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

celldetective/gui/classifier_widget.py

@@ -1,7 +1,7 @@
-from PyQt5.QtWidgets import QWidget, QLineEdit, QMessageBox, QHBoxLayout, QVBoxLayout, QPushButton, QLabel, \
+from PyQt5.QtWidgets import QLineEdit, QMessageBox, QHBoxLayout, QVBoxLayout, QPushButton, QLabel, \
 	QCheckBox, QRadioButton, QButtonGroup, QComboBox
 from PyQt5.QtCore import Qt, QSize
-from superqt import QLabeledSlider,QLabeledDoubleSlider, QSearchableComboBox
+from superqt import QLabeledSlider, QLabeledDoubleSlider, QSearchableComboBox
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
 
@@ -11,11 +11,11 @@ import matplotlib.pyplot as plt
 import json
 
 from celldetective.gui.gui_utils import FigureCanvas, center_window, color_from_status, help_generic
-from celldetective.gui import Styles
+from celldetective.gui.base_components import CelldetectiveWidget
 from celldetective.utils import get_software_location
 from celldetective.measure import classify_cells_from_query, interpret_track_classification
 
-class ClassifierWidget(QWidget, Styles):
+class ClassifierWidget(CelldetectiveWidget):
 
 	def __init__(self, parent_window):
 
@@ -33,7 +33,7 @@ class ClassifierWidget(QWidget, Styles):
 
 		is_number = np.vectorize(lambda x: np.issubdtype(x, np.number))
 		is_number_test = is_number(self.df.dtypes)
-		self.cols = [col for t,col in zip(is_number_test,self.df.columns) if t]
+		self.cols = [col for t, col in zip(is_number_test, self.df.columns) if t]
 
 		self.class_name = 'custom'
 		self.name_le = QLineEdit(self.class_name)
@@ -44,7 +44,7 @@ class ClassifierWidget(QWidget, Styles):
 
 		
 		layout = QVBoxLayout(self)
-		layout.setContentsMargins(30,30,30,30)
+		layout.setContentsMargins(30, 30, 30, 30)
 
 		name_layout = QHBoxLayout()
 		name_layout.addWidget(QLabel('class name: '), 33)
@@ -55,7 +55,7 @@ class ClassifierWidget(QWidget, Styles):
 		fig_btn_hbox.addWidget(QLabel(''), 95)
 		self.project_times_btn = QPushButton('')
 		self.project_times_btn.setStyleSheet(self.parent_window.parent_window.parent_window.button_select_all)
-		self.project_times_btn.setIcon(icon(MDI6.math_integral,color="black"))
+		self.project_times_btn.setIcon(icon(MDI6.math_integral, color="black"))
 		self.project_times_btn.setToolTip("Project measurements at all times.")
 		self.project_times_btn.setIconSize(QSize(20, 20))
 		self.project_times = False
@@ -70,8 +70,8 @@ class ClassifierWidget(QWidget, Styles):
 		# slider
 		self.frame_slider = QLabeledSlider()
 		self.frame_slider.setSingleStep(1)
-		self.frame_slider.setOrientation(1)
-		self.frame_slider.setRange(0,int(self.df.FRAME.max()) - 1)
+		self.frame_slider.setOrientation(Qt.Horizontal)
+		self.frame_slider.setRange(0, int(self.df.FRAME.max()) - 1)
 		self.frame_slider.setValue(0)
 		self.currentFrame = 0
 
@@ -84,8 +84,8 @@ class ClassifierWidget(QWidget, Styles):
 		# transparency slider
 		self.alpha_slider = QLabeledDoubleSlider()
 		self.alpha_slider.setSingleStep(0.001)
-		self.alpha_slider.setOrientation(1)
-		self.alpha_slider.setRange(0,1)
+		self.alpha_slider.setOrientation(Qt.Horizontal)
+		self.alpha_slider.setRange(0, 1)
 		self.alpha_slider.setValue(1.0)
 		self.alpha_slider.setDecimals(3)
 
@@ -95,8 +95,8 @@ class ClassifierWidget(QWidget, Styles):
 		layout.addLayout(slider_alpha_hbox)
 
 
-		self.features_cb = [QSearchableComboBox() for i in range(2)]
-		self.log_btns = [QPushButton() for i in range(2)]
+		self.features_cb = [QSearchableComboBox() for _ in range(2)]
+		self.log_btns = [QPushButton() for _ in range(2)]
 
 		for i in range(2):
 			hbox_feat = QHBoxLayout()
@@ -106,7 +106,7 @@ class ClassifierWidget(QWidget, Styles):
 			layout.addLayout(hbox_feat)
 
 			self.features_cb[i].clear()
-			self.features_cb[i].addItems(sorted(list(self.cols),key=str.lower))
+			self.features_cb[i].addItems(sorted(list(self.cols), key=str.lower))
 			self.features_cb[i].currentTextChanged.connect(self.update_props_scatter)
 			self.features_cb[i].setCurrentIndex(i)
 
@@ -134,15 +134,15 @@ class ClassifierWidget(QWidget, Styles):
 			self.time_corr.setEnabled(False)
 
 		time_prop_hbox = QHBoxLayout()
-		time_prop_hbox.addWidget(self.time_corr,alignment=Qt.AlignCenter)
+		time_prop_hbox.addWidget(self.time_corr, alignment=Qt.AlignCenter)
 
 		self.help_propagate_btn = QPushButton()
-		self.help_propagate_btn.setIcon(icon(MDI6.help_circle,color=self.help_color))
+		self.help_propagate_btn.setIcon(icon(MDI6.help_circle, color=self.help_color))
 		self.help_propagate_btn.setIconSize(QSize(20, 20))
 		self.help_propagate_btn.clicked.connect(self.help_propagate)
 		self.help_propagate_btn.setStyleSheet(self.button_select_all)
 		self.help_propagate_btn.setToolTip("Help.")
-		time_prop_hbox.addWidget(self.help_propagate_btn,5,alignment=Qt.AlignRight)
+		time_prop_hbox.addWidget(self.help_propagate_btn, 5, alignment=Qt.AlignRight)
 
 		layout.addLayout(time_prop_hbox)
 
@@ -154,23 +154,23 @@ class ClassifierWidget(QWidget, Styles):
 
 		time_corr_layout = QHBoxLayout()
 		time_corr_layout.addWidget(self.unique_state_btn, 33, alignment=Qt.AlignCenter)
-		time_corr_layout.addWidget(self.irreversible_event_btn, 33,alignment=Qt.AlignCenter)
-		time_corr_layout.addWidget(self.transient_event_btn, 33,alignment=Qt.AlignCenter)
+		time_corr_layout.addWidget(self.irreversible_event_btn, 33, alignment=Qt.AlignCenter)
+		time_corr_layout.addWidget(self.transient_event_btn, 33, alignment=Qt.AlignCenter)
 		layout.addLayout(time_corr_layout)
 
 		self.prereq_event_check = QCheckBox('prerequisite event:')
 		self.prereq_event_check.toggled.connect(self.activate_prereq_cb)
 		self.prereq_event_cb = QComboBox()
-		event_cols = ['--'] + [c.replace('t_','') for c in self.cols if c.startswith('t_')]
+		event_cols = ['--'] + [c.replace('t_', '') for c in self.cols if c.startswith('t_')]
 		self.prereq_event_cb.addItems(event_cols)
 		self.prereq_event_check.setEnabled(False)
 		self.prereq_event_cb.setEnabled(False)
 
 		self.r2_slider = QLabeledDoubleSlider()
 		self.r2_slider.setValue(0.75)
-		self.r2_slider.setRange(0,1)
+		self.r2_slider.setRange(0, 1)
 		self.r2_slider.setSingleStep(0.01)
-		self.r2_slider.setOrientation(1)
+		self.r2_slider.setOrientation(Qt.Horizontal)
 		self.r2_label = QLabel('R2 tolerance:')
 		self.r2_label.setToolTip('Minimum R2 between the fit sigmoid and the binary response to the filters to accept the event.')
 
@@ -196,7 +196,7 @@ class ClassifierWidget(QWidget, Styles):
 			wg.setEnabled(False)
 
 		prereq_layout = QHBoxLayout()
-		prereq_layout.setContentsMargins(30,0,0,0)
+		prereq_layout.setContentsMargins(30, 0, 0, 0)
 		prereq_layout.addWidget(self.prereq_event_check, 20)
 		prereq_layout.addWidget(self.prereq_event_cb, 80)
 		layout.addLayout(prereq_layout)
@@ -212,7 +212,6 @@ class ClassifierWidget(QWidget, Styles):
 		self.frame_slider.valueChanged.connect(self.set_frame)
 		self.alpha_slider.valueChanged.connect(self.set_transparency)
 
-		self.setAttribute(Qt.WA_DeleteOnClose)
 
 	def activate_prereq_cb(self):
 		if self.prereq_event_check.isChecked():
@@ -270,11 +269,10 @@ class ClassifierWidget(QWidget, Styles):
 		Define properties scatter.
 		"""
 
-		self.fig_props, self.ax_props = plt.subplots(figsize=(4,4),tight_layout=True)
+		self.fig_props, self.ax_props = plt.subplots(figsize=(4, 4), tight_layout=True)
 		self.propscanvas = FigureCanvas(self.fig_props, interactive=True)
 		self.fig_props.set_facecolor('none')
-		self.fig_props.canvas.setStyleSheet("background-color: transparent;")
-		self.scat_props = self.ax_props.scatter([],[], color="k", alpha=self.currentAlpha)
+		self.scat_props = self.ax_props.scatter([], [], color="k", alpha=self.currentAlpha)
 		self.propscanvas.canvas.draw_idle()
 		self.propscanvas.canvas.setMinimumHeight(self.screen_height//5)
 
@@ -295,25 +293,24 @@ class ClassifierWidget(QWidget, Styles):
 				self.log_btns[0].setEnabled(True)
 
 			if np.any(self.df[self.features_cb[1].currentText()].to_numpy() <= 0.):
-				if self.ax_props.get_xscale()=='log':
+				if self.ax_props.get_xscale() == 'log':
 					self.log_btns[1].click()
 				self.log_btns[1].setEnabled(False)
 			else:
 				self.log_btns[1].setEnabled(True)
 		except Exception as e:
-			#print(e)
-			pass
+			print(e)
 
 		class_name = self.class_name
 
 		try:
 
 			if not self.project_times:
-				self.scat_props.set_offsets(self.df.loc[self.df['FRAME']==self.currentFrame,[self.features_cb[1].currentText(),self.features_cb[0].currentText()]].to_numpy())
-				colors = [color_from_status(c) for c in self.df.loc[self.df['FRAME']==self.currentFrame,class_name].to_numpy()]
+				self.scat_props.set_offsets(self.df.loc[self.df['FRAME'] == self.currentFrame, [self.features_cb[1].currentText(), self.features_cb[0].currentText()]].to_numpy())
+				colors = [color_from_status(c) for c in self.df.loc[self.df['FRAME'] == self.currentFrame, class_name].to_numpy()]
 				self.scat_props.set_facecolor(colors)
 			else:
-				self.scat_props.set_offsets(self.df[[self.features_cb[1].currentText(),self.features_cb[0].currentText()]].to_numpy())
+				self.scat_props.set_offsets(self.df[[self.features_cb[1].currentText(), self.features_cb[0].currentText()]].to_numpy())
 				colors = [color_from_status(c) for c in self.df[class_name].to_numpy()]
 				self.scat_props.set_facecolor(colors)
 			
@@ -333,18 +330,18 @@ class ClassifierWidget(QWidget, Styles):
 				
 				x_padding = (max_x - min_x) * 0.05
 				y_padding = (max_y - min_y) * 0.05
-				if x_padding==0:
+				if x_padding == 0:
 					x_padding = 0.05
-				if y_padding==0:
+				if y_padding == 0:
 					y_padding = 0.05
 
-				if min_x==min_x and max_x==max_x:
-					if self.ax_props.get_xscale()=='linear':
+				if min_x == min_x and max_x == max_x:
+					if self.ax_props.get_xscale() == 'linear':
 						self.ax_props.set_xlim(min_x - x_padding, max_x + x_padding)
 					else:
 						self.ax_props.set_xlim(min_x, max_x)
-				if min_y==min_y and max_y==max_y:
-					if self.ax_props.get_yscale()=='linear':
+				if min_y == min_y and max_y == max_y:
+					if self.ax_props.get_yscale() == 'linear':
 						self.ax_props.set_ylim(min_y - y_padding, max_y + y_padding)
 					else:
 						self.ax_props.set_ylim(min_y, max_y)						
@@ -379,7 +376,7 @@ class ClassifierWidget(QWidget, Styles):
 		if self.df is None:
 			msgBox = QMessageBox()
 			msgBox.setIcon(QMessageBox.Warning)
-			msgBox.setText(f"The query could not be understood. No filtering was applied. {e}")
+			msgBox.setText(f"The query could not be understood. No filtering was applied.")
 			msgBox.setWindowTitle("Warning")
 			msgBox.setStandardButtons(QMessageBox.Ok)
 			returnValue = msgBox.exec()
@@ -390,22 +387,18 @@ class ClassifierWidget(QWidget, Styles):
 		self.update_props_scatter(feature_changed=False)
 
 	def set_frame(self, value):
-		xlim=self.ax_props.get_xlim()
-		ylim=self.ax_props.get_ylim()
+		xlim = self.ax_props.get_xlim()
+		ylim = self.ax_props.get_ylim()
 		self.currentFrame = value
 		self.update_props_scatter(feature_changed=False)
 		self.ax_props.set_xlim(xlim)
 		self.ax_props.set_ylim(ylim)
 
-
 	def set_transparency(self, value):
-		xlim=self.ax_props.get_xlim()
-		ylim=self.ax_props.get_ylim()
+		xlim = self.ax_props.get_xlim()
+		ylim = self.ax_props.get_ylim()
 		self.currentAlpha = value
-		#fc = self.scat_props.get_facecolors()
-		#fc[:, 3] = value
-		#self.scat_props.set_facecolors(fc)
-		#self.propscanvas.canvas.draw_idle()
+
 		self.update_props_scatter(feature_changed=False)
 		self.ax_props.set_xlim(xlim)
 		self.ax_props.set_ylim(ylim)
@@ -413,12 +406,12 @@ class ClassifierWidget(QWidget, Styles):
 	def switch_projection(self):
 		if self.project_times:
 			self.project_times = False
-			self.project_times_btn.setIcon(icon(MDI6.math_integral,color="black"))
+			self.project_times_btn.setIcon(icon(MDI6.math_integral, color="black"))
 			self.project_times_btn.setIconSize(QSize(20, 20))
 			self.frame_slider.setEnabled(True)
 		else:
 			self.project_times = True
-			self.project_times_btn.setIcon(icon(MDI6.math_integral_box,color="black"))
+			self.project_times_btn.setIcon(icon(MDI6.math_integral_box, color="black"))
 			self.project_times_btn.setIconSize(QSize(20, 20))
 			self.frame_slider.setEnabled(False)
 		self.update_props_scatter(feature_changed=False)
@@ -432,12 +425,13 @@ class ClassifierWidget(QWidget, Styles):
 
 		if self.time_corr.isChecked():
 			self.class_name_user = 'class_'+self.name_le.text()
-			print(f'User defined class name: {self.class_name_user}.')
+			print(f'User defined class name: {self.class_name_user}...')
 			if self.class_name_user in self.df.columns:
 
 				msgBox = QMessageBox()
 				msgBox.setIcon(QMessageBox.Information)
-				msgBox.setText(f"The class column {self.class_name_user} already exists in the table.\nProceeding will reclassify. Do you want to continue?")
+				msgBox.setText(f"The class column {self.class_name_user} already exists in the table.\nProceeding will "
+							   f"reclassify. Do you want to continue?")
 				msgBox.setWindowTitle("Warning")
 				msgBox.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
 				returnValue = msgBox.exec()
@@ -447,7 +441,6 @@ class ClassifierWidget(QWidget, Styles):
 					return None
 
 			name_map = {self.class_name: self.class_name_user}
-			print(f"{name_map=}")
 			self.df = self.df.drop(list(set(name_map.values()) & set(self.df.columns)), axis=1).rename(columns=name_map)
 			self.df.reset_index(inplace=True, drop=True)
 
@@ -455,7 +448,7 @@ class ClassifierWidget(QWidget, Styles):
 			if self.prereq_event_check.isChecked() and "t_"+self.prereq_event_cb.currentText() in self.cols:
 				pre_event = self.prereq_event_cb.currentText()
 
-			self.df = interpret_track_classification(self.df, self.class_name_user, irreversible_event=self.irreversible_event_btn.isChecked(), unique_state=self.unique_state_btn.isChecked(), transient_event=self.transient_event_btn.isChecked(),r2_threshold=self.r2_slider.value(), pre_event=pre_event)
+			self.df = interpret_track_classification(self.df, self.class_name_user, irreversible_event=self.irreversible_event_btn.isChecked(), unique_state=self.unique_state_btn.isChecked(), transient_event=self.transient_event_btn.isChecked(), r2_threshold=self.r2_slider.value(), pre_event=pre_event)
 		
 		else:
 			self.group_name_user = 'group_' + self.name_le.text()
@@ -465,7 +458,8 @@ class ClassifierWidget(QWidget, Styles):
 				msgBox = QMessageBox()
 				msgBox.setIcon(QMessageBox.Information)
 				msgBox.setText(
-					f"The group column {self.group_name_user} already exists in the table.\nProceeding will reclassify. Do you want to continue?")
+					f"The group column {self.group_name_user} already exists in the table.\nProceeding will "
+					f"reclassify. Do you want to continue?")
 				msgBox.setWindowTitle("Warning")
 				msgBox.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
 				returnValue = msgBox.exec()
@@ -477,14 +471,18 @@ class ClassifierWidget(QWidget, Styles):
 			name_map = {self.class_name: self.group_name_user}
 			self.df = self.df.drop(list(set(name_map.values()) & set(self.df.columns)), axis=1).rename(columns=name_map)
 			print(self.df.columns)
-			#self.df[self.group_name_user] = self.df[self.group_name_user].replace({0: 1, 1: 0})
+			# self.df[self.group_name_user] = self.df[self.group_name_user].replace({0: 1, 1: 0})
 			self.df.reset_index(inplace=True, drop=True)
 
 		if 'custom' in list(self.df.columns):
-			self.df = self.df.drop(['custom'],axis=1)
-
-		for pos,pos_group in self.df.groupby('position'):
-			pos_group.to_csv(pos+os.sep.join(['output', 'tables', f'trajectories_{self.mode}.csv']), index=False)
+			self.df = self.df.drop(['custom'], axis=1)
+		
+		self.fig_props.set_size_inches(4, 3)
+		self.fig_props.suptitle(self.property_query_le.text(), fontsize=10)
+		self.fig_props.tight_layout()
+		for pos, pos_group in self.df.groupby('position'):
+			self.fig_props.savefig(str(pos)+os.sep.join(['output', f'{self.class_name}.png']), bbox_inches='tight', dpi=300)
+			pos_group.to_csv(str(pos)+os.sep.join(['output', 'tables', f'trajectories_{self.mode}.csv']), index=False)
 
 		self.parent_window.parent_window.update_position_options()
 		self.close()
@@ -496,7 +494,7 @@ class ClassifierWidget(QWidget, Styles):
 		Helper for segmentation strategy between threshold-based and Deep learning.
 		"""
 
-		dict_path = os.sep.join([get_software_location(),'celldetective','gui','help','propagate-classification.json'])
+		dict_path = os.sep.join([get_software_location(), 'celldetective', 'gui', 'help', 'propagate-classification.json'])
 
 		with open(dict_path) as f:
 			d = json.load(f)
@@ -520,53 +518,46 @@ class ClassifierWidget(QWidget, Styles):
 		Switch threshold histogram to log scale. Auto adjust.
 		"""
 
-		if i==1:
+		if i == 1:
 			try:
 				feat_x = self.features_cb[1].currentText()
 				min_x = self.df.dropna(subset=feat_x)[feat_x].min()
 				max_x = self.df.dropna(subset=feat_x)[feat_x].max()
 				x_padding = (max_x - min_x) * 0.05
-				if x_padding==0:
+				if x_padding == 0:
 					x_padding = 0.05
 
-				if self.ax_props.get_xscale()=='linear':
+				if self.ax_props.get_xscale() == 'linear':
 					self.ax_props.set_xlim(min_x, max_x)
 					self.ax_props.set_xscale('log')
-					self.log_btns[i].setIcon(icon(MDI6.math_log,color="#1565c0"))
+					self.log_btns[i].setIcon(icon(MDI6.math_log, color="#1565c0"))
 				else:
 					self.ax_props.set_xscale('linear')
 					self.ax_props.set_xlim(min_x - x_padding, max_x + x_padding)
-					self.log_btns[i].setIcon(icon(MDI6.math_log,color="black"))
+					self.log_btns[i].setIcon(icon(MDI6.math_log, color="black"))
 			except Exception as e:
 				print(e)
-		elif i==0:
+		elif i == 0:
 			try:
 				feat_y = self.features_cb[0].currentText()
 				min_y = self.df.dropna(subset=feat_y)[feat_y].min()
 				max_y = self.df.dropna(subset=feat_y)[feat_y].max()
 				y_padding = (max_y - min_y) * 0.05
-				if y_padding==0:
+				if y_padding == 0:
 					y_padding = 0.05
 
-				if self.ax_props.get_yscale()=='linear':
+				if self.ax_props.get_yscale() == 'linear':
 					self.ax_props.set_ylim(min_y, max_y)
 					self.ax_props.set_yscale('log')
-					self.log_btns[i].setIcon(icon(MDI6.math_log,color="#1565c0"))
+					self.log_btns[i].setIcon(icon(MDI6.math_log, color="#1565c0"))
 				else:
 					self.ax_props.set_yscale('linear')
 					self.ax_props.set_ylim(min_y - y_padding, max_y + y_padding)
-					self.log_btns[i].setIcon(icon(MDI6.math_log,color="black"))
+					self.log_btns[i].setIcon(icon(MDI6.math_log, color="black"))
 			except Exception as e:
 				print(e)
 
 		self.ax_props.autoscale()
 		self.propscanvas.canvas.draw_idle()
 
-		print('Done.')
-
-
-
-
-
-
-
+		print('Done.')

celldetective/gui/configure_new_exp.py

@@ -1,7 +1,6 @@
-from PyQt5.QtWidgets import QMainWindow, QApplication, QMessageBox, QHBoxLayout, QFileDialog, QVBoxLayout, QScrollArea, QCheckBox, QGridLayout, QLabel, QLineEdit, QPushButton, QWidget
+from PyQt5.QtWidgets import QApplication, 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.gui.styles import Styles
 from celldetective.utils import get_software_location
 import json
 
@@ -13,9 +12,10 @@ from configparser import ConfigParser
 import os
 from functools import partial
 import numpy as np
-from celldetective.gui import Styles
+from celldetective.gui import CelldetectiveMainWindow, CelldetectiveWidget
 
-class ConfigNewExperiment(QMainWindow, Styles):
+
+class ConfigNewExperiment(CelldetectiveMainWindow):
 
 	def __init__(self, parent_window=None):
 		
@@ -34,11 +34,11 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		
 		# Create button widget and layout
 		self.scroll_area = QScrollArea(self)
-		button_widget = QWidget()
+		button_widget = CelldetectiveWidget()
 		self.grid = QGridLayout()
 		button_widget.setLayout(self.grid)
 
-		self.grid.setContentsMargins(30,30,30,30)
+		self.grid.setContentsMargins(30, 30, 30, 30)
 		self.grid.addWidget(QLabel("Folder:"), 0, 0, 1, 3)
 		self.supFolder = QLineEdit()
 		self.supFolder.setAlignment(Qt.AlignLeft)	
@@ -64,17 +64,20 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		self.grid.addWidget(self.expName, 3, 0, 1, 3)
 
 		self.generate_movie_settings()
-		self.grid.addLayout(self.ms_grid,29,0,1,3)
+		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.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, 31, 0, 1, 3, alignment = Qt.AlignBottom)		
+		self.grid.addWidget(self.validate_button, 32, 0, 1, 3, alignment = Qt.AlignBottom)		
 		button_widget.adjustSize()
 
 		self.scroll_area.setAlignment(Qt.AlignCenter)
@@ -128,10 +131,9 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		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(32)
+		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:")
@@ -139,7 +141,7 @@ class ConfigNewExperiment(QMainWindow, Styles):
 
 		self.SliderPos = QLabeledSlider(Qt.Horizontal, self)
 		self.SliderPos.setMinimum(1)
-		self.SliderPos.setMaximum(50)
+		self.SliderPos.setMaximum(512)
 
 		self.ms_grid.addWidget(self.SliderPos, 4, 0, 1, 3)
 
@@ -168,7 +170,7 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		self.ms_grid.addWidget(self.movie_length,9, 0, 1, 3)
 		self.MovieLengthSlider = QLabeledSlider(Qt.Horizontal, self)
 		self.MovieLengthSlider.setMinimum(2)
-		self.MovieLengthSlider.setMaximum(128)
+		#self.MovieLengthSlider.setMaximum(128)
 		self.ms_grid.addWidget(self.MovieLengthSlider, 10, 0, 1, 3)
 
 		self.prefix_lbl = QLabel("Prefix for the movies:")
@@ -181,7 +183,7 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		self.movie_prefix_field.setText("")
 		self.ms_grid.addWidget(self.movie_prefix_field, 12, 0, 1, 3)
 
-		self.ms_grid.addWidget(QLabel("X shape in pixels:"), 13, 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)	
@@ -190,7 +192,7 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		self.shape_x_field.setText("2048")
 		self.ms_grid.addWidget(self.shape_x_field, 14, 0, 1, 3)
 
-		self.ms_grid.addWidget(QLabel("Y shape in pixels:"), 15, 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)	
@@ -271,7 +273,7 @@ class ConfigNewExperiment(QMainWindow, Styles):
 
 	def add_custom_channel(self):
 
-		self.CustomChannelWidget = QWidget()
+		self.CustomChannelWidget = CelldetectiveWidget()
 		self.CustomChannelWidget.setWindowTitle("Custom channel")
 		layout = QVBoxLayout()
 		self.CustomChannelWidget.setLayout(layout)
@@ -323,6 +325,83 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		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):
 
 		"""
@@ -362,6 +441,17 @@ class ConfigNewExperiment(QMainWindow, Styles):
 			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)
@@ -429,8 +519,13 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		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(',','.'))
@@ -456,6 +551,7 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		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)
@@ -464,7 +560,7 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		print(f'New experiment successfully configured in folder {self.directory}...')
 		self.close()
 
-class SetupConditionLabels(QWidget, Styles):
+class SetupConditionLabels(CelldetectiveWidget):
 	def __init__(self, parent_window, n_wells):
 		super().__init__()
 		self.parent_window = parent_window