celldetective 1.2.1__py3-none-any.whl → 1.2.2__py3-none-any.whl

celldetective/gui/process_block.py

@@ -1,46 +1,41 @@
-from PyQt5.QtWidgets import QFrame, QGridLayout, QRadioButton, QButtonGroup, QGroupBox, QComboBox,QTabWidget,QSizePolicy,QListWidget, QDialog, QLabel, QPushButton, QVBoxLayout, QHBoxLayout, QCheckBox, \
-	QMessageBox, QWidget, QLineEdit, QScrollArea, QSpacerItem, QLayout, QSizePolicy
+from PyQt5.QtWidgets import QFrame, QGridLayout, QComboBox, QListWidget, QLabel, QPushButton, QVBoxLayout, QHBoxLayout, QCheckBox, \
+	QMessageBox, QWidget
 from PyQt5.QtCore import Qt, QSize
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
 import gc
-from PyQt5.QtGui import QIcon, QDoubleValidator, QIntValidator
+from PyQt5.QtGui import QDoubleValidator, QIntValidator
 
 from celldetective.gui.signal_annotator import MeasureAnnotator
 from celldetective.gui.signal_annotator2 import SignalAnnotator2
 from celldetective.io import get_segmentation_models_list, control_segmentation_napari, get_signal_models_list, \
-	control_tracking_btrack, load_experiment_tables, get_pair_signal_models_list, get_position_pickle, get_position_table
-from celldetective.io import locate_segmentation_model, auto_load_number_of_frames, load_frames, locate_signal_model
+	control_tracking_btrack, load_experiment_tables, get_pair_signal_models_list
+from celldetective.io import locate_segmentation_model, fix_missing_labels, auto_load_number_of_frames, load_frames, locate_signal_model
 from celldetective.gui import SegmentationModelLoader, ClassifierWidget, ConfigNeighborhoods, ConfigSegmentationModelTraining, ConfigTracking, SignalAnnotator, ConfigSignalModelTraining, ConfigMeasurements, ConfigSignalAnnotator, TableUI
 from celldetective.gui.gui_utils import QHSeperationLine
 from celldetective.relative_measurements import rel_measure_at_position
 from celldetective.segmentation import segment_at_position, segment_from_threshold_at_position
 from celldetective.tracking import track_at_position
 from celldetective.measure import measure_at_position
-from celldetective.signals import analyze_signals_at_position, analyze_pair_signals, analyze_pair_signals_at_position
+from celldetective.signals import analyze_signals_at_position, analyze_pair_signals_at_position
 from celldetective.utils import extract_experiment_channels
 import numpy as np
 from glob import glob
 from natsort import natsorted
-from superqt import QLabeledDoubleSlider, QLabeledSlider, QLabeledRangeSlider, QLabeledSlider, QLabeledDoubleRangeSlider
 import os
 import pandas as pd
-from tqdm import tqdm
 from celldetective.gui.gui_utils import center_window
 from tifffile import imwrite
 import json
 import psutil
 from celldetective.neighborhood import compute_neighborhood_at_position, compute_contact_neighborhood_at_position
 from celldetective.gui.gui_utils import FigureCanvas
-import matplotlib.pyplot as plt
-from celldetective.filters import std_filter, median_filter, gauss_filter
-from stardist import fill_label_holes
-from celldetective.preprocessing import correct_background_model_free, estimate_background_per_condition, correct_background_model
+from celldetective.preprocessing import correct_background_model_free, correct_background_model
 from celldetective.utils import _estimate_scale_factor, _extract_channel_indices_from_config, _extract_channel_indices, ConfigSectionMap, _extract_nbr_channels_from_config, _get_img_num_per_channel, normalize_per_channel
-from celldetective.gui.gui_utils import ThresholdLineEdit, QuickSliderLayout
-from celldetective.gui.viewers import StackVisualizer, CellSizeViewer, ThresholdedStackVisualizer
-from celldetective.gui.layouts import BackgroundModelFreeCorrectionLayout, ProtocolDesignerLayout, BackgroundFitCorrectionLayout, OperationLayout
+from celldetective.gui.gui_utils import ThresholdLineEdit, QuickSliderLayout, help_generic
+from celldetective.gui.layouts import CellposeParamsWidget, StarDistParamsWidget, BackgroundModelFreeCorrectionLayout, ProtocolDesignerLayout, BackgroundFitCorrectionLayout
 from celldetective.gui import Styles
+from celldetective.utils import get_software_location
 
 class ProcessPanel(QFrame, Styles):
 	def __init__(self, parent_window, mode):
@@ -70,29 +65,45 @@ class ProcessPanel(QFrame, Styles):
 
 		"""
 
-		panel_title = QLabel(f"PROCESS {self.mode.upper()}")
+		panel_title = QLabel(f"PROCESS {self.mode.upper()}   ")
 		panel_title.setStyleSheet("""
 			font-weight: bold;
 			padding: 0px;
 			""")
 
+		title_hbox = QHBoxLayout()
 		self.grid.addWidget(panel_title, 0, 0, 1, 4, alignment=Qt.AlignCenter)
 
+		self.help_pop_btn = QPushButton()
+		self.help_pop_btn.setIcon(icon(MDI6.help_circle,color=self.help_color))
+		self.help_pop_btn.setIconSize(QSize(20, 20))
+		self.help_pop_btn.clicked.connect(self.help_population)
+		self.help_pop_btn.setStyleSheet(self.button_select_all)
+		self.help_pop_btn.setToolTip("Help.")
+		#self.grid.addWidget(self.help_pop_btn, 0, 0, 1, 3, alignment=Qt.AlignRight)
+
+
 		self.select_all_btn = QPushButton()
 		self.select_all_btn.setIcon(icon(MDI6.checkbox_blank_outline,color="black"))
 		self.select_all_btn.setIconSize(QSize(20, 20))
 		self.all_ticked = False
 		self.select_all_btn.clicked.connect(self.tick_all_actions)
 		self.select_all_btn.setStyleSheet(self.button_select_all)
-		self.grid.addWidget(self.select_all_btn, 0, 0, 1, 4, alignment=Qt.AlignLeft)
+		#self.grid.addWidget(self.select_all_btn, 0, 0, 1, 4, alignment=Qt.AlignLeft)
 		#self.to_disable.append(self.all_tc_actions)
 
 		self.collapse_btn = QPushButton()
 		self.collapse_btn.setIcon(icon(MDI6.chevron_down,color="black"))
 		self.collapse_btn.setIconSize(QSize(25, 25))
 		self.collapse_btn.setStyleSheet(self.button_select_all)
-		self.grid.addWidget(self.collapse_btn, 0, 0, 1, 4, alignment=Qt.AlignRight)
+		#self.grid.addWidget(self.collapse_btn, 0, 0, 1, 4, alignment=Qt.AlignRight)
+
+		title_hbox.addWidget(self.select_all_btn, 5)
+		title_hbox.addWidget(QLabel(), 85, alignment=Qt.AlignCenter)
+		title_hbox.addWidget(self.help_pop_btn, 5)
+		title_hbox.addWidget(self.collapse_btn, 5)
 
+		self.grid.addLayout(title_hbox, 0,0,1,4)
 		self.populate_contents()
 
 		self.grid.addWidget(self.ContentsFrame, 1, 0, 1, 4, alignment=Qt.AlignTop)
@@ -101,22 +112,48 @@ class ProcessPanel(QFrame, Styles):
 		self.ContentsFrame.hide()
 
 	def collapse_advanced(self):
+
+		effector_open = not self.parent_window.ProcessEffectors.ContentsFrame.isHidden()
+		targets_open = not self.parent_window.ProcessTargets.ContentsFrame.isHidden()
+		interactions_open = not self.parent_window.NeighPanel.ContentsFrame.isHidden()
+		preprocessing_open = not self.parent_window.PreprocessingPanel.ContentsFrame.isHidden()
+		is_open = np.array([effector_open, targets_open, interactions_open, preprocessing_open])
+
 		if self.ContentsFrame.isHidden():
 			self.collapse_btn.setIcon(icon(MDI6.chevron_down,color="black"))
 			self.collapse_btn.setIconSize(QSize(20, 20))
-			self.parent_window.scroll.setMinimumHeight(int(550))
-			#self.parent.w.adjustSize()
-			self.parent_window.adjustSize()
-			#self.parent.scroll.adjustSize()
+			if len(is_open[is_open])==0:
+				self.parent_window.scroll.setMinimumHeight(int(550))
+				self.parent_window.adjustSize()
 		else:
 			self.collapse_btn.setIcon(icon(MDI6.chevron_up,color="black"))
 			self.collapse_btn.setIconSize(QSize(20, 20))
-			#self.parent.w.adjustSize()
-			#self.parent.adjustSize()
 			self.parent_window.scroll.setMinimumHeight(min(int(930), int(0.9*self.parent_window.screen_height)))
-			self.parent_window.scroll.setMinimumWidth(425)
 
-			#self.parent.scroll.adjustSize()
+
+	def help_population(self):
+
+		"""
+		Helper to choose a proper cell population structure.
+		"""
+
+		dict_path = os.sep.join([get_software_location(),'celldetective','gui','help','cell-populations.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)
+			msgBox.setWindowTitle("Info")
+			msgBox.setStandardButtons(QMessageBox.Ok)
+			returnValue = msgBox.exec()
+			if returnValue == QMessageBox.Ok:
+				return None			
 
 	def populate_contents(self):
 		self.ContentsFrame = QFrame()
@@ -265,7 +302,7 @@ class ProcessPanel(QFrame, Styles):
 			padding-left: 10px;
 			padding-top: 5px;
 			""")
-		grid_track.addWidget(self.track_action, 80)
+		grid_track.addWidget(self.track_action, 75)
 		#self.to_disable.append(self.track_action_tc)
 
 		# self.show_track_table_btn = QPushButton()
@@ -304,6 +341,14 @@ class ProcessPanel(QFrame, Styles):
 		self.track_config_btn.clicked.connect(self.open_tracking_configuration_ui)
 		grid_track.addWidget(self.track_config_btn, 6) #4,2,1,1, alignment=Qt.AlignRight
 
+		self.help_track_btn = QPushButton()
+		self.help_track_btn.setIcon(icon(MDI6.help_circle,color=self.help_color))
+		self.help_track_btn.setIconSize(QSize(20, 20))
+		self.help_track_btn.clicked.connect(self.help_tracking)
+		self.help_track_btn.setStyleSheet(self.button_select_all)
+		self.help_track_btn.setToolTip("Help.")
+		grid_track.addWidget(self.help_track_btn, 6) #4,2,1,1, alignment=Qt.AlignRight
+
 		self.grid_contents.addLayout(grid_track, 4, 0, 1,4)
 
 	def delete_tracks(self):
@@ -352,9 +397,15 @@ class ProcessPanel(QFrame, Styles):
 		self.check_seg_btn.clicked.connect(self.check_segmentation)
 		self.check_seg_btn.setStyleSheet(self.button_select_all)
 		self.check_seg_btn.setToolTip("View segmentation output in napari.")
-		#self.check_seg_btn.setEnabled(False)
-		#self.to_disable.append(self.control_target_seg)
-		grid_segment.addWidget(self.check_seg_btn, 10)
+		grid_segment.addWidget(self.check_seg_btn, 5)
+
+		self.help_seg_btn = QPushButton()
+		self.help_seg_btn.setIcon(icon(MDI6.help_circle,color=self.help_color))
+		self.help_seg_btn.setIconSize(QSize(20, 20))
+		self.help_seg_btn.clicked.connect(self.help_segmentation)
+		self.help_seg_btn.setStyleSheet(self.button_select_all)
+		self.help_seg_btn.setToolTip("Help.")
+		grid_segment.addWidget(self.help_seg_btn, 5)
 		self.grid_contents.addLayout(grid_segment, 0,0,1,4)
 
 		seg_option_vbox = QVBoxLayout()
@@ -391,6 +442,107 @@ class ProcessPanel(QFrame, Styles):
 		self.seg_model_list.setEnabled(False)
 		self.grid_contents.addLayout(seg_option_vbox, 2, 0, 1, 4)
 
+	def help_segmentation(self):
+
+		"""
+		Widget with different decision helper decision trees.
+		"""
+
+		self.help_w = QWidget()
+		self.help_w.setWindowTitle('Helper')
+		layout = QVBoxLayout()
+		seg_strategy_btn = QPushButton('A guide to choose a segmentation strategy.')
+		seg_strategy_btn.setIcon(icon(MDI6.help_circle,color=self.celldetective_blue))
+		seg_strategy_btn.setIconSize(QSize(40, 40))
+		seg_strategy_btn.setStyleSheet(self.button_style_sheet_5)
+		seg_strategy_btn.clicked.connect(self.help_seg_strategy)
+
+		dl_strategy_btn = QPushButton('A guide to choose your Deep learning segmentation strategy.')
+		dl_strategy_btn.setIcon(icon(MDI6.help_circle,color=self.celldetective_blue))
+		dl_strategy_btn.setIconSize(QSize(40, 40))
+		dl_strategy_btn.setStyleSheet(self.button_style_sheet_5)
+		dl_strategy_btn.clicked.connect(self.help_seg_dl_strategy)
+
+		layout.addWidget(seg_strategy_btn)
+		layout.addWidget(dl_strategy_btn)
+
+		self.help_w.setLayout(layout)
+		center_window(self.help_w)
+		self.help_w.show()
+
+		return None
+
+	def help_seg_strategy(self):
+
+		"""
+		Helper for segmentation strategy between threshold-based and Deep learning.
+		"""
+
+		dict_path = os.sep.join([get_software_location(),'celldetective','gui','help','Threshold-vs-DL.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(f"The suggested technique is {suggestion}.\nSee a tutorial <a href='https://celldetective.readthedocs.io/en/latest/segment.html'>here</a>.")
+			msgBox.setWindowTitle("Info")
+			msgBox.setStandardButtons(QMessageBox.Ok)
+			returnValue = msgBox.exec()
+			if returnValue == QMessageBox.Ok:
+				return None
+
+	def help_seg_dl_strategy(self):
+		
+		"""
+		Helper for DL segmentation strategy, between pretrained models and custom models.
+		"""
+
+		dict_path = os.sep.join([get_software_location(),'celldetective','gui','help','DL-segmentation-strategy.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.setText(f"The suggested technique is {suggestion}.")
+			msgBox.setWindowTitle("Info")
+			msgBox.setStandardButtons(QMessageBox.Ok)
+			returnValue = msgBox.exec()
+			if returnValue == QMessageBox.Ok:
+				return None
+
+	def help_tracking(self):
+
+		"""
+		Helper for segmentation strategy between threshold-based and Deep learning.
+		"""
+
+		dict_path = os.sep.join([get_software_location(),'celldetective','gui','help','tracking.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(f"{suggestion}")
+			msgBox.setWindowTitle("Info")
+			msgBox.setStandardButtons(QMessageBox.Ok)
+			returnValue = msgBox.exec()
+			if returnValue == QMessageBox.Ok:
+				return None
+
 	def check_segmentation(self):
 
 		if not os.path.exists(os.sep.join([self.parent_window.pos,f'labels_{self.mode}', os.sep])):
@@ -422,6 +574,24 @@ class ProcessPanel(QFrame, Styles):
 				msgBox.setWindowTitle("Warning")
 				msgBox.setStandardButtons(QMessageBox.Ok)
 				returnValue = msgBox.exec()
+
+				msgBox = QMessageBox()
+				msgBox.setIcon(QMessageBox.Question)
+				msgBox.setText("Would you like to pass empty frames to fix the asymmetry?")
+				msgBox.setWindowTitle("Question")
+				msgBox.setStandardButtons(QMessageBox.Yes | QMessageBox.No | QMessageBox.Cancel)
+				returnValue = msgBox.exec()
+				if returnValue == QMessageBox.Yes:
+					print('Fixing the missing labels...')
+					fix_missing_labels(self.parent_window.pos, prefix=self.parent_window.movie_prefix,population=self.mode)
+					try:
+						control_segmentation_napari(self.parent_window.pos, prefix=self.parent_window.movie_prefix, population=self.mode,flush_memory=True)
+					except Exception as e:
+						print(f'Error {e}')
+						return None
+				else:
+					return None
+
 			gc.collect()
 
 	def check_signals(self):
@@ -507,27 +677,27 @@ class ProcessPanel(QFrame, Styles):
 			self.all_ticked = True
 
 	def upload_segmentation_model(self):
-
+		print('Load a segmentation model or pipeline...')
 		self.SegModelLoader = SegmentationModelLoader(self)
 		self.SegModelLoader.show()
 
 	def open_tracking_configuration_ui(self):
-
+		print('Set the tracking parameters...')
 		self.ConfigTracking = ConfigTracking(self)
 		self.ConfigTracking.show()
 
 	def open_signal_model_config_ui(self):
-
+		print('Set the training parameters for new signal models...')
 		self.ConfigSignalTrain = ConfigSignalModelTraining(self)
 		self.ConfigSignalTrain.show()
 
 	def open_segmentation_model_config_ui(self):
-
+		print('Set the training parameters for a new segmentation model...')
 		self.ConfigSegmentationTrain = ConfigSegmentationModelTraining(self)
 		self.ConfigSegmentationTrain.show()
 
 	def open_measurement_configuration_ui(self):
-
+		print('Set the measurements to be performed...')
 		self.ConfigMeasurements = ConfigMeasurements(self)
 		self.ConfigMeasurements.show()
 
@@ -611,120 +781,14 @@ class ProcessPanel(QFrame, Styles):
 
 		if self.model_name.startswith('CP') and self.model_name in self.seg_models_generic and not self.cellpose_calibrated:
 
-			self.diamWidget = QWidget()
-			self.diamWidget.setWindowTitle('Estimate diameter')
-
-			layout = QVBoxLayout()
-			self.diamWidget.setLayout(layout)
-
-			self.view_diameter_btn = QPushButton()
-			self.view_diameter_btn.setStyleSheet(self.button_select_all)
-			self.view_diameter_btn.setIcon(icon(MDI6.image_check, color="black"))
-			self.view_diameter_btn.setToolTip("View stack.")
-			self.view_diameter_btn.setIconSize(QSize(20, 20))
-			self.view_diameter_btn.clicked.connect(self.view_current_stack_with_scale_bar)
-
-			self.diameter_le = ThresholdLineEdit(init_value=40, connected_buttons=[self.view_diameter_btn],placeholder='cell diameter in pixels', value_type='float')
-
-			self.cellpose_channel_cb = [QComboBox() for i in range(2)]
-			self.cellpose_channel_template = ['brightfield_channel', 'live_nuclei_channel']
-			if self.model_name=="CP_nuclei":
-				self.cellpose_channel_template = ['live_nuclei_channel', 'None']
-
-
-			for k in range(2):
-				hbox_channel = QHBoxLayout()
-				hbox_channel.addWidget(QLabel(f'channel {k+1}: '))
-				hbox_channel.addWidget(self.cellpose_channel_cb[k])
-				if k==1:
-					self.cellpose_channel_cb[k].addItems(list(self.exp_channels)+['None'])
-				else:
-					self.cellpose_channel_cb[k].addItems(list(self.exp_channels))
-				idx = self.cellpose_channel_cb[k].findText(self.cellpose_channel_template[k])
-				if idx>0:
-					self.cellpose_channel_cb[k].setCurrentIndex(idx)
-				else:
-					self.cellpose_channel_cb[k].setCurrentIndex(0)
-
-				if k==1:
-					idx = self.cellpose_channel_cb[k].findText('None')
-					self.cellpose_channel_cb[k].setCurrentIndex(idx)
-
-				layout.addLayout(hbox_channel)
-
-			hbox = QHBoxLayout()
-			hbox.addWidget(QLabel('diameter [px]: '), 33)
-			hbox.addWidget(self.diameter_le, 61)
-			hbox.addWidget(self.view_diameter_btn)
-			layout.addLayout(hbox)
-
-			self.flow_slider = QLabeledDoubleSlider()
-			self.flow_slider.setOrientation(1)
-			self.flow_slider.setRange(-6,6)
-			self.flow_slider.setValue(0.4)
-
-			hbox = QHBoxLayout()
-			hbox.addWidget(QLabel('flow threshold: '), 33)
-			hbox.addWidget(self.flow_slider, 66)
-			layout.addLayout(hbox)
-
-			self.cellprob_slider = QLabeledDoubleSlider()
-			self.cellprob_slider.setOrientation(1)
-			self.cellprob_slider.setRange(-6,6)
-			self.cellprob_slider.setValue(0.)
-
-			hbox = QHBoxLayout()
-			hbox.addWidget(QLabel('cellprob threshold: '), 33)
-			hbox.addWidget(self.cellprob_slider, 66)
-			layout.addLayout(hbox)
-
-			self.set_cellpose_scale_btn = QPushButton('set')
-			self.set_cellpose_scale_btn.clicked.connect(self.set_cellpose_scale)
-			layout.addWidget(self.set_cellpose_scale_btn)
-
+			self.diamWidget = CellposeParamsWidget(self, model_name=self.model_name)
 			self.diamWidget.show()
-			center_window(self.diamWidget)
 			return None
 
-
 		if self.model_name.startswith('SD') and self.model_name in self.seg_models_generic and not self.stardist_calibrated:
 
-			self.diamWidget = QWidget()
-			self.diamWidget.setWindowTitle('Channels')
-
-			layout = QVBoxLayout()
-			self.diamWidget.setLayout(layout)
-
-			self.stardist_channel_cb = [QComboBox() for i in range(1)]
-			self.stardist_channel_template = ['live_nuclei_channel']
-			max_i = 1
-			if self.model_name=="SD_versatile_he":
-				self.stardist_channel_template = ["H&E_1","H&E_2","H&E_3"]
-				self.stardist_channel_cb = [QComboBox() for i in range(3)]
-				max_i = 3
-
-			for k in range(max_i):
-				hbox_channel = QHBoxLayout()
-				hbox_channel.addWidget(QLabel(f'channel {k+1}: '))
-				hbox_channel.addWidget(self.stardist_channel_cb[k])
-				if k==1:
-					self.stardist_channel_cb[k].addItems(list(self.exp_channels)+['None'])
-				else:
-					self.stardist_channel_cb[k].addItems(list(self.exp_channels))
-				idx = self.stardist_channel_cb[k].findText(self.stardist_channel_template[k])
-				if idx>0:
-					self.stardist_channel_cb[k].setCurrentIndex(idx)
-				else:
-					self.stardist_channel_cb[k].setCurrentIndex(0)
-
-				layout.addLayout(hbox_channel)
-
-			self.set_stardist_scale_btn = QPushButton('set')
-			self.set_stardist_scale_btn.clicked.connect(self.set_stardist_scale)
-			layout.addWidget(self.set_stardist_scale_btn)
-
+			self.diamWidget = StarDistParamsWidget(self, model_name = self.model_name)
 			self.diamWidget.show()
-			center_window(self.diamWidget)
 			return None
 
 
@@ -823,27 +887,28 @@ class ProcessPanel(QFrame, Styles):
 		# QApplication.restoreOverrideCursor()
 		# self.unfreeze()
 
-	def view_current_stack_with_scale_bar(self):
+	# def view_current_stack_with_scale_bar(self):
 
-		self.parent_window.locate_image()
-		if self.parent_window.current_stack is not None:
-			self.viewer = CellSizeViewer(
-										  initial_diameter = float(self.diameter_le.text().replace(',', '.')),
-				parent_le = self.diameter_le,
-										  stack_path=self.parent_window.current_stack,
-										  window_title=f'Position {self.parent_window.position_list.currentText()}',
-										  frame_slider = True,
-										  contrast_slider = True,
-										  channel_cb = True,
-										  channel_names = self.parent_window.exp_channels,
-										  n_channels = self.parent_window.nbr_channels,
-										  PxToUm = 1,
-										 )
-			self.viewer.show()
+	# 	self.parent_window.locate_image()
+	# 	if self.parent_window.current_stack is not None:
+	# 		self.viewer = CellSizeViewer(
+	# 									  initial_diameter = float(self.diameter_le.text().replace(',', '.')),
+	# 			parent_le = self.diameter_le,
+	# 									  stack_path=self.parent_window.current_stack,
+	# 									  window_title=f'Position {self.parent_window.position_list.currentText()}',
+	# 									  frame_slider = True,
+	# 									  contrast_slider = True,
+	# 									  channel_cb = True,
+	# 									  channel_names = self.parent_window.exp_channels,
+	# 									  n_channels = self.parent_window.nbr_channels,
+	# 									  PxToUm = 1,
+	# 									 )
+	# 		self.viewer.show()
 
 
 
 	def open_napari_tracking(self):
+		print(f'View the tracks before post-processing for position {self.parent_window.pos} in napari...')
 		control_tracking_btrack(self.parent_window.pos, prefix=self.parent_window.movie_prefix, population=self.mode, threads=self.parent_window.parent_window.n_threads)
 
 	def view_table_ui(self):
@@ -910,14 +975,14 @@ class ProcessPanel(QFrame, Styles):
 
 	def set_cellpose_scale(self):
 
-		scale = self.parent_window.PxToUm * float(self.diameter_le.get_threshold()) / 30.0
+		scale = self.parent_window.PxToUm * float(self.diamWidget.diameter_le.get_threshold()) / 30.0
 		if self.model_name=="CP_nuclei":
-			scale = self.parent_window.PxToUm * float(self.diameter_le.get_threshold()) / 17.0
-		flow_thresh = self.flow_slider.value()
-		cellprob_thresh = self.cellprob_slider.value()
+			scale = self.parent_window.PxToUm * float(self.diamWidget.diameter_le.get_threshold()) / 17.0
+		flow_thresh = self.diamWidget.flow_slider.value()
+		cellprob_thresh = self.diamWidget.cellprob_slider.value()
 		model_complete_path = locate_segmentation_model(self.model_name)
 		input_config_path = model_complete_path+"config_input.json"
-		new_channels = [self.cellpose_channel_cb[i].currentText() for i in range(2)]
+		new_channels = [self.diamWidget.cellpose_channel_cb[i].currentText() for i in range(2)]
 		print(new_channels)
 		with open(input_config_path) as config_file:
 			input_config = json.load(config_file)
@@ -936,21 +1001,13 @@ class ProcessPanel(QFrame, Styles):
 
 	def set_stardist_scale(self):
 
-		# scale = self.parent.PxToUm * float(self.diameter_le.text()) / 30.0
-		# if self.model_name=="CP_nuclei":
-		# 	scale = self.parent.PxToUm * float(self.diameter_le.text()) / 17.0
-		# flow_thresh = self.flow_slider.value()
-		# cellprob_thresh = self.cellprob_slider.value()
 		model_complete_path = locate_segmentation_model(self.model_name)
 		input_config_path = model_complete_path+"config_input.json"
-		new_channels = [self.stardist_channel_cb[i].currentText() for i in range(len(self.stardist_channel_cb))]
+		new_channels = [self.diamWidget.stardist_channel_cb[i].currentText() for i in range(len(self.diamWidget.stardist_channel_cb))]
 		with open(input_config_path) as config_file:
 			input_config = json.load(config_file)
 
-		# input_config['spatial_calibration'] = scale
 		input_config['channels'] = new_channels
-		# input_config['flow_threshold'] = flow_thresh
-		# input_config['cellprob_threshold'] = cellprob_thresh
 		with open(input_config_path, 'w') as f:
 			json.dump(input_config, f, indent=4)
 
@@ -1008,19 +1065,22 @@ class NeighPanel(QFrame, Styles):
 
 	def collapse_advanced(self):
 
+		effector_open = not self.parent_window.ProcessEffectors.ContentsFrame.isHidden()
+		targets_open = not self.parent_window.ProcessTargets.ContentsFrame.isHidden()
+		interactions_open = not self.parent_window.NeighPanel.ContentsFrame.isHidden()
+		preprocessing_open = not self.parent_window.PreprocessingPanel.ContentsFrame.isHidden()
+		is_open = np.array([effector_open, targets_open, interactions_open, preprocessing_open])
+
 		if self.ContentsFrame.isHidden():
 			self.collapse_btn.setIcon(icon(MDI6.chevron_down,color="black"))
 			self.collapse_btn.setIconSize(QSize(20, 20))
-			self.parent_window.scroll.setMinimumHeight(int(550))
-			#self.parent.w.adjustSize()
-			self.parent_window.adjustSize()
+			if len(is_open[is_open])==0:
+				self.parent_window.scroll.setMinimumHeight(int(550))
+				self.parent_window.adjustSize()
 		else:
 			self.collapse_btn.setIcon(icon(MDI6.chevron_up,color="black"))
 			self.collapse_btn.setIconSize(QSize(20, 20))
-			#self.parent.w.adjustSize()
-			#self.parent.adjustSize()
 			self.parent_window.scroll.setMinimumHeight(min(int(1000), int(0.9*self.parent_window.screen_height)))
-			self.parent_window.scroll.setMinimumWidth(425)
 
 
 	def populate_contents(self):
@@ -1042,9 +1102,21 @@ class NeighPanel(QFrame, Styles):
 		#self.neigh_action.setIconSize(QSize(20, 20))
 		self.neigh_action.setToolTip(
 			"Compute neighborhoods in list below.")
+
 		neigh_option_hbox.addWidget(self.neigh_action,90)
+
+
+		self.help_neigh_btn = QPushButton()
+		self.help_neigh_btn.setIcon(icon(MDI6.help_circle,color=self.help_color))
+		self.help_neigh_btn.setIconSize(QSize(20, 20))
+		self.help_neigh_btn.clicked.connect(self.help_neighborhood)
+		self.help_neigh_btn.setStyleSheet(self.button_select_all)
+		self.help_neigh_btn.setToolTip("Help.")
+		neigh_option_hbox.addWidget(self.help_neigh_btn,5,alignment=Qt.AlignRight)
+
 		self.grid_contents.addLayout(neigh_option_hbox, 1,0,1,4)
 
+
 		neigh_options_layout = QVBoxLayout()
 
 		neigh_options_vbox = QVBoxLayout()
@@ -1233,6 +1305,31 @@ class NeighPanel(QFrame, Styles):
 		self.neigh_action.setChecked(False)
 
 
+	def help_neighborhood(self):
+
+		"""
+		Helper for neighborhood strategy.
+		"""
+
+		dict_path = os.sep.join([get_software_location(),'celldetective','gui','help','neighborhood.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(f"{suggestion}\nSee a tutorial <a href='https://celldetective.readthedocs.io/en/latest/interactions.html#neighborhood'>here</a>.")
+			msgBox.setWindowTitle("Info")
+			msgBox.setStandardButtons(QMessageBox.Ok)
+			returnValue = msgBox.exec()
+			if returnValue == QMessageBox.Ok:
+				return None
+
+
 	def load_available_tables(self):
 
 		"""
@@ -1520,19 +1617,22 @@ class PreprocessingPanel(QFrame, Styles):
 
 	def collapse_advanced(self):
 
+		effector_open = not self.parent_window.ProcessEffectors.ContentsFrame.isHidden()
+		targets_open = not self.parent_window.ProcessTargets.ContentsFrame.isHidden()
+		interactions_open = not self.parent_window.NeighPanel.ContentsFrame.isHidden()
+		preprocessing_open = not self.parent_window.PreprocessingPanel.ContentsFrame.isHidden()
+		is_open = np.array([effector_open, targets_open, interactions_open, preprocessing_open])
+
 		if self.ContentsFrame.isHidden():
 			self.collapse_btn.setIcon(icon(MDI6.chevron_down,color="black"))
 			self.collapse_btn.setIconSize(QSize(20, 20))
-			self.parent_window.scroll.setMinimumHeight(int(550))
-			#self.parent.w.adjustSize()
-			self.parent_window.adjustSize()
+			if len(is_open[is_open])==0:
+				self.parent_window.scroll.setMinimumHeight(int(550))
+				self.parent_window.adjustSize()
 		else:
 			self.collapse_btn.setIcon(icon(MDI6.chevron_up,color="black"))
 			self.collapse_btn.setIconSize(QSize(20, 20))
-			#self.parent.w.adjustSize()
-			#self.parent.adjustSize()
 			self.parent_window.scroll.setMinimumHeight(min(int(930), int(0.9*self.parent_window.screen_height)))
-			self.parent_window.scroll.setMinimumWidth(425)
 
 	def populate_contents(self):
 
@@ -1547,6 +1647,16 @@ class PreprocessingPanel(QFrame, Styles):
 											  tab_names=['Fit', 'Model-free'],
 											  title='BACKGROUND CORRECTION',
 											  list_title='Corrections to apply:')
+		
+		self.help_background_btn = QPushButton()
+		self.help_background_btn.setIcon(icon(MDI6.help_circle,color=self.help_color))
+		self.help_background_btn.setIconSize(QSize(20, 20))
+		self.help_background_btn.clicked.connect(self.help_background)
+		self.help_background_btn.setStyleSheet(self.button_select_all)
+		self.help_background_btn.setToolTip("Help.")
+
+		self.protocol_layout.title_layout.addWidget(self.help_background_btn, 5, alignment=Qt.AlignRight)
+
 		self.grid_contents.addLayout(self.protocol_layout,0,0,1,4)
 		self.submit_preprocessing_btn = QPushButton("Submit")
 		self.submit_preprocessing_btn.setStyleSheet(self.button_style_sheet_2)
@@ -1650,4 +1760,28 @@ class PreprocessingPanel(QFrame, Styles):
 				self.current_stack = None
 				return None
 		else:
-			self.current_stack = movies[0]
+			self.current_stack = movies[0]
+
+	def help_background(self):
+
+		"""
+		Helper to choose a proper cell population structure.
+		"""
+
+		dict_path = os.sep.join([get_software_location(),'celldetective','gui','help','preprocessing.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)
+			msgBox.setWindowTitle("Info")
+			msgBox.setStandardButtons(QMessageBox.Ok)
+			returnValue = msgBox.exec()
+			if returnValue == QMessageBox.Ok:
+				return None