celldetective 1.4.2__py3-none-any.whl → 1.5.0b1__py3-none-any.whl

celldetective/gui/viewers.py

@@ -1,1354 +0,0 @@
-from celldetective.io import auto_load_number_of_frames, load_frames
-from celldetective.filters import *
-from celldetective.segmentation import filter_image, threshold_image
-from celldetective.measure import contour_of_instance_segmentation, extract_blobs_in_image
-from celldetective.utils import _get_img_num_per_channel, estimate_unreliable_edge, is_integer_array
-from tifffile import imread
-import matplotlib.pyplot as plt 
-from pathlib import Path
-from natsort import natsorted
-from glob import glob
-import os
-
-from PyQt5.QtWidgets import QHBoxLayout, QMessageBox, QPushButton, QLabel, QComboBox, QLineEdit, QListWidget, QShortcut
-from PyQt5.QtCore import Qt, QSize
-from PyQt5.QtGui import QKeySequence, QDoubleValidator
-from celldetective.gui.gui_utils import FigureCanvas, QuickSliderLayout, QHSeperationLine, ThresholdLineEdit, PreprocessingLayout2
-from celldetective.gui import CelldetectiveWidget
-from superqt import QLabeledDoubleSlider, QLabeledSlider, QLabeledDoubleRangeSlider
-from superqt.fonticon import icon
-from fonticon_mdi6 import MDI6
-from matplotlib_scalebar.scalebar import ScaleBar
-import gc
-from scipy.ndimage import shift
-
-class StackVisualizer(CelldetectiveWidget):
-
-	"""
-	A widget for visualizing image stacks with interactive sliders and channel selection.
-
-	Parameters:
-	- stack (numpy.ndarray or None): The stack of images.
-	- stack_path (str or None): The path to the stack of images if provided as a file.
-	- frame_slider (bool): Enable frame navigation slider.
-	- contrast_slider (bool): Enable contrast adjustment slider.
-	- channel_cb (bool): Enable channel selection dropdown.
-	- channel_names (list or None): Names of the channels if `channel_cb` is True.
-	- n_channels (int): Number of channels.
-	- target_channel (int): Index of the target channel.
-	- window_title (str): Title of the window.
-	- PxToUm (float or None): Pixel to micrometer conversion factor.
-	- background_color (str): Background color of the widget.
-	- imshow_kwargs (dict): Additional keyword arguments for imshow function.
-
-	Methods:
-	- show(): Display the widget.
-	- load_stack(): Load the stack of images.
-	- locate_image_virtual(): Locate the stack of images if provided as a file.
-	- generate_figure_canvas(): Generate the figure canvas for displaying images.
-	- generate_channel_cb(): Generate the channel dropdown if enabled.
-	- generate_contrast_slider(): Generate the contrast slider if enabled.
-	- generate_frame_slider(): Generate the frame slider if enabled.
-	- set_target_channel(value): Set the target channel.
-	- change_contrast(value): Change contrast based on slider value.
-	- set_channel_index(value): Set the channel index based on dropdown value.
-	- change_frame(value): Change the displayed frame based on slider value.
-	- closeEvent(event): Event handler for closing the widget.
-
-	Notes:
-	- This class provides a convenient interface for visualizing image stacks with frame navigation,
-	  contrast adjustment, and channel selection functionalities.
-	"""
-	
-	def __init__(self, stack=None, stack_path=None, frame_slider=True, contrast_slider=True, channel_cb=False, channel_names=None, n_channels=1, target_channel=0, window_title='View', PxToUm=None, background_color='transparent',imshow_kwargs={}):
-		super().__init__()
-
-		#self.setWindowTitle(window_title)
-		self.window_title = window_title
-
-		self.stack = stack
-		self.stack_path = stack_path
-		self.create_frame_slider = frame_slider
-		self.background_color = background_color
-		self.create_contrast_slider = contrast_slider
-		self.create_channel_cb = channel_cb
-		self.n_channels = n_channels
-		self.channel_names = channel_names
-		self.target_channel = target_channel
-		self.imshow_kwargs = imshow_kwargs
-		self.PxToUm = PxToUm
-		self.init_contrast = False
-		self.channel_trigger = False
-
-		self.load_stack() # need to get stack, frame etc
-		self.generate_figure_canvas()
-		if self.create_channel_cb:
-			self.generate_channel_cb()
-		if self.create_contrast_slider:
-			self.generate_contrast_slider()
-		if self.create_frame_slider:
-			self.generate_frame_slider()
-
-		self.canvas.layout.setContentsMargins(15,15,15,30)
-		#center_window(self)
-
-	def show(self):
-		# Display the widget
-		self.canvas.show()
-
-	def load_stack(self):
-		# Load the stack of images
-		if self.stack is not None:
-
-			if isinstance(self.stack, list):
-				self.stack = np.array(self.stack)
-
-			if self.stack.ndim==3:
-				print('No channel axis found...')
-				self.stack = self.stack[:,:,:,np.newaxis]
-				self.target_channel = 0
-			
-			self.mode = 'direct'
-			self.stack_length = len(self.stack)
-			self.mid_time = self.stack_length // 2
-			self.init_frame = self.stack[self.mid_time,:,:,self.target_channel]
-			self.last_frame = self.stack[-1,:,:,self.target_channel]
-		else:
-			self.mode = 'virtual'
-			assert isinstance(self.stack_path, str)
-			assert self.stack_path.endswith('.tif')
-			self.locate_image_virtual()
-
-	def locate_image_virtual(self):
-		# Locate the stack of images if provided as a file
-
-		self.stack_length = auto_load_number_of_frames(self.stack_path)
-		self.mid_time = self.stack_length // 2
-		self.img_num_per_channel = _get_img_num_per_channel(np.arange(self.n_channels), self.stack_length, self.n_channels)
-
-		self.init_frame = load_frames(self.img_num_per_channel[self.target_channel, self.mid_time], 
-									  self.stack_path,
-									  normalize_input=False).astype(float)[:,:,0]
-		self.last_frame = load_frames(self.img_num_per_channel[self.target_channel, self.stack_length-1], 
-									  self.stack_path,
-									  normalize_input=False).astype(float)[:,:,0]
-
-
-	def generate_figure_canvas(self):
-		# Generate the figure canvas for displaying images
-
-		self.fig, self.ax = plt.subplots(figsize=(5,5),tight_layout=True) #figsize=(5, 5)
-		self.canvas = FigureCanvas(self.fig, title=self.window_title, interactive=True)
-		self.ax.clear()
-		self.im = self.ax.imshow(self.init_frame, cmap='gray', interpolation='none', zorder=0, **self.imshow_kwargs)
-		if self.PxToUm is not None:
-			scalebar = ScaleBar(self.PxToUm,
-								"um",
-								length_fraction=0.25,
-								location='upper right',
-								border_pad=0.4,
-								box_alpha=0.95,
-								color='white',
-								box_color='black',
-								)
-			if self.PxToUm==1:
-				scalebar = ScaleBar(1,
-								"px",
-								dimension="pixel-length",
-								length_fraction=0.25,
-								location='upper right',
-								border_pad=0.4,
-								box_alpha=0.95,
-								color='white',
-								box_color='black',
-								)
-			self.ax.add_artist(scalebar)
-		self.ax.set_xticks([])
-		self.ax.set_yticks([])
-		self.fig.set_facecolor('none')  # or 'None'
-		self.fig.canvas.setStyleSheet(f"background-color: {self.background_color};")
-		self.canvas.canvas.draw()
-
-	def generate_channel_cb(self):
-		# Generate the channel dropdown if enabled
-
-		assert self.channel_names is not None
-		assert len(self.channel_names)==self.n_channels
-
-		channel_layout = QHBoxLayout()
-		channel_layout.setContentsMargins(15,0,15,0)
-		channel_layout.addWidget(QLabel('Channel: '), 25)
-
-		self.channels_cb = QComboBox()
-		self.channels_cb.addItems(self.channel_names)
-		self.channels_cb.currentIndexChanged.connect(self.set_channel_index)
-		channel_layout.addWidget(self.channels_cb, 75)
-		self.canvas.layout.addLayout(channel_layout)
-
-	def set_contrast_decimals(self):
-		if is_integer_array(self.init_frame):
-			self.contrast_slider.setDecimals(0)
-			self.contrast_slider.setSingleStep(1.0)
-			self.contrast_slider.setTickInterval(1.0)
-		else:
-			self.contrast_slider.setDecimals(3)
-			self.contrast_slider.setSingleStep(1.0E-03)
-			self.contrast_slider.setTickInterval(1.0E-03)
-
-	def generate_contrast_slider(self):
-		# Generate the contrast slider if enabled
-		
-		self.contrast_slider = QLabeledDoubleRangeSlider()
-		contrast_layout = QuickSliderLayout(
-											label='Contrast: ',
-											slider=self.contrast_slider,
-											slider_initial_value=[np.nanpercentile(self.init_frame, 0.1),np.nanpercentile(self.init_frame, 99.99)],
-											slider_range=(np.nanmin(self.init_frame),np.nanmax(self.init_frame)),
-											decimal_option=True,
-											precision=2,
-											)
-		self.set_contrast_decimals()
-
-		contrast_layout.setContentsMargins(15,0,15,0)
-		self.im.set_clim(vmin=np.nanpercentile(self.init_frame, 0.1),vmax=np.nanpercentile(self.init_frame, 99.99))
-		self.contrast_slider.valueChanged.connect(self.change_contrast)
-		self.canvas.layout.addLayout(contrast_layout)
-
-	def generate_frame_slider(self):
-		# Generate the frame slider if enabled
-	
-		self.frame_slider = QLabeledSlider()
-		frame_layout = QuickSliderLayout(
-										label='Frame: ',
-										slider=self.frame_slider,
-										slider_initial_value=int(self.mid_time),
-										slider_range=(0,self.stack_length-1),
-										decimal_option=False,
-										)
-		frame_layout.setContentsMargins(15,0,15,0)
-		self.frame_slider.valueChanged.connect(self.change_frame)
-		self.canvas.layout.addLayout(frame_layout)
-
-	def set_target_channel(self, value):
-		# Set the target channel
-		
-		self.target_channel = value
-		self.change_frame(self.frame_slider.value())
-
-	def change_contrast(self, value):
-		# Change contrast based on slider value
-
-		vmin = value[0]
-		vmax = value[1]
-		self.im.set_clim(vmin=vmin, vmax=vmax)
-		self.fig.canvas.draw_idle()
-
-	def set_channel_index(self, value):
-		# Set the channel index based on dropdown value
-
-		self.target_channel = value
-		self.init_contrast = True
-		if self.mode == 'direct':
-			self.last_frame = self.stack[-1,:,:,self.target_channel]
-		elif self.mode == 'virtual':
-			self.last_frame = load_frames(self.img_num_per_channel[self.target_channel, self.stack_length-1], 
-										  self.stack_path,
-										  normalize_input=False).astype(float)[:,:,0]
-		self.change_frame_from_channel_switch(self.frame_slider.value())
-		self.channel_trigger = False
-		self.init_contrast = False
-
-		self.set_contrast_decimals()
-
-	def change_frame_from_channel_switch(self, value):
-		
-		self.channel_trigger = True
-		self.change_frame(value)
-
-	def change_frame(self, value):
-
-		# Change the displayed frame based on slider value
-		if self.channel_trigger:
-			self.switch_from_channel = True
-		else:
-			self.switch_from_channel = False
-
-		if self.mode=='virtual':
-
-			self.init_frame = load_frames(self.img_num_per_channel[self.target_channel, value], 
-								self.stack_path,
-								normalize_input=False
-								).astype(float)[:,:,0]
-		elif self.mode=='direct':
-			self.init_frame = self.stack[value,:,:,self.target_channel].copy()
-		
-		self.im.set_data(self.init_frame)
-		
-		if self.init_contrast:
-			imgs = np.array([self.init_frame,self.last_frame])
-			vmin = np.nanpercentile(imgs.flatten(), 1.0)
-			vmax = np.nanpercentile(imgs.flatten(), 99.99)
-			self.contrast_slider.setRange(np.nanmin(imgs),np.nanmax(imgs))
-			self.contrast_slider.setValue((vmin,vmax))
-			self.im.set_clim(vmin,vmax)
-
-		if self.create_contrast_slider:
-			self.change_contrast(self.contrast_slider.value())
-
-
-	def closeEvent(self, event):
-		# Event handler for closing the widget
-		self.canvas.close()	
-
-
-class ThresholdedStackVisualizer(StackVisualizer):
-	
-	"""
-	A widget for visualizing thresholded image stacks with interactive sliders and channel selection.
-
-	Parameters:
-	- preprocessing (list or None): A list of preprocessing filters to apply to the image before thresholding.
-	- parent_le: The parent QLineEdit instance to set the threshold value.
-	- initial_threshold (float): Initial threshold value.
-	- initial_mask_alpha (float): Initial mask opacity value.
-	- args, kwargs: Additional arguments to pass to the parent class constructor.
-
-	Methods:
-	- generate_apply_btn(): Generate the apply button to set the threshold in the parent QLineEdit.
-	- set_threshold_in_parent_le(): Set the threshold value in the parent QLineEdit.
-	- generate_mask_imshow(): Generate the mask imshow.
-	- generate_threshold_slider(): Generate the threshold slider.
-	- generate_opacity_slider(): Generate the opacity slider for the mask.
-	- change_mask_opacity(value): Change the opacity of the mask.
-	- change_threshold(value): Change the threshold value.
-	- change_frame(value): Change the displayed frame and update the threshold.
-	- compute_mask(threshold_value): Compute the mask based on the threshold value.
-	- preprocess_image(): Preprocess the image before thresholding.
-
-	Notes:
-	- This class extends the functionality of StackVisualizer to visualize thresholded image stacks
-	  with interactive sliders for threshold and mask opacity adjustment.
-	"""
-
-	def __init__(self, preprocessing=None, parent_le=None, initial_threshold=5, initial_mask_alpha=0.5, show_opacity_slider=True, show_threshold_slider=True, *args, **kwargs):
-		# Initialize the widget and its attributes		
-		super().__init__(*args, **kwargs)
-		self.preprocessing = preprocessing
-		self.thresh = initial_threshold
-		self.mask_alpha = initial_mask_alpha
-		self.parent_le = parent_le
-		self.show_opacity_slider = show_opacity_slider
-		self.show_threshold_slider = show_threshold_slider
-		self.thresholded = False
-		self.mask = np.zeros_like(self.init_frame)
-		self.thresh_min = 0.0
-		self.thresh_max = 30.0
-
-		self.generate_threshold_slider()
-
-		if self.thresh is not None:
-			self.compute_mask(self.thresh)
-
-		self.generate_mask_imshow()
-		self.generate_scatter()
-		self.generate_opacity_slider()
-		if isinstance(self.parent_le, QLineEdit):
-			self.generate_apply_btn()
-
-	def generate_apply_btn(self):
-		# Generate the apply button to set the threshold in the parent QLineEdit		
-		apply_hbox = QHBoxLayout()
-		self.apply_threshold_btn = QPushButton('Apply')
-		self.apply_threshold_btn.clicked.connect(self.set_threshold_in_parent_le)
-		self.apply_threshold_btn.setStyleSheet(self.button_style_sheet)
-		apply_hbox.addWidget(QLabel(''),33)
-		apply_hbox.addWidget(self.apply_threshold_btn, 33)
-		apply_hbox.addWidget(QLabel(''),33)		
-		self.canvas.layout.addLayout(apply_hbox)
-
-	def set_threshold_in_parent_le(self):
-		# Set the threshold value in the parent QLineEdit
-		self.parent_le.set_threshold(self.threshold_slider.value())
-		self.close()
-
-	def generate_mask_imshow(self):
-		# Generate the mask imshow
-
-		self.im_mask = self.ax.imshow(np.ma.masked_where(self.mask==0, self.mask), alpha=self.mask_alpha, interpolation='none')
-		self.canvas.canvas.draw()
-
-	def generate_scatter(self):
-		self.scat_markers = self.ax.scatter([], [], color="tab:red")
-
-	def generate_threshold_slider(self):
-		# Generate the threshold slider
-		self.threshold_slider = QLabeledDoubleSlider()
-		if self.thresh is None:
-			init_value = 1.0E5
-		else:
-			init_value = self.thresh
-		thresh_layout = QuickSliderLayout(label='Threshold: ',
-										slider=self.threshold_slider,
-										slider_initial_value=init_value,
-										slider_range=(self.thresh_min,np.amax([self.thresh_max, init_value])),
-										decimal_option=True,
-										precision=4,
-										)
-		thresh_layout.setContentsMargins(15,0,15,0)
-		self.threshold_slider.valueChanged.connect(self.change_threshold)
-		if self.show_threshold_slider:
-			self.canvas.layout.addLayout(thresh_layout)
-
-	def generate_opacity_slider(self):
-		# Generate the opacity slider for the mask
-		self.opacity_slider = QLabeledDoubleSlider()
-		opacity_layout = QuickSliderLayout(label='Opacity: ',
-										slider=self.opacity_slider,
-										slider_initial_value=0.5,
-										slider_range=(0,1),
-										decimal_option=True,
-										precision=3,
-										)
-		opacity_layout.setContentsMargins(15,0,15,0)
-		self.opacity_slider.valueChanged.connect(self.change_mask_opacity)
-		if self.show_opacity_slider:
-			self.canvas.layout.addLayout(opacity_layout)
-
-	def change_mask_opacity(self, value):
-		# Change the opacity of the mask
-		self.mask_alpha = value
-		self.im_mask.set_alpha(self.mask_alpha)
-		self.canvas.canvas.draw_idle()
-
-	def change_threshold(self, value):
-		# Change the threshold value		
-		self.thresh = value
-		if self.thresh is not None:
-			self.compute_mask(self.thresh)
-			mask = np.ma.masked_where(self.mask == 0, self.mask)
-			self.im_mask.set_data(mask)
-			self.canvas.canvas.draw_idle()
-
-	def change_frame(self, value):
-		# Change the displayed frame and update the threshold
-		if self.thresholded:
-			self.init_contrast = True
-		super().change_frame(value)
-		self.change_threshold(self.threshold_slider.value())
-		if self.thresholded:
-			self.thresholded = False
-			self.init_contrast = False
-
-	def compute_mask(self, threshold_value):
-		# Compute the mask based on the threshold value
-		self.preprocess_image()
-		edge = estimate_unreliable_edge(self.preprocessing)
-		if isinstance(threshold_value, (list,np.ndarray,tuple)):
-			self.mask = threshold_image(self.processed_image, threshold_value[0], threshold_value[1], foreground_value=1, fill_holes=True, edge_exclusion=edge).astype(int)
-		else:
-			self.mask = threshold_image(self.processed_image, threshold_value, np.inf, foreground_value=1, fill_holes=True, edge_exclusion=edge).astype(int)
-
-	def preprocess_image(self):
-		# Preprocess the image before thresholding		
-		if self.preprocessing is not None:
-
-			assert isinstance(self.preprocessing, list)
-			self.processed_image = filter_image(self.init_frame.copy().astype(float),filters=self.preprocessing)
-			min_ = np.amin(self.processed_image)
-			max_ = np.amax(self.processed_image)
-
-			if min_ < self.thresh_min:
-				self.thresh_min = min_
-			if max_ > self.thresh_max:
-				self.thresh_max = max_
-
-			self.threshold_slider.setRange(self.thresh_min, self.thresh_max)
-
-	def set_preprocessing(self, activation_protocol):
-
-		self.preprocessing = activation_protocol
-		self.preprocess_image()
-
-		self.im.set_data(self.processed_image)
-		vmin = np.nanpercentile(self.processed_image, 1.0)
-		vmax = np.nanpercentile(self.processed_image, 99.99)
-		self.contrast_slider.setRange(np.nanmin(self.processed_image),
-									  np.nanmax(self.processed_image))
-		self.contrast_slider.setValue((vmin, vmax))
-		self.im.set_clim(vmin,vmax)
-		self.canvas.canvas.draw_idle()
-		self.thresholded = True
-
-
-class CellEdgeVisualizer(StackVisualizer):
-
-	"""
-	A widget for visualizing cell edges with interactive sliders and channel selection.
-
-	Parameters:
-	- cell_type (str): Type of cells ('effectors' by default).
-	- edge_range (tuple): Range of edge sizes (-30, 30) by default.
-	- invert (bool): Flag to invert the edge size (False by default).
-	- parent_list_widget: The parent QListWidget instance to add edge measurements.
-	- parent_le: The parent QLineEdit instance to set the edge size.
-	- labels (array or None): Array of labels for cell segmentation.
-	- initial_edge (int): Initial edge size (5 by default).
-	- initial_mask_alpha (float): Initial mask opacity value (0.5 by default).
-	- args, kwargs: Additional arguments to pass to the parent class constructor.
-
-	Methods:
-	- load_labels(): Load the cell labels.
-	- locate_labels_virtual(): Locate virtual labels.
-	- generate_add_to_list_btn(): Generate the add to list button.
-	- generate_add_to_le_btn(): Generate the set measurement button for QLineEdit.
-	- set_measurement_in_parent_le(): Set the edge size in the parent QLineEdit.
-	- set_measurement_in_parent_list(): Add the edge size to the parent QListWidget.
-	- generate_label_imshow(): Generate the label imshow.
-	- generate_edge_slider(): Generate the edge size slider.
-	- generate_opacity_slider(): Generate the opacity slider for the mask.
-	- change_mask_opacity(value): Change the opacity of the mask.
-	- change_edge_size(value): Change the edge size.
-	- change_frame(value): Change the displayed frame and update the edge labels.
-	- compute_edge_labels(): Compute the edge labels.
-
-	Notes:
-	- This class extends the functionality of StackVisualizer to visualize cell edges
-	  with interactive sliders for edge size adjustment and mask opacity control.
-	"""
-
-	def __init__(self, cell_type="effectors", edge_range=(-30,30), invert=False, parent_list_widget=None, parent_le=None, labels=None, initial_edge=5, initial_mask_alpha=0.5, *args, **kwargs):
-		
-		# Initialize the widget and its attributes
-		super().__init__(*args, **kwargs)
-		self.edge_size = initial_edge
-		self.mask_alpha = initial_mask_alpha
-		self.cell_type = cell_type
-		self.labels = labels
-		self.edge_range = edge_range
-		self.invert = invert
-		self.parent_list_widget = parent_list_widget
-		self.parent_le = parent_le
-
-		self.load_labels()
-		self.generate_label_imshow()
-		self.generate_edge_slider()
-		self.generate_opacity_slider()
-		if isinstance(self.parent_list_widget, QListWidget):
-			self.generate_add_to_list_btn()
-		if isinstance(self.parent_le, QLineEdit):
-			self.generate_add_to_le_btn()
-
-	def load_labels(self):
-		# Load the cell labels
-
-		if self.labels is not None:
-
-			if isinstance(self.labels, list):
-				self.labels = np.array(self.labels)
-
-			assert self.labels.ndim==3,'Wrong dimensions for the provided labels, expect TXY'
-			assert len(self.labels)==self.stack_length
-
-			self.mode = 'direct'
-			self.init_label = self.labels[self.mid_time,:,:]
-		else:
-			self.mode = 'virtual'
-			assert isinstance(self.stack_path, str)
-			assert self.stack_path.endswith('.tif')
-			self.locate_labels_virtual()
-		
-		self.compute_edge_labels()
-
-	def locate_labels_virtual(self):
-		# Locate virtual labels
-
-		labels_path = str(Path(self.stack_path).parent.parent) + os.sep + f'labels_{self.cell_type}' + os.sep
-		self.mask_paths = natsorted(glob(labels_path + '*.tif'))
-		
-		if len(self.mask_paths) == 0:
-
-			msgBox = QMessageBox()
-			msgBox.setIcon(QMessageBox.Critical)
-			msgBox.setText("No labels were found for the selected cells. Abort.")
-			msgBox.setWindowTitle("Critical")
-			msgBox.setStandardButtons(QMessageBox.Ok)
-			returnValue = msgBox.exec()
-			self.close()
-
-		self.init_label = imread(self.mask_paths[self.frame_slider.value()])
-
-	def generate_add_to_list_btn(self):
-		# Generate the add to list button
-		
-		add_hbox = QHBoxLayout()
-		self.add_measurement_btn = QPushButton('Add measurement')
-		self.add_measurement_btn.clicked.connect(self.set_measurement_in_parent_list)
-		self.add_measurement_btn.setIcon(icon(MDI6.plus,color="white"))
-		self.add_measurement_btn.setIconSize(QSize(20, 20))
-		self.add_measurement_btn.setStyleSheet(self.button_style_sheet)
-		add_hbox.addWidget(QLabel(''),33)
-		add_hbox.addWidget(self.add_measurement_btn, 33)
-		add_hbox.addWidget(QLabel(''),33)		
-		self.canvas.layout.addLayout(add_hbox)
-
-	def generate_add_to_le_btn(self):
-		# Generate the set measurement button for QLineEdit
-		
-		add_hbox = QHBoxLayout()
-		self.set_measurement_btn = QPushButton('Set')
-		self.set_measurement_btn.clicked.connect(self.set_measurement_in_parent_le)
-		self.set_measurement_btn.setStyleSheet(self.button_style_sheet)
-		add_hbox.addWidget(QLabel(''),33)
-		add_hbox.addWidget(self.set_measurement_btn, 33)
-		add_hbox.addWidget(QLabel(''),33)		
-		self.canvas.layout.addLayout(add_hbox)
-
-	def set_measurement_in_parent_le(self):
-		# Set the edge size in the parent QLineEdit
-		
-		self.parent_le.setText(str(int(self.edge_slider.value())))
-		self.close()
-
-	def set_measurement_in_parent_list(self):
-		# Add the edge size to the parent QListWidget
-		
-		self.parent_list_widget.addItems([str(self.edge_slider.value())])
-		self.close()
-
-	def generate_label_imshow(self):
-		# Generate the label imshow
-		
-		self.im_mask = self.ax.imshow(np.ma.masked_where(self.edge_labels==0, self.edge_labels), alpha=self.mask_alpha, interpolation='none', cmap="viridis")
-		self.canvas.canvas.draw()
-
-	def generate_edge_slider(self):
-		# Generate the edge size slider
-
-		self.edge_slider = QLabeledSlider()
-		edge_layout = QuickSliderLayout(label='Edge: ',
-										slider=self.edge_slider,
-										slider_initial_value=self.edge_size,
-										slider_range=self.edge_range,
-										decimal_option=False,
-										)
-		edge_layout.setContentsMargins(15,0,15,0)
-		self.edge_slider.valueChanged.connect(self.change_edge_size)
-		self.canvas.layout.addLayout(edge_layout)
-
-	def generate_opacity_slider(self):
-		# Generate the opacity slider for the mask
-
-		self.opacity_slider = QLabeledDoubleSlider()
-		opacity_layout = QuickSliderLayout(label='Opacity: ',
-										slider=self.opacity_slider,
-										slider_initial_value=0.5,
-										slider_range=(0,1),
-										decimal_option=True,
-										precision=3,
-										)
-		opacity_layout.setContentsMargins(15,0,15,0)
-		self.opacity_slider.valueChanged.connect(self.change_mask_opacity)
-		self.canvas.layout.addLayout(opacity_layout)
-
-	def change_mask_opacity(self, value):
-		# Change the opacity of the mask
-
-		self.mask_alpha = value
-		self.im_mask.set_alpha(self.mask_alpha)
-		self.canvas.canvas.draw_idle()
-
-	def change_edge_size(self, value):
-		# Change the edge size
-		
-		self.edge_size = value
-		self.compute_edge_labels()
-		mask = np.ma.masked_where(self.edge_labels == 0, self.edge_labels)
-		self.im_mask.set_data(mask)
-		self.canvas.canvas.draw_idle()
-
-	def change_frame(self, value):
-		# Change the displayed frame and update the edge labels
-		
-		super().change_frame(value)
-
-		if self.mode=='virtual':
-			self.init_label = imread(self.mask_paths[value])
-		elif self.mode=='direct':
-			self.init_label = self.labels[value,:,:]
-		
-		self.compute_edge_labels()
-		mask = np.ma.masked_where(self.edge_labels == 0, self.edge_labels)
-		self.im_mask.set_data(mask)
-
-	def compute_edge_labels(self):
-		# Compute the edge labels
-		
-		if self.invert:
-			edge_size = - self.edge_size
-		else:
-			edge_size = self.edge_size
-
-		self.edge_labels = contour_of_instance_segmentation(self.init_label, edge_size)
-
-class SpotDetectionVisualizer(StackVisualizer):
-	
-	def __init__(self, parent_channel_cb=None, parent_diameter_le=None, parent_threshold_le=None, parent_preprocessing_list=None, cell_type='targets', labels=None, *args, **kwargs):
-
-		super().__init__(*args, **kwargs)
-		
-		self.cell_type = cell_type
-		self.labels = labels
-		self.detection_channel = self.target_channel
-
-		self.parent_channel_cb = parent_channel_cb
-		self.parent_diameter_le = parent_diameter_le
-		self.parent_threshold_le = parent_threshold_le
-		self.parent_preprocessing_list = parent_preprocessing_list
-
-		self.spot_sizes = []
-		self.floatValidator = QDoubleValidator()
-		self.init_scatter()
-		
-		self.generate_detection_channel()		
-		self.detection_channel = self.detection_channel_cb.currentIndex()
-
-		self.generate_spot_detection_params()
-		self.generate_add_measurement_btn()
-		self.load_labels()
-		self.change_frame(self.mid_time)
-
-		self.ax.callbacks.connect('xlim_changed', self.update_marker_sizes)
-		self.ax.callbacks.connect('ylim_changed', self.update_marker_sizes)
-
-		self.apply_diam_btn.clicked.connect(self.detect_and_display_spots)
-		self.apply_thresh_btn.clicked.connect(self.detect_and_display_spots)
-		
-		self.channels_cb.setCurrentIndex(self.target_channel)
-		self.detection_channel_cb.setCurrentIndex(self.target_channel)
-
-	def update_marker_sizes(self, event=None):
-		
-		# Get axis bounds
-		xlim = self.ax.get_xlim()
-		ylim = self.ax.get_ylim()
-
-		# Data-to-pixel scale
-		ax_width_in_pixels = self.ax.bbox.width
-		ax_height_in_pixels =self.ax.bbox.height
-
-		x_scale = (float(xlim[1]) - float(xlim[0])) / ax_width_in_pixels
-		y_scale = (float(ylim[1]) - float(ylim[0])) / ax_height_in_pixels
-
-		# Choose the smaller scale for square pixels
-		scale = min(x_scale, y_scale)
-
-		# Convert radius_px to data units
-		if len(self.spot_sizes)>0:
-
-			radius_data_units = self.spot_sizes / float(scale)
-
-			# Convert to scatter `s` size (points squared)
-			radius_pts = radius_data_units * (72. / self.fig.dpi )
-			size = np.pi * (radius_pts ** 2)
-
-			# Update scatter sizes
-			self.spot_scat.set_sizes(size)
-			self.fig.canvas.draw_idle()
-
-	def init_scatter(self):
-		self.spot_scat = self.ax.scatter([],[], s=50, facecolors='none', edgecolors='tab:red',zorder=100)
-		self.canvas.canvas.draw()
-
-	def change_frame(self, value):
-
-		super().change_frame(value)
-		if not self.switch_from_channel:
-			self.reset_detection()
-
-		if self.mode=='virtual':
-			self.init_label = imread(self.mask_paths[value])
-			self.target_img = load_frames(self.img_num_per_channel[self.detection_channel, value], 
-								self.stack_path,normalize_input=False).astype(float)[:,:,0]
-		elif self.mode=='direct':
-			self.init_label = self.labels[value,:,:]
-			self.target_img = self.stack[value,:,:,self.detection_channel].copy()
-
-	def detect_and_display_spots(self):
-
-		self.reset_detection()
-		self.control_valid_parameters() # set current diam and threshold
-		#self.change_frame(self.frame_slider.value())
-		#self.set_detection_channel_index(self.detection_channel_cb.currentIndex())
-
-		image_preprocessing = self.preprocessing.list.items
-		if image_preprocessing==[]:
-			image_preprocessing = None
-
-		blobs_filtered = extract_blobs_in_image(self.target_img, self.init_label,threshold=self.thresh, diameter=self.diameter, image_preprocessing=image_preprocessing)
-		if blobs_filtered is not None:
-			self.spot_positions = np.array([[x,y] for y,x,_ in blobs_filtered])
-			if len(self.spot_positions)>0:
-				self.spot_sizes = np.sqrt(2)*np.array([sig for _,_,sig in blobs_filtered])
-			#radius_pts = self.spot_sizes * (self.fig.dpi / 72.0)
-			#sizes = np.pi*(radius_pts**2)
-			if len(self.spot_positions)>0:
-				self.spot_scat.set_offsets(self.spot_positions)
-			else:
-				empty_offset = np.ma.masked_array([0, 0], mask=True)
-				self.spot_scat.set_offsets(empty_offset)
-			#self.spot_scat.set_sizes(sizes)
-			if len(self.spot_positions)>0:
-				self.update_marker_sizes()
-			self.canvas.canvas.draw()
-
-	def reset_detection(self):
-		
-		self.ax.scatter([], []).get_offsets()
-		empty_offset = np.ma.masked_array([0, 0], mask=True)
-		self.spot_scat.set_offsets(empty_offset)
-		self.canvas.canvas.draw()
-
-	def load_labels(self):
-
-		# Load the cell labels
-		if self.labels is not None:
-
-			if isinstance(self.labels, list):
-				self.labels = np.array(self.labels)
-
-			assert self.labels.ndim==3,'Wrong dimensions for the provided labels, expect TXY'
-			assert len(self.labels)==self.stack_length
-
-			self.mode = 'direct'
-			self.init_label = self.labels[self.mid_time,:,:]
-		else:
-			self.mode = 'virtual'
-			assert isinstance(self.stack_path, str)
-			assert self.stack_path.endswith('.tif')
-			self.locate_labels_virtual()
-	
-	def locate_labels_virtual(self):
-		# Locate virtual labels
-
-		labels_path = str(Path(self.stack_path).parent.parent) + os.sep + f'labels_{self.cell_type}' + os.sep
-		self.mask_paths = natsorted(glob(labels_path + '*.tif'))
-		
-		if len(self.mask_paths) == 0:
-
-			msgBox = QMessageBox()
-			msgBox.setIcon(QMessageBox.Critical)
-			msgBox.setText("No labels were found for the selected cells. Abort.")
-			msgBox.setWindowTitle("Critical")
-			msgBox.setStandardButtons(QMessageBox.Ok)
-			returnValue = msgBox.exec()
-			self.close()
-
-		self.init_label = imread(self.mask_paths[self.frame_slider.value()])
-	
-	def generate_detection_channel(self):
-
-		assert self.channel_names is not None
-		assert len(self.channel_names)==self.n_channels
-
-		channel_layout = QHBoxLayout()
-		channel_layout.setContentsMargins(15,0,15,0)
-		channel_layout.addWidget(QLabel('Detection\nchannel: '), 25)
-
-		self.detection_channel_cb = QComboBox()
-		self.detection_channel_cb.addItems(self.channel_names)
-		self.detection_channel_cb.currentIndexChanged.connect(self.set_detection_channel_index)
-		channel_layout.addWidget(self.detection_channel_cb, 75)
-
-		# self.invert_check = QCheckBox('invert')
-		# if self.invert:
-		# 	self.invert_check.setChecked(True)
-		# self.invert_check.toggled.connect(self.set_invert)
-		# channel_layout.addWidget(self.invert_check, 10)
-
-		self.canvas.layout.addLayout(channel_layout)
-		
-		self.preprocessing = PreprocessingLayout2(fraction=25, parent_window=self)
-		self.preprocessing.setContentsMargins(15,0,15,0)
-		self.canvas.layout.addLayout(self.preprocessing)
-
-
-	# def set_invert(self):
-	# 	if self.invert_check.isChecked():
-	# 		self.invert = True
-	# 	else:
-	# 		self.invert = False
-
-	def set_detection_channel_index(self, value):
-
-		self.detection_channel = value
-		if self.mode == 'direct':
-			self.target_img = self.stack[-1,:,:,self.detection_channel]
-		elif self.mode == 'virtual':
-			self.target_img = load_frames(self.img_num_per_channel[self.detection_channel, self.frame_slider.value()], 
-										  self.stack_path,normalize_input=False).astype(float)[:,:,0]
-
-	def generate_spot_detection_params(self):
-
-		self.spot_diam_le = QLineEdit('1')
-		self.spot_diam_le.setValidator(self.floatValidator)
-		self.apply_diam_btn = QPushButton('Set')
-		self.apply_diam_btn.setStyleSheet(self.button_style_sheet_2)
-
-		self.spot_thresh_le = QLineEdit('0')
-		self.spot_thresh_le.setValidator(self.floatValidator)
-		self.apply_thresh_btn = QPushButton('Set')
-		self.apply_thresh_btn.setStyleSheet(self.button_style_sheet_2)		
-
-		self.spot_diam_le.textChanged.connect(self.control_valid_parameters)
-		self.spot_thresh_le.textChanged.connect(self.control_valid_parameters)
-
-		spot_diam_layout = QHBoxLayout()
-		spot_diam_layout.setContentsMargins(15,0,15,0)
-		spot_diam_layout.addWidget(QLabel('Spot diameter: '), 25)
-		spot_diam_layout.addWidget(self.spot_diam_le, 65)
-		spot_diam_layout.addWidget(self.apply_diam_btn, 10)
-		self.canvas.layout.addLayout(spot_diam_layout)
-
-		spot_thresh_layout = QHBoxLayout()
-		spot_thresh_layout.setContentsMargins(15,0,15,0)
-		spot_thresh_layout.addWidget(QLabel('Detection\nthreshold: '), 25)
-		spot_thresh_layout.addWidget(self.spot_thresh_le, 65)
-		spot_thresh_layout.addWidget(self.apply_thresh_btn, 10)
-		self.canvas.layout.addLayout(spot_thresh_layout)
-
-	def generate_add_measurement_btn(self):
-
-		add_hbox = QHBoxLayout()
-		self.add_measurement_btn = QPushButton('Add measurement')
-		self.add_measurement_btn.clicked.connect(self.set_measurement_in_parent_list)
-		self.add_measurement_btn.setIcon(icon(MDI6.plus,color="white"))
-		self.add_measurement_btn.setIconSize(QSize(20, 20))
-		self.add_measurement_btn.setStyleSheet(self.button_style_sheet)
-		add_hbox.addWidget(QLabel(''),33)
-		add_hbox.addWidget(self.add_measurement_btn, 33)
-		add_hbox.addWidget(QLabel(''),33)		
-		self.canvas.layout.addLayout(add_hbox)
-
-	def control_valid_parameters(self):
-		
-		valid_diam = False
-		try:
-			self.diameter = float(self.spot_diam_le.text().replace(',','.'))
-			valid_diam = True
-		except:
-			valid_diam = False
-
-		valid_thresh = False
-		try:
-			self.thresh = float(self.spot_thresh_le.text().replace(',','.'))
-			valid_thresh = True
-		except:
-			valid_thresh = False
-
-		if valid_diam and valid_thresh:
-			self.apply_diam_btn.setEnabled(True)
-			self.apply_thresh_btn.setEnabled(True)
-			self.add_measurement_btn.setEnabled(True)
-		else:
-			self.apply_diam_btn.setEnabled(False)
-			self.apply_thresh_btn.setEnabled(False)
-			self.add_measurement_btn.setEnabled(False)
-
-	def set_measurement_in_parent_list(self):
-
-		if self.parent_channel_cb is not None:
-			self.parent_channel_cb.setCurrentIndex(self.detection_channel)
-		if self.parent_diameter_le is not None:
-			self.parent_diameter_le.setText(self.spot_diam_le.text())
-		if self.parent_threshold_le is not None:
-			self.parent_threshold_le.setText(self.spot_thresh_le.text())
-		if self.parent_preprocessing_list is not None:
-			self.parent_preprocessing_list.clear()
-			items = self.preprocessing.list.getItems()
-			for item in items:
-				self.parent_preprocessing_list.addItemToList(item)
-			self.parent_preprocessing_list.items = self.preprocessing.list.items
-		self.close()
-
-class CellSizeViewer(StackVisualizer):
-
-	"""
-	A widget for visualizing cell size with interactive sliders and circle display.
-
-	Parameters:
-	- initial_diameter (int): Initial diameter of the circle (40 by default).
-	- set_radius_in_list (bool): Flag to set radius instead of diameter in the list (False by default).
-	- diameter_slider_range (tuple): Range of the diameter slider (0, 200) by default.
-	- parent_le: The parent QLineEdit instance to set the diameter.
-	- parent_list_widget: The parent QListWidget instance to add diameter measurements.
-	- args, kwargs: Additional arguments to pass to the parent class constructor.
-
-	Methods:
-	- generate_circle(): Generate the circle for visualization.
-	- generate_add_to_list_btn(): Generate the add to list button.
-	- set_measurement_in_parent_list(): Add the diameter to the parent QListWidget.
-	- on_xlims_or_ylims_change(event_ax): Update the circle position on axis limits change.
-	- generate_set_btn(): Generate the set button for QLineEdit.
-	- set_threshold_in_parent_le(): Set the diameter in the parent QLineEdit.
-	- generate_diameter_slider(): Generate the diameter slider.
-	- change_diameter(value): Change the diameter of the circle.
-
-	Notes:
-	- This class extends the functionality of StackVisualizer to visualize cell size
-	  with interactive sliders for diameter adjustment and circle display.
-	"""
-
-	def __init__(self, initial_diameter=40, set_radius_in_list=False, diameter_slider_range=(0,500), parent_le=None, parent_list_widget=None, *args, **kwargs):
-		# Initialize the widget and its attributes
-		
-		super().__init__(*args, **kwargs)
-		self.diameter = initial_diameter
-		self.parent_le = parent_le
-		self.diameter_slider_range = diameter_slider_range
-		self.parent_list_widget = parent_list_widget
-		self.set_radius_in_list = set_radius_in_list
-		self.generate_circle()
-		self.generate_diameter_slider()
-
-		if isinstance(self.parent_le, QLineEdit):
-			self.generate_set_btn()
-		if isinstance(self.parent_list_widget, QListWidget):
-			self.generate_add_to_list_btn()
-
-	def generate_circle(self):
-		# Generate the circle for visualization
-
-		self.circ = plt.Circle((self.init_frame.shape[0]//2,self.init_frame.shape[1]//2), self.diameter//2 / self.PxToUm, ec="tab:red",fill=False)
-		self.ax.add_patch(self.circ)
-
-		self.ax.callbacks.connect('xlim_changed',self.on_xlims_or_ylims_change)
-		self.ax.callbacks.connect('ylim_changed', self.on_xlims_or_ylims_change)
-
-	def generate_add_to_list_btn(self):
-		# Generate the add to list button
-		
-		add_hbox = QHBoxLayout()
-		self.add_measurement_btn = QPushButton('Add measurement')
-		self.add_measurement_btn.clicked.connect(self.set_measurement_in_parent_list)
-		self.add_measurement_btn.setIcon(icon(MDI6.plus,color="white"))
-		self.add_measurement_btn.setIconSize(QSize(20, 20))
-		self.add_measurement_btn.setStyleSheet(self.button_style_sheet)
-		add_hbox.addWidget(QLabel(''),33)
-		add_hbox.addWidget(self.add_measurement_btn, 33)
-		add_hbox.addWidget(QLabel(''),33)		
-		self.canvas.layout.addLayout(add_hbox)
-
-	def set_measurement_in_parent_list(self):
-		# Add the diameter to the parent QListWidget
-
-		if self.set_radius_in_list:
-			val = int(self.diameter_slider.value()//2)
-		else:
-			val = int(self.diameter_slider.value()) 
-		
-		self.parent_list_widget.addItems([str(val)])
-		self.close()
-
-	def on_xlims_or_ylims_change(self, event_ax):
-		# Update the circle position on axis limits change
-
-		xmin,xmax = event_ax.get_xlim()
-		ymin,ymax = event_ax.get_ylim()
-		self.circ.center = np.mean([xmin,xmax]), np.mean([ymin,ymax])
-
-	def generate_set_btn(self):
-		# Generate the set button for QLineEdit
-		
-		apply_hbox = QHBoxLayout()
-		self.apply_threshold_btn = QPushButton('Set')
-		self.apply_threshold_btn.clicked.connect(self.set_threshold_in_parent_le)
-		self.apply_threshold_btn.setStyleSheet(self.button_style_sheet)
-		apply_hbox.addWidget(QLabel(''),33)
-		apply_hbox.addWidget(self.apply_threshold_btn, 33)
-		apply_hbox.addWidget(QLabel(''),33)		
-		self.canvas.layout.addLayout(apply_hbox)
-
-	def set_threshold_in_parent_le(self):
-		# Set the diameter in the parent QLineEdit
-
-		self.parent_le.set_threshold(self.diameter_slider.value())
-		self.close()
-
-	def generate_diameter_slider(self):
-		# Generate the diameter slider
-
-		self.diameter_slider = QLabeledDoubleSlider()
-		diameter_layout = QuickSliderLayout(label='Diameter: ',
-										slider=self.diameter_slider,
-										slider_initial_value=self.diameter,
-										slider_range=self.diameter_slider_range,
-										decimal_option=True,
-										precision=5,
-										)
-		diameter_layout.setContentsMargins(15,0,15,0)
-		self.diameter_slider.valueChanged.connect(self.change_diameter)
-		self.canvas.layout.addLayout(diameter_layout)
-
-	def change_diameter(self, value):
-		# Change the diameter of the circle
-		self.diameter = value
-		self.circ.set_radius(self.diameter//2 / self.PxToUm)
-		self.canvas.canvas.draw_idle()
-
-
-class ChannelOffsetViewer(StackVisualizer):
-
-	def __init__(self, parent_window=None, *args, **kwargs):
-		
-		self.parent_window = parent_window
-		self.overlay_target_channel = -1
-		self.shift_vertical = 0
-		self.shift_horizontal = 0
-		super().__init__(*args, **kwargs)
-
-		self.load_stack()
-		self.canvas.layout.addWidget(QHSeperationLine())
-		
-		self.generate_overlay_channel_cb()
-		self.generate_overlay_imshow()
-		
-		self.generate_overlay_alpha_slider()
-		self.generate_overlay_contrast_slider()
-
-		self.generate_overlay_shift()
-		self.generate_add_to_parent_btn()
-
-		if self.overlay_target_channel==-1:
-			index = len(self.channel_names) -1
-		else:
-			index = self.overlay_target_channel
-		self.channels_overlay_cb.setCurrentIndex(index)
-		self.frame_slider.valueChanged.connect(self.change_overlay_frame)
-
-		self.define_keyboard_shortcuts()
-
-		self.channels_overlay_cb.setCurrentIndex(self.parent_window.channels_cb.currentIndex())
-		self.set_channel_index(0)
-
-		self.setAttribute(Qt.WA_DeleteOnClose)
-
-	def generate_overlay_imshow(self):
-		self.im_overlay = self.ax.imshow(self.overlay_init_frame, cmap='Blues', interpolation='none',alpha=0.5, **self.imshow_kwargs)
-
-	def generate_overlay_alpha_slider(self):
-		# Generate the contrast slider if enabled
-		
-		self.overlay_alpha_slider = QLabeledDoubleSlider()
-		alpha_layout = QuickSliderLayout(
-											label='Overlay\ntransparency: ',
-											slider=self.overlay_alpha_slider,
-											slider_initial_value=0.5,
-											slider_range=(0,1.0),
-											decimal_option=True,
-											precision=5,
-											)
-		alpha_layout.setContentsMargins(15,0,15,0)
-		self.overlay_alpha_slider.valueChanged.connect(self.change_alpha_overlay)
-		self.canvas.layout.addLayout(alpha_layout)
-
-
-	def generate_overlay_contrast_slider(self):
-		# Generate the contrast slider if enabled
-		
-		self.overlay_contrast_slider = QLabeledDoubleRangeSlider()
-		contrast_layout = QuickSliderLayout(
-											label='Overlay contrast: ',
-											slider=self.overlay_contrast_slider,
-											slider_initial_value=[np.nanpercentile(self.overlay_init_frame, 0.1),np.nanpercentile(self.overlay_init_frame, 99.99)],
-											slider_range=(np.nanmin(self.overlay_init_frame),np.nanmax(self.overlay_init_frame)),
-											decimal_option=True,
-											precision=5,
-											)
-		contrast_layout.setContentsMargins(15,0,15,0)
-		self.im_overlay.set_clim(vmin=np.nanpercentile(self.overlay_init_frame, 0.1),vmax=np.nanpercentile(self.overlay_init_frame, 99.99))
-		self.overlay_contrast_slider.valueChanged.connect(self.change_contrast_overlay)
-		self.canvas.layout.addLayout(contrast_layout)
-
-	def set_overlay_channel_index(self, value):
-		# Set the channel index based on dropdown value
-
-		self.overlay_target_channel = value
-		self.overlay_init_contrast = True
-		if self.mode == 'direct':
-			self.overlay_last_frame = self.stack[-1,:,:,self.overlay_target_channel]
-		elif self.mode == 'virtual':
-			self.overlay_last_frame = load_frames(self.img_num_per_channel[self.overlay_target_channel, self.stack_length-1], 
-										  self.stack_path,
-										  normalize_input=False).astype(float)[:,:,0]
-		self.change_overlay_frame(self.frame_slider.value())
-		self.overlay_init_contrast = False
-
-	def generate_overlay_channel_cb(self):
-
-		assert self.channel_names is not None
-		assert len(self.channel_names)==self.n_channels
-
-		channel_layout = QHBoxLayout()
-		channel_layout.setContentsMargins(15,0,15,0)
-		channel_layout.addWidget(QLabel('Overlay channel: '), 25)
-
-		self.channels_overlay_cb = QComboBox()
-		self.channels_overlay_cb.addItems(self.channel_names)
-		self.channels_overlay_cb.currentIndexChanged.connect(self.set_overlay_channel_index)
-		channel_layout.addWidget(self.channels_overlay_cb, 75)
-		self.canvas.layout.addLayout(channel_layout)
-
-	def generate_overlay_shift(self):
-
-		shift_layout = QHBoxLayout()
-		shift_layout.setContentsMargins(15,0,15,0)
-		shift_layout.addWidget(QLabel('shift (h): '), 20, alignment=Qt.AlignRight)
-
-		self.apply_shift_btn = QPushButton('Apply')
-		self.apply_shift_btn.setStyleSheet(self.button_style_sheet_2)
-		self.apply_shift_btn.setToolTip('Apply the shift to the overlay channel.')
-		self.apply_shift_btn.clicked.connect(self.shift_generic)
-
-		self.set_shift_btn = QPushButton('Set')
-
-		self.horizontal_shift_le = ThresholdLineEdit(init_value=self.shift_horizontal, connected_buttons=[self.apply_shift_btn, self.set_shift_btn],placeholder='horizontal shift [pixels]', value_type='float')
-		shift_layout.addWidget(self.horizontal_shift_le, 20)
-
-		shift_layout.addWidget(QLabel('shift (v): '), 20, alignment=Qt.AlignRight)
-
-		self.vertical_shift_le = ThresholdLineEdit(init_value=self.shift_vertical, connected_buttons=[self.apply_shift_btn, self.set_shift_btn],placeholder='vertical shift [pixels]', value_type='float')
-		shift_layout.addWidget(self.vertical_shift_le, 20)
-
-		shift_layout.addWidget(self.apply_shift_btn, 20)
-
-		self.canvas.layout.addLayout(shift_layout)
-
-
-	def change_overlay_frame(self, value):
-		# Change the displayed frame based on slider value
-		
-		if self.mode=='virtual':
-
-			self.overlay_init_frame = load_frames(self.img_num_per_channel[self.overlay_target_channel, value], 
-								self.stack_path,
-								normalize_input=False
-								).astype(float)[:,:,0]
-		elif self.mode=='direct':
-			self.overlay_init_frame = self.stack[value,:,:,self.overlay_target_channel].copy()
-		
-		self.im_overlay.set_data(self.overlay_init_frame)
-		
-		if self.overlay_init_contrast:
-			self.im_overlay.autoscale()
-			I_min, I_max = self.im_overlay.get_clim()
-			self.overlay_contrast_slider.setRange(np.nanmin([self.overlay_init_frame,self.overlay_last_frame]),np.nanmax([self.overlay_init_frame,self.overlay_last_frame]))
-			self.overlay_contrast_slider.setValue((I_min,I_max))
-
-		if self.create_contrast_slider:
-			self.change_contrast_overlay(self.overlay_contrast_slider.value())
-	
-	def locate_image_virtual(self):
-		# Locate the stack of images if provided as a file
-		self.stack_length = auto_load_number_of_frames(self.stack_path)
-		if self.stack_length is None:
-			stack = imread(self.stack_path)
-			self.stack_length = len(stack)
-			del stack
-			gc.collect()
-
-		self.mid_time = self.stack_length // 2
-		self.img_num_per_channel = _get_img_num_per_channel(np.arange(self.n_channels), self.stack_length, self.n_channels)
-
-		self.init_frame = load_frames(self.img_num_per_channel[self.target_channel, self.mid_time], 
-									  self.stack_path,
-									  normalize_input=False).astype(float)[:,:,0]
-		self.last_frame = load_frames(self.img_num_per_channel[self.target_channel, self.stack_length-1], 
-									  self.stack_path,
-									  normalize_input=False).astype(float)[:,:,0]
-		self.overlay_init_frame = load_frames(self.img_num_per_channel[self.overlay_target_channel, self.mid_time], 
-									  self.stack_path,
-									  normalize_input=False).astype(float)[:,:,0]
-		self.overlay_last_frame = load_frames(self.img_num_per_channel[self.overlay_target_channel, self.stack_length-1], 
-									  self.stack_path,
-									  normalize_input=False).astype(float)[:,:,0]
-	
-	def change_contrast_overlay(self, value):
-		# Change contrast based on slider value
-
-		vmin = value[0]
-		vmax = value[1]
-		self.im_overlay.set_clim(vmin=vmin, vmax=vmax)
-		self.fig.canvas.draw_idle()
-
-	def change_alpha_overlay(self, value):
-		# Change contrast based on slider value
-
-		alpha = value
-		self.im_overlay.set_alpha(alpha)
-		self.fig.canvas.draw_idle()
-
-
-	def define_keyboard_shortcuts(self):
-		
-		self.shift_up_shortcut = QShortcut(QKeySequence(Qt.Key_Up), self.canvas)
-		self.shift_up_shortcut.activated.connect(self.shift_overlay_up)
-		
-		self.shift_down_shortcut = QShortcut(QKeySequence(Qt.Key_Down), self.canvas)
-		self.shift_down_shortcut.activated.connect(self.shift_overlay_down)
-
-		self.shift_left_shortcut = QShortcut(QKeySequence(Qt.Key_Left), self.canvas)
-		self.shift_left_shortcut.activated.connect(self.shift_overlay_left)
-		
-		self.shift_right_shortcut = QShortcut(QKeySequence(Qt.Key_Right), self.canvas)
-		self.shift_right_shortcut.activated.connect(self.shift_overlay_right)
-
-
-	def shift_overlay_up(self):
-		self.shift_vertical -= 2
-		self.vertical_shift_le.set_threshold(self.shift_vertical)
-		#self.shift_generic()
-		self.apply_shift_btn.click()
-
-	def shift_overlay_down(self):
-		self.shift_vertical += 2
-		self.vertical_shift_le.set_threshold(self.shift_vertical)
-		#self.shift_generic()
-		self.apply_shift_btn.click()
-
-	def shift_overlay_left(self):
-		self.shift_horizontal -= 2
-		self.horizontal_shift_le.set_threshold(self.shift_horizontal)
-		#self.shift_generic()
-		self.apply_shift_btn.click()
-
-	def shift_overlay_right(self):
-		self.shift_horizontal += 2
-		self.horizontal_shift_le.set_threshold(self.shift_horizontal)
-		#self.shift_generic()
-		self.apply_shift_btn.click()
-
-	def shift_generic(self):
-		self.shift_vertical = self.vertical_shift_le.get_threshold()
-		self.shift_horizontal = self.horizontal_shift_le.get_threshold()
-		self.shifted_frame = shift(self.overlay_init_frame, [self.shift_vertical, self.shift_horizontal],prefilter=False)
-		self.im_overlay.set_data(self.shifted_frame)
-		self.fig.canvas.draw_idle()
-
-	def generate_add_to_parent_btn(self):
-		
-		add_hbox = QHBoxLayout()
-		add_hbox.setContentsMargins(0,5,0,5)
-		self.set_shift_btn.clicked.connect(self.set_parent_attributes)
-		self.set_shift_btn.setStyleSheet(self.button_style_sheet)
-		add_hbox.addWidget(QLabel(''),33)
-		add_hbox.addWidget(self.set_shift_btn, 33)
-		add_hbox.addWidget(QLabel(''),33)		
-		self.canvas.layout.addLayout(add_hbox)
-
-	def set_parent_attributes(self):
-
-		idx = self.channels_overlay_cb.currentIndex()
-		self.parent_window.channels_cb.setCurrentIndex(idx)
-		self.parent_window.vertical_shift_le.set_threshold(self.vertical_shift_le.get_threshold())
-		self.parent_window.horizontal_shift_le.set_threshold(self.horizontal_shift_le.get_threshold())
-		self.close()