@@ -302,9 +310,10 @@ class AppInitWindow(QMainWindow):
 		QDesktopServices.openUrl(doc_url)
 
 	def open_models_folder(self):
+		
 		path = os.sep.join([self.soft_path,'celldetective','models',os.sep])
 		try:
-			subprocess.Popen(f'explorer {os.path.realpath(path)}')
+			Popen(f'explorer {os.path.realpath(path)}')
 		except:
 
 			try:
@@ -312,9 +321,6 @@ class AppInitWindow(QMainWindow):
 			except:
 				return None
 
-
-		#os.system(f'start {os.path.realpath(path)}')
-
 	def create_buttons_hbox(self):
 
 		self.buttons_layout = QHBoxLayout()
@@ -344,18 +350,6 @@ class AppInitWindow(QMainWindow):
 		else:
 			self.validate_button.setEnabled(False)
 
-	def init_styles(self):
-
-		"""
-		Initialize styles.
-		"""
-		
-		self.qtab_style = self.Styles.qtab_style
-		self.button_style_sheet = self.Styles.button_style_sheet
-		self.button_style_sheet_2 = self.Styles.button_style_sheet_2
-		self.button_style_sheet_2_not_done = self.Styles.button_style_sheet_2_not_done
-		self.button_style_sheet_3 = self.Styles.button_style_sheet_3
-		self.button_select_all = self.Styles.button_select_all
 
 	def set_experiment_path(self, path):
 		self.experiment_path_selection.setText(path)
@@ -414,7 +408,7 @@ class AppInitWindow(QMainWindow):
 			self.experiment_path_selection.setText(self.foldername)
 		else:
 			return None
-		if not os.path.exists(self.foldername+"/config.ini"):
+		if not os.path.exists(os.sep.join([self.foldername,"config.ini"])):
 			msgBox = QMessageBox()
 			msgBox.setIcon(QMessageBox.Warning)
 			msgBox.setText("No configuration can be found in the selected folder...")

celldetective-1.3.4/celldetective/gui/analyze_block.py

@@ -0,0 +1,81 @@
+from PyQt5.QtWidgets import QFrame, QLabel, QPushButton, QVBoxLayout, \
+    QSpacerItem, QSizePolicy
+from PyQt5.QtCore import Qt, QSize
+from PyQt5.QtGui import QIcon
+from celldetective.gui.plot_measurements import ConfigMeasurementsPlot
+from celldetective.gui import ConfigSurvival, ConfigSignalPlot
+import os
+from celldetective.gui import Styles
+
+class AnalysisPanel(QFrame, Styles):
+	def __init__(self, parent_window, title=None):
+
+		super().__init__()		
+		self.parent_window = parent_window
+		self.title = title
+		if self.title is None:
+			self.title=''
+		self.exp_channels = self.parent_window.exp_channels
+		self.exp_dir = self.parent_window.exp_dir
+		self.soft_path = self.parent_window.parent_window.soft_path
+
+		self.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
+		self.grid = QVBoxLayout(self)
+		self.grid.setSpacing(20)
+		self.generate_header()
+	
+	def generate_header(self):
+
+		"""
+		Read the mode and prepare a collapsable block to process a specific cell population.
+
+		"""
+
+		panel_title = QLabel("Survival")
+		panel_title.setStyleSheet("""
+			font-weight: bold;
+			padding: 0px;
+			""")
+
+		self.grid.addWidget(panel_title, alignment=Qt.AlignCenter)
+
+		self.survival_btn = QPushButton("plot survival")
+		self.survival_btn.setIcon(QIcon(QIcon(os.sep.join([self.soft_path,'celldetective','icons','survival2.png']))))
+		self.survival_btn.setStyleSheet(self.button_style_sheet_2)
+		self.survival_btn.setIconSize(QSize(35, 35))
+		self.survival_btn.clicked.connect(self.configure_survival)
+		self.grid.addWidget(self.survival_btn)
+
+		signal_lbl = QLabel("Single-cell signals")
+		signal_lbl.setStyleSheet("""
+			font-weight: bold;
+			padding: 0px;
+			""")
+
+		self.grid.addWidget(signal_lbl, alignment=Qt.AlignCenter)
+
+		self.plot_signal_btn = QPushButton("plot signals")
+		self.plot_signal_btn.setIcon(QIcon(QIcon(os.sep.join([self.soft_path,'celldetective','icons','signals_icon.png']))))
+		self.plot_signal_btn.setStyleSheet(self.button_style_sheet_2)
+		self.plot_signal_btn.setIconSize(QSize(35, 35))
+		self.plot_signal_btn.clicked.connect(self.configure_plot_signals)
+		self.grid.addWidget(self.plot_signal_btn)
+
+		verticalSpacer = QSpacerItem(20, 40, QSizePolicy.Minimum, QSizePolicy.Expanding)
+		self.grid.addItem(verticalSpacer)
+
+	def configure_survival(self):
+		print('survival analysis starting!!!')
+		self.configSurvival = ConfigSurvival(self)
+		self.configSurvival.show()
+
+	def configure_plot_signals(self):
+		print('Configure a signal collapse representation...')
+		self.ConfigSignalPlot = ConfigSignalPlot(self)
+		self.ConfigSignalPlot.show()
+
+	def configure_plot_measurements(self):
+
+		print('plot measurements analysis starting!!!')
+		self.ConfigMeasurementsPlot_wg = ConfigMeasurementsPlot(self)
+		self.ConfigMeasurementsPlot_wg.show()

{celldetective-1.3.3.post1 → celldetective-1.3.4}/celldetective/gui/classifier_widget.py

@@ -10,7 +10,7 @@ import numpy as np
 import matplotlib.pyplot as plt
 import json
 
-from celldetective.gui.gui_utils import FigureCanvas, center_window, color_from_status, help_generic, color_from_class
+from celldetective.gui.gui_utils import FigureCanvas, center_window, color_from_status, help_generic
 from celldetective.gui import Styles
 from celldetective.utils import get_software_location
 from celldetective.measure import classify_cells_from_query, interpret_track_classification

{celldetective-1.3.3.post1 → celldetective-1.3.4}/celldetective/gui/control_panel.py

@@ -1,7 +1,7 @@
-from PyQt5.QtWidgets import QMainWindow, QComboBox, QPushButton, QHBoxLayout, QLabel, QWidget, QGridLayout, QFrame, \
+from PyQt5.QtWidgets import QMainWindow, QPushButton, QHBoxLayout, QLabel, QWidget, QGridLayout, QFrame, \
 	QTabWidget, QVBoxLayout, QMessageBox, QScrollArea, QDesktopWidget
 from PyQt5.QtCore import Qt, QSize
-from celldetective.gui.gui_utils import center_window, QHSeperationLine
+from celldetective.gui.gui_utils import center_window, QHSeperationLine, QCheckableComboBox
 from celldetective.utils import _extract_labels_from_config, ConfigSectionMap, extract_experiment_channels, extract_identity_col
 from celldetective.gui import ConfigEditor, ProcessPanel, PreprocessingPanel, AnalysisPanel, NeighPanel
 from celldetective.io import get_experiment_wells, get_config, get_spatial_calibration, get_temporal_calibration, get_experiment_concentrations, get_experiment_cell_types, get_experiment_antibodies, get_experiment_pharmaceutical_agents
@@ -18,6 +18,7 @@ from celldetective.utils import extract_experiment_channels
 from celldetective.gui import Styles
 import pandas as pd
 
+
 class ControlPanel(QMainWindow, Styles):
 
 	def __init__(self, parent_window=None, exp_dir=""):
@@ -90,7 +91,7 @@ class ControlPanel(QMainWindow, Styles):
 		self.initial_width = self.size().width()
 		self.screen_height = desktop.screenGeometry().height()
 		self.screen_width = desktop.screenGeometry().width()
-		self.scroll.setMinimumWidth(425)
+		self.scroll.setMinimumWidth(440)
 
 	def init_wells_and_positions(self):
 
@@ -138,23 +139,23 @@ class ControlPanel(QMainWindow, Styles):
 		self.edit_config_button.clicked.connect(self.open_config_editor)
 		self.edit_config_button.setStyleSheet(self.button_select_all)
 
-		self.well_list = QComboBox()
+		self.well_list = QCheckableComboBox(obj='well', parent_window=self)
 		thresh = 32
-		self.well_truncated = [w[:thresh - 3]+'...' if len(w)>thresh else w for w in self.well_labels]		
-		self.well_list.addItems(self.well_truncated) #self.well_labels
-		for i in range(len(self.well_labels)):
-			self.well_list.setItemData(i, self.well_labels[i], Qt.ToolTipRole)
-		self.well_list.addItems(["*"])
-		self.well_list.activated.connect(self.display_positions)
-		self.to_disable.append(self.well_list)
+		self.well_truncated = [w[:thresh - 3]+'...' if len(w)>thresh else w for w in self.well_labels]
+		for i in range(len(self.well_truncated)):
+			self.well_list.addItem(self.well_truncated[i], tooltip=self.well_labels[i])
 
-		self.position_list = QComboBox()
-		self.position_list.addItems(["*"])
+		self.position_list = QCheckableComboBox(obj='position', parent_window=self)
 		self.position_list.addItems(self.positions[0])
-		self.position_list.activated.connect(self.update_position_options)
 		self.to_disable.append(self.position_list)
 		#self.locate_selected_position()
 
+		self.well_list.activated.connect(self.display_positions)
+		self.well_list.setCurrentIndex(0)
+
+		self.position_list.activated.connect(self.update_position_options)
+		self.position_list.setCurrentIndex(0)
+
 		self.view_stack_btn = QPushButton()
 		self.view_stack_btn.setStyleSheet(self.button_select_all)
 		self.view_stack_btn.setIcon(icon(MDI6.image_check, color="black"))
@@ -163,6 +164,24 @@ class ControlPanel(QMainWindow, Styles):
 		self.view_stack_btn.clicked.connect(self.view_current_stack)
 		self.view_stack_btn.setEnabled(False)
 
+		self.select_all_wells_btn = QPushButton()
+		self.select_all_wells_btn.setIcon(icon(MDI6.select_all,color="black"))
+		self.select_all_wells_btn.setIconSize(QSize(20, 20))
+		self.select_all_wells_btn.setToolTip("Select all wells.")
+		self.select_all_wells_btn.clicked.connect(self.select_all_wells)
+		self.select_all_wells_btn.setStyleSheet(self.button_select_all)
+		self.select_all_wells_option = False
+
+
+		self.select_all_pos_btn = QPushButton()
+		self.select_all_pos_btn.setIcon(icon(MDI6.select_all,color="black"))
+		self.select_all_pos_btn.setIconSize(QSize(20, 20))
+		self.select_all_pos_btn.setToolTip("Select all positions.")
+		self.select_all_pos_btn.clicked.connect(self.select_all_positions)
+		self.select_all_pos_btn.setStyleSheet(self.button_select_all)
+		self.select_all_pos_option = False
+
+
 		well_lbl = QLabel('Well: ')
 		well_lbl.setAlignment(Qt.AlignRight)
 
@@ -196,20 +215,52 @@ class ControlPanel(QMainWindow, Styles):
 		# Well row
 		well_hbox = QHBoxLayout()
 		well_hbox.addWidget(well_lbl, 25, alignment=Qt.AlignVCenter)
-		well_hbox.addWidget(self.well_list, 75)
+		well_subhbox = QHBoxLayout()
+		well_subhbox.addWidget(self.well_list, 95)
+		well_subhbox.addWidget(self.select_all_wells_btn, 5)
+		well_hbox.addLayout(well_subhbox, 75)
 		vbox.addLayout(well_hbox)
 
 		# Position row
 		position_hbox = QHBoxLayout()
 		position_hbox.addWidget(pos_lbl, 25, alignment=Qt.AlignVCenter)
 		pos_subhbox = QHBoxLayout()
-		pos_subhbox.addWidget(self.position_list, 95)
+		pos_subhbox.addWidget(self.position_list, 90)
+		pos_subhbox.addWidget(self.select_all_pos_btn, 5)
 		pos_subhbox.addWidget(self.view_stack_btn, 5)
 		position_hbox.addLayout(pos_subhbox, 75)
 		vbox.addLayout(position_hbox)
 
 		vbox.addWidget(hsep)
 
+	def select_all_wells(self):
+
+		if not self.select_all_wells_option:
+			self.well_list.selectAll()
+			self.select_all_wells_option = True
+			self.select_all_wells_btn.setIcon(icon(MDI6.select_all,color=self.celldetective_blue))
+			self.select_all_wells_btn.setIconSize(QSize(20, 20))
+			self.display_positions()
+		else:
+			self.well_list.unselectAll()
+			self.select_all_wells_option = False
+			self.select_all_wells_btn.setIcon(icon(MDI6.select_all,color="black"))
+			self.select_all_wells_btn.setIconSize(QSize(20, 20))
+			self.display_positions()
+
+	def select_all_positions(self):
+
+		if not self.select_all_pos_option:
+			self.position_list.selectAll()
+			self.select_all_pos_option = True
+			self.select_all_pos_btn.setIcon(icon(MDI6.select_all,color=self.celldetective_blue))
+			self.select_all_pos_btn.setIconSize(QSize(20, 20))
+		else:
+			self.position_list.unselectAll()
+			self.select_all_pos_option = False
+			self.select_all_pos_btn.setIcon(icon(MDI6.select_all,color="black"))
+			self.select_all_pos_btn.setIconSize(QSize(20, 20))
+
 	def locate_image(self):
 
 		"""
@@ -341,17 +392,30 @@ class ControlPanel(QMainWindow, Styles):
 		Show the positions as the well is changed.
 		"""
 
-		if self.well_list.currentText()=="*":
+		if self.well_list.isMultipleSelection():
+
 			self.position_list.clear()
-			self.position_list.addItems(["*"])
 			position_linspace = np.linspace(0,len(self.positions[0])-1,len(self.positions[0]),dtype=int)
 			position_linspace = [str(s) for s in position_linspace]
 			self.position_list.addItems(position_linspace)
+			if self.select_all_pos_option:
+				self.select_all_pos_btn.click()
+			self.select_all_pos_btn.click()
+		
+		elif not self.well_list.isAnySelected():
+
+			self.position_list.unselectAll()
+			if self.select_all_pos_option:
+				self.select_all_pos_btn.click()
+
 		else:
-			pos_index = self.well_list.currentIndex()
+			pos_index = self.well_list.getSelectedIndices()[0]
 			self.position_list.clear()
-			self.position_list.addItems(["*"])
 			self.position_list.addItems(self.positions[pos_index])
+			if self.select_all_pos_option:
+				self.select_all_pos_btn.click()
+			self.position_list.setCurrentIndex(0)
+		
 		self.update_position_options()
 	
 	def open_config_editor(self):
@@ -366,7 +430,7 @@ class ControlPanel(QMainWindow, Styles):
 
 		"""
 
-		if self.well_list.currentText()=="*":
+		if self.well_list.isMultipleSelection():
 			msgBox = QMessageBox()
 			msgBox.setIcon(QMessageBox.Critical)
 			msgBox.setText("Please select a single well...")
@@ -376,12 +440,12 @@ class ControlPanel(QMainWindow, Styles):
 			if returnValue == QMessageBox.Ok:
 				return False
 		else:
-			self.well_index = [self.well_list.currentIndex()]
+			self.well_index = self.well_list.getSelectedIndices() #[self.well_list.currentIndex()]
 
 		for w_idx in self.well_index:
 
 			pos = self.positions[w_idx]
-			if self.position_list.currentText()=="*":
+			if not self.position_list.isSingleSelection():
 				msgBox = QMessageBox()
 				msgBox.setIcon(QMessageBox.Critical)
 				msgBox.setText("Please select a single position...")
@@ -391,11 +455,12 @@ class ControlPanel(QMainWindow, Styles):
 				if returnValue == QMessageBox.Ok:
 					return False
 			else:
-				pos_indices = natsorted([pos.index(self.position_list.currentText())])
+				pos_indices = self.position_list.getSelectedIndices()
 
 			well = self.wells[w_idx]
 
 			for pos_idx in pos_indices:
+
 				self.pos = natsorted(glob(well+f"{os.path.split(well)[-1].replace('W','').replace(os.sep,'')}*{os.sep}"))[pos_idx]
 				if not os.path.exists(self.pos + 'output'):
 					os.mkdir(self.pos + 'output')
@@ -405,6 +470,7 @@ class ControlPanel(QMainWindow, Styles):
 		return True
 
 	def create_config_dir(self):
+
 		self.config_folder = self.exp_dir+'configs'+os.sep
 		if not os.path.exists(self.config_folder):
 			os.mkdir(self.config_folder)
@@ -413,7 +479,8 @@ class ControlPanel(QMainWindow, Styles):
 		
 		self.pos = self.position_list.currentText()
 		panels = [self.ProcessEffectors, self.ProcessTargets]
-		if self.position_list.currentText()=="*":
+
+		if self.position_list.isMultipleSelection() or not self.position_list.isAnySelected():
 			
 			for p in panels:
 				p.check_seg_btn.setEnabled(False)
@@ -443,7 +510,9 @@ class ControlPanel(QMainWindow, Styles):
 			self.ProcessEffectors.delete_tracks_btn.hide()
 
 			self.view_stack_btn.setEnabled(False)
-		elif self.well_list.currentText()=='*':
+
+		elif self.well_list.isMultipleSelection():
+
 			self.ProcessTargets.view_tab_btn.setEnabled(True)
 			self.ProcessEffectors.view_tab_btn.setEnabled(True)	
 			self.NeighPanel.view_tab_btn.setEnabled(True)
@@ -455,7 +524,9 @@ class ControlPanel(QMainWindow, Styles):
 			self.ProcessTargets.delete_tracks_btn.hide()
 			self.ProcessEffectors.delete_tracks_btn.hide()
 		else:
-			if not self.well_list.currentText()=="*":
+
+			if self.well_list.isAnySelected() and self.position_list.isAnySelected():
+
 				self.locate_selected_position()
 				self.view_stack_btn.setEnabled(True)
 				# if os.path.exists(os.sep.join([self.pos,'labels_effectors', os.sep])):