celldetective 1.3.5__tar.gz → 1.3.6.post2__tar.gz

{celldetective-1.3.5 → celldetective-1.3.6.post2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: celldetective
-Version: 1.3.5
+Version: 1.3.6.post2
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro
@@ -42,6 +42,7 @@ Requires-Dist: pytest-qt
 Requires-Dist: h5py
 Requires-Dist: cliffs_delta
 Requires-Dist: requests
+Requires-Dist: trackpy
 
 # Celldetective
 

celldetective-1.3.6.post2/celldetective/_version.py

@@ -0,0 +1 @@
+__version__ = "1.3.6.post2"

{celldetective-1.3.5 → celldetective-1.3.6.post2}/celldetective/filters.py

@@ -88,9 +88,13 @@ def laplace_filter(img, output=float, interpolate=True, *kwargs):
 		img = interpolate_nan(img.astype(float))
 	return snd.laplace(img.astype(float), *kwargs)
 
-def dog_filter(img, sigma_low, sigma_high, interpolate=True, *kwargs):
+def dog_filter(img, blob_size=None, sigma_low=1, sigma_high=2, interpolate=True, *kwargs):
+	
 	if interpolate:
 		img = interpolate_nan(img.astype(float))
+	if blob_size is not None:
+		sigma_low = 1.0 / (1.0 + np.sqrt(2)) * blob_size
+		sigma_high = np.sqrt(2)*sigma_low
 	return difference_of_gaussians(img.astype(float), sigma_low, sigma_high, *kwargs)
 
 def otsu_filter(img, *kwargs):
@@ -115,15 +119,31 @@ def sauvola_filter(img, *kwargs):
 	binary = img >= thresh
 	return binary.astype(float)
 
-def log_filter(img, sigma, *kwargs):
+def log_filter(img, blob_size=None, sigma=1, interpolate=True, *kwargs):
 
 	if interpolate:
 		img = interpolate_nan(img.astype(float))
+	if blob_size is not None:
+		sigma_low = 1.0 / (1.0 + np.sqrt(2)) * blob_size
+		sigma_high = np.sqrt(2)*sigma_low
+
 	return snd.gaussian_laplace(img.astype(float), sigma, *kwargs)
 
 def tophat_filter(img, size, connectivity=4, interpolate=True, *kwargs):
+	
 	if interpolate:
 		img = interpolate_nan(img.astype(float))
 	structure = snd.generate_binary_structure(rank=2, connectivity=connectivity)
 	img = snd.white_tophat(img.astype(float), structure=structure, size=size, *kwargs)
 	return img
+
+def invert_filter(img, value=65535, *kwargs):
+	
+	img = img.astype(float)
+
+	image_fill = np.zeros_like(img)
+	image_fill[:,:] = value
+
+	inverted = np.subtract(image_fill, img, where=img==img)
+	return inverted
+

{celldetective-1.3.5 → celldetective-1.3.6.post2}/celldetective/gui/btrack_options.py

@@ -1,5 +1,7 @@
-from PyQt5.QtWidgets import QMainWindow, QApplication, QMessageBox, QScrollArea, QComboBox, QFrame, QCheckBox, QFileDialog, QGridLayout, QTextEdit, QLineEdit, QVBoxLayout, QWidget, QLabel, QHBoxLayout, QPushButton
+from PyQt5.QtWidgets import QRadioButton, QButtonGroup, QMainWindow, QApplication, QMessageBox, QScrollArea, QComboBox, QFrame, QCheckBox, QFileDialog, QGridLayout, QTextEdit, QLineEdit, QVBoxLayout, QWidget, QLabel, QHBoxLayout, QPushButton
 from PyQt5.QtCore import Qt, QSize
+from PyQt5.QtGui import QDoubleValidator
+
 from celldetective.gui.gui_utils import center_window, FeatureChoice, ListWidget, QHSeperationLine, FigureCanvas, help_generic
 from superqt import QLabeledDoubleSlider,QLabeledSlider
 from superqt.fonticon import icon
@@ -30,6 +32,8 @@ class ConfigTracking(QMainWindow, Styles):
 		self.setWindowTitle("Configure tracking")
 		self.mode = self.parent_window.mode
 		self.exp_dir = self.parent_window.exp_dir
+		self.floatValidator = QDoubleValidator()
+
 		if self.mode=="targets":
 			self.config_name = os.sep.join(["configs", "btrack_config_targets.json"])
 			self.track_instructions_write_path = self.parent_window.exp_dir + os.sep.join(["configs","tracking_instructions_targets.json"])
@@ -68,9 +72,25 @@ class ConfigTracking(QMainWindow, Styles):
 		main_layout.setContentsMargins(30,30,30,30)
 
 		# First collapsable Frame CONFIG
+
+		self.btrack_option = QRadioButton('bTrack')
+		self.btrack_option.setChecked(True)
+
+		self.trackpy_option = QRadioButton('trackpy')
+		self.tracker_option_group = QButtonGroup()
+		self.tracker_option_group.addButton(self.btrack_option)
+		self.tracker_option_group.addButton(self.trackpy_option)
+
 		self.config_frame = QFrame()
 		self.config_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
 		self.populate_config_frame()
+
+		tracker_hbox = QHBoxLayout()
+		tracker_hbox.setContentsMargins(15,15,15,15)
+		tracker_hbox.addWidget(self.btrack_option, 50, alignment=Qt.AlignCenter)
+		tracker_hbox.addWidget(self.trackpy_option, 50, alignment=Qt.AlignCenter)
+		main_layout.addLayout(tracker_hbox)
+
 		main_layout.addWidget(self.config_frame)
 
 		# Second collapsable frame FEATURES
@@ -79,6 +99,12 @@ class ConfigTracking(QMainWindow, Styles):
 		self.populate_features_frame()
 		main_layout.addWidget(self.features_frame)
 
+		self.config_trackpy_frame = QFrame()
+		self.config_trackpy_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
+		self.populate_config_trackpy_frame()
+		main_layout.addWidget(self.config_trackpy_frame)
+		self.config_trackpy_frame.hide()
+
 		# Third collapsable frame POST-PROCESSING
 		self.post_proc_frame = QFrame()
 		self.post_proc_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
@@ -102,9 +128,27 @@ class ConfigTracking(QMainWindow, Styles):
 		self.setCentralWidget(self.scroll_area)
 		self.show()
 
+		self.btrack_option.toggled.connect(self.show_tracking_options)
+		self.trackpy_option.toggled.connect(self.show_tracking_options)
+
 		QApplication.processEvents()
 		self.adjustScrollArea()
 
+	def show_tracking_options(self):
+
+		if self.btrack_option.isChecked():
+			self.config_frame.show()
+			self.features_frame.show()
+			self.config_trackpy_frame.hide()
+			#self.scroll_area.setMinimumHeight(min(int(930), int(0.9*self.screen_height)))
+			#self.adjustSize()
+		else:
+			self.config_frame.hide()
+			self.features_frame.hide()
+			self.config_trackpy_frame.show()
+			#self.scroll_area.setMinimumHeight(self.minimum_height)
+			#self.adjustSize()
+
 
 	def populate_post_proc_frame(self):
 
@@ -539,6 +583,29 @@ class ConfigTracking(QMainWindow, Styles):
 		self.collapse_config_btn.clicked.connect(self.collapse_config_advanced)
 		#self.ContentsConfig.hide()
 
+	def populate_config_trackpy_frame(self):
+
+		grid = QGridLayout(self.config_trackpy_frame)
+		panel_title = QLabel(f"CONFIGURATION")
+		panel_title.setStyleSheet("""
+			font-weight: bold;
+			padding: 0px;
+			""")
+
+		grid.addWidget(panel_title, 0, 0, 1, 4, alignment=Qt.AlignCenter)
+
+		self.collapse_config_trackpy_btn = QPushButton()
+		self.collapse_config_trackpy_btn.setIcon(icon(MDI6.chevron_down,color="black"))
+		self.collapse_config_trackpy_btn.setIconSize(QSize(20, 20))
+		self.collapse_config_trackpy_btn.setStyleSheet(self.button_select_all)
+		grid.addWidget(self.collapse_config_trackpy_btn, 0, 0, 1, 4, alignment=Qt.AlignRight)
+		self.generate_config_trackpy_panel_contents()
+		grid.addWidget(self.ContentsConfigTrackpy, 1, 0, 1, 4, alignment=Qt.AlignTop)
+		self.collapse_config_trackpy_btn.clicked.connect(lambda: self.ContentsConfigTrackpy.setHidden(not self.ContentsConfigTrackpy.isHidden()))
+		self.collapse_config_trackpy_btn.clicked.connect(self.collapse_config_trackpy_advanced)
+		#self.ContentsConfig.hide()
+
+
 	def collapse_config_advanced(self):
 
 		"""
@@ -561,6 +628,56 @@ class ConfigTracking(QMainWindow, Styles):
 			self.collapse_config_btn.setIconSize(QSize(20, 20))
 			self.scroll_area.setMinimumHeight(min(int(930), int(0.9*self.screen_height)))
 
+	def collapse_config_trackpy_advanced(self):
+
+		"""
+		Switch the chevron icon and adjust the size for the CONFIG frame.
+		"""
+
+
+		post_open = not self.ContentsPostProc.isHidden()
+		is_open = np.array([post_open])
+
+		if self.ContentsConfigTrackpy.isHidden():
+			self.collapse_config_trackpy_btn.setIcon(icon(MDI6.chevron_down,color="black"))
+			self.collapse_config_trackpy_btn.setIconSize(QSize(20, 20))
+			if len(is_open[is_open])==0:
+				self.scroll_area.setMinimumHeight(int(self.minimum_height))
+				self.adjustSize()
+		else:
+			self.collapse_config_trackpy_btn.setIcon(icon(MDI6.chevron_up,color="black"))
+			self.collapse_config_trackpy_btn.setIconSize(QSize(20, 20))
+			self.scroll_area.setMinimumHeight(min(int(930), int(0.9*self.screen_height)))
+
+
+	def generate_config_trackpy_panel_contents(self):
+
+		self.ContentsConfigTrackpy = QFrame()
+		layout = QVBoxLayout(self.ContentsConfigTrackpy)
+		layout.setContentsMargins(0,0,0,0)
+
+		sr_layout = QHBoxLayout()
+		self.search_range_lbl = QLabel("search range [px]: ")
+		self.search_range_le = QLineEdit('30')
+		self.search_range_le.setPlaceholderText('search distance in pixels')
+		self.search_range_le.setValidator(self.floatValidator)
+		sr_layout.addWidget(self.search_range_lbl, 30)
+		sr_layout.addWidget(self.search_range_le, 70)
+		layout.addLayout(sr_layout)
+
+		memory_layout = QHBoxLayout()
+		self.memory_lbl = QLabel("memory [# frames]: ")
+		self.memory_slider = QLabeledSlider()
+		self.memory_slider.setSingleStep(1)
+		self.memory_slider.setTickInterval(1)
+		self.memory_slider.setSingleStep(1)
+		self.memory_slider.setOrientation(1)
+		self.memory_slider.setRange(0,self.parent_window.parent_window.len_movie)
+		self.memory_slider.setValue(0)
+		memory_layout.addWidget(self.memory_lbl, 30)
+		memory_layout.addWidget(self.memory_slider, 70)
+		layout.addLayout(memory_layout)
+
 
 	def generate_config_panel_contents(self):
 		
@@ -741,7 +858,23 @@ class ConfigTracking(QMainWindow, Styles):
 		"""
 
 		print('Writing instructions...')
+		
+		if self.btrack_option.isChecked():
+			btrack_option = True
+		else:
+			btrack_option = False
+
+		# Fetch trackpky params
+		if not btrack_option:
+			search_range = int(self.search_range_le.text().replace(',','.'))
+			memory = self.memory_slider.value()
+		else:
+			search_range = None
+			memory = None	
+
 		tracking_options = {'btrack_config_path': self.config_path}
+		tracking_options.update({'btrack_option': btrack_option, 'search_range': search_range, 'memory': memory})
+
 		if not self.features_ticked:
 			features = None
 			masked_channels = None
@@ -850,6 +983,23 @@ class ConfigTracking(QMainWindow, Styles):
 					self.ContentsFeatures.hide()
 					self.uncheck_features()
 
+				btrack_option = True
+				if 'btrack_option' in tracking_instructions:
+					btrack_option = tracking_instructions['btrack_option']
+				if btrack_option:
+					self.btrack_option.click()
+				else:
+					self.trackpy_option.click()
+
+				if 'search_range' in tracking_instructions:
+					search_range = tracking_instructions['search_range']
+					if search_range is not None:
+						self.search_range_le.setText(str(search_range).replace('.',','))				
+				if 'memory' in tracking_instructions:
+					memory = tracking_instructions['memory']
+					if memory is not None:
+						self.memory_slider.setValue(memory)
+
 				# Uncheck channels that are masked
 				mask_channels = tracking_instructions['mask_channels']
 				if (mask_channels is not None) and len(mask_channels)>0:

{celldetective-1.3.5 → celldetective-1.3.6.post2}/celldetective/gui/classifier_widget.py

@@ -95,7 +95,6 @@ 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)]
 
@@ -129,7 +128,6 @@ class ClassifierWidget(QWidget, Styles):
 		layout.addLayout(hbox_classify)
 
 		self.time_corr = QCheckBox('Time correlated')
-		self.time_corr.toggled.connect(self.activate_time_corr_options)
 		if "TRACK_ID" in self.df.columns:
 			self.time_corr.setEnabled(True)
 		else:
@@ -150,17 +148,14 @@ class ClassifierWidget(QWidget, Styles):
 
 		self.irreversible_event_btn = QRadioButton('irreversible event')
 		self.unique_state_btn = QRadioButton('unique state')
+		self.transient_event_btn = QRadioButton('transient event')
 		time_corr_btn_group = QButtonGroup()
 		self.unique_state_btn.click()
-		self.time_corr_options = [self.irreversible_event_btn, self.unique_state_btn]
-
-		for btn in self.time_corr_options:
-			time_corr_btn_group.addButton(btn)
-			btn.setEnabled(False)
 
 		time_corr_layout = QHBoxLayout()
-		time_corr_layout.addWidget(self.unique_state_btn, 50, alignment=Qt.AlignCenter)
-		time_corr_layout.addWidget(self.irreversible_event_btn, 50,alignment=Qt.AlignCenter)
+		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)
 		layout.addLayout(time_corr_layout)
 
 		self.prereq_event_check = QCheckBox('prerequisite event:')
@@ -171,12 +166,6 @@ class ClassifierWidget(QWidget, Styles):
 		self.prereq_event_check.setEnabled(False)
 		self.prereq_event_cb.setEnabled(False)
 
-		prereq_layout = QHBoxLayout()
-		prereq_layout.addWidget(QLabel(''), 50)
-		prereq_layout.addWidget(self.prereq_event_check, 15)
-		prereq_layout.addWidget(self.prereq_event_cb, 35)
-		layout.addLayout(prereq_layout)
-
 		self.r2_slider = QLabeledDoubleSlider()
 		self.r2_slider.setValue(0.75)
 		self.r2_slider.setRange(0,1)
@@ -186,17 +175,32 @@ class ClassifierWidget(QWidget, Styles):
 		self.r2_label.setToolTip('Minimum R2 between the fit sigmoid and the binary response to the filters to accept the event.')
 
 		r2_threshold_layout = QHBoxLayout()
-		r2_threshold_layout.addWidget(QLabel(''), 50)
-		r2_threshold_layout.addWidget(self.r2_label, 15)
-		r2_threshold_layout.addWidget(self.r2_slider, 35)
-		layout.addLayout(r2_threshold_layout)	
+		r2_threshold_layout.addWidget(QLabel(''), 33)
+		r2_threshold_layout.addWidget(self.r2_label, 13)
+		r2_threshold_layout.addWidget(self.r2_slider, 20)
+		r2_threshold_layout.addWidget(QLabel(''), 33)
+
+		layout.addLayout(r2_threshold_layout)
 		
+		self.time_corr_options = [self.irreversible_event_btn, self.unique_state_btn, self.prereq_event_check, self.prereq_event_cb, self.transient_event_btn]
+		for btn in [self.irreversible_event_btn, self.unique_state_btn, self.transient_event_btn]:
+			time_corr_btn_group.addButton(btn)
+			btn.setEnabled(False)
+		self.time_corr.toggled.connect(self.activate_time_corr_options)
+
 		self.irreversible_event_btn.clicked.connect(self.activate_r2)
 		self.unique_state_btn.clicked.connect(self.activate_r2)
+		self.transient_event_btn.clicked.connect(self.activate_r2)
 
 		for wg in [self.r2_slider, self.r2_label]:
 			wg.setEnabled(False)
 
+		prereq_layout = QHBoxLayout()
+		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)
+
 		layout.addWidget(QLabel())
 
 		self.submit_btn = QPushButton('apply')
@@ -225,10 +229,10 @@ class ClassifierWidget(QWidget, Styles):
 
 	def activate_r2(self):
 		if self.irreversible_event_btn.isChecked() and self.time_corr.isChecked():
-			for wg in [self.r2_slider, self.r2_label, self.prereq_event_check]:
+			for wg in [self.r2_slider, self.r2_label]:
 				wg.setEnabled(True)
 		else:
-			for wg in [self.r2_slider, self.r2_label, self.prereq_event_check]:
+			for wg in [self.r2_slider, self.r2_label]:
 				wg.setEnabled(False)				
 
 	def activate_time_corr_options(self):
@@ -441,7 +445,7 @@ 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(), 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()

{celldetective-1.3.5 → celldetective-1.3.6.post2}/celldetective/gui/configure_new_exp.py

@@ -453,6 +453,9 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		config.set('Labels', 'concentrations', self.concentrations)
 		config.set('Labels', 'pharmaceutical_agents', self.pharmaceutical_agents)
 
+		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)
@@ -480,6 +483,8 @@ class SetupConditionLabels(QWidget, Styles):
 		self.antibodies_cbs = [QLineEdit() for i in range(self.n_wells)]
 		self.concentrations_cbs = [QLineEdit() for i in range(self.n_wells)]
 		self.pharmaceutical_agents_cbs = [QLineEdit() for i in range(self.n_wells)]
+		self.concentration_units_le = QLineEdit('pM')
+		self.concentration_units_le.setPlaceholderText('concentration units')
 
 		for i in range(self.n_wells):
 			hbox = QHBoxLayout()
@@ -504,6 +509,12 @@ class SetupConditionLabels(QWidget, Styles):
 
 			self.layout.addLayout(hbox)
 
+		concentration_units_layout = QHBoxLayout()
+		concentration_units_layout.addWidget(QLabel('concentration\nunits: '),5,alignment=Qt.AlignLeft)
+		concentration_units_layout.addWidget(self.concentration_units_le,10)
+		concentration_units_layout.addWidget(QLabel(''), 85)
+		self.layout.addLayout(concentration_units_layout)
+
 		btn_hbox = QHBoxLayout()
 		btn_hbox.setContentsMargins(0,20,0,0)
 		self.skip_btn = QPushButton('Skip')
@@ -556,6 +567,8 @@ class SetupConditionLabels(QWidget, Styles):
 		pharamaceutical_text = [c.text() for c in self.pharmaceutical_agents_cbs]
 		self.parent_window.pharmaceutical_agents = ','.join(pharamaceutical_text)
 
+		self.parent_window.concentration_units = self.concentration_units_le.text()
+
 
 
 

{celldetective-1.3.5 → celldetective-1.3.6.post2}/celldetective/gui/control_panel.py

@@ -338,6 +338,7 @@ class ControlPanel(QMainWindow, Styles):
 		self.antibodies = get_experiment_antibodies(self.exp_dir)
 		self.pharmaceutical_agents = get_experiment_pharmaceutical_agents(self.exp_dir)
 
+		self.metadata = ConfigSectionMap(self.exp_config,"Metadata")
 		print('Experiment configuration successfully read...')
 
 	def closeEvent(self, event):

{celldetective-1.3.5 → celldetective-1.3.6.post2}/celldetective/gui/gui_utils.py

@@ -1,5 +1,5 @@
 import numpy as np
-from PyQt5.QtWidgets import QApplication, QMessageBox, QFrame, QSizePolicy, QWidget, QLineEdit, QListWidget, QVBoxLayout, QComboBox, \
+from PyQt5.QtWidgets import QGridLayout, QApplication, QMessageBox, QFrame, QSizePolicy, QWidget, QLineEdit, QListWidget, QVBoxLayout, QComboBox, \
 	QPushButton, QLabel, QHBoxLayout, QCheckBox, QFileDialog, QToolButton, QMenu, QStylePainter, QStyleOptionComboBox, QStyle
 from PyQt5.QtCore import Qt, QSize, QAbstractTableModel, QEvent, pyqtSignal
 from PyQt5.QtGui import QDoubleValidator, QIntValidator, QStandardItemModel, QPalette
@@ -15,6 +15,125 @@ import celldetective.extra_properties as extra_properties
 from inspect import getmembers, isfunction
 from celldetective.filters import *
 from os import sep
+import json
+
+
+class PreprocessingLayout(QVBoxLayout, Styles):
+
+	"""
+	A widget that allows user to choose preprocessing filters for an image
+	"""
+
+	def __init__(self, parent_window=None, apply_btn_option=True, *args, **kwargs):
+		super().__init__(*args, **kwargs)
+
+		self.parent_window = parent_window
+		self.apply_btn_option = apply_btn_option
+		self.generate_components()
+		self.add_to_layout()
+
+	def add_to_layout(self):
+		
+		self.setContentsMargins(20, 20, 20, 20)
+		
+		button_layout = QHBoxLayout()
+		button_layout.addWidget(self.preprocess_lbl, 85, alignment=Qt.AlignLeft)
+		button_layout.addWidget(self.delete_filter_btn, 5)
+		button_layout.addWidget(self.add_filter_btn, 5)
+		button_layout.addWidget(self.help_prefilter_btn, 5)
+		self.addLayout(button_layout, 25)
+
+		self.addWidget(self.list, 70)
+		if self.apply_btn_option:
+			self.addWidget(self.apply_btn, 5)
+
+	def generate_components(self):
+		
+		self.list = ListWidget(FilterChoice, [])
+
+		self.preprocess_lbl = QLabel('Preprocessing')
+		self.preprocess_lbl.setStyleSheet("font-weight: bold;")
+
+		self.delete_filter_btn = QPushButton()
+		self.delete_filter_btn.setStyleSheet(self.button_select_all)
+		self.delete_filter_btn.setIcon(icon(MDI6.trash_can, color="black"))
+		self.delete_filter_btn.setToolTip("Remove filter")
+		self.delete_filter_btn.setIconSize(QSize(20, 20))
+		self.delete_filter_btn.clicked.connect(self.list.removeSel)
+
+		self.add_filter_btn = QPushButton()
+		self.add_filter_btn.setStyleSheet(self.button_select_all)
+		self.add_filter_btn.setIcon(icon(MDI6.filter_plus, color="black"))
+		self.add_filter_btn.setToolTip("Add filter")
+		self.add_filter_btn.setIconSize(QSize(20, 20))
+		self.add_filter_btn.clicked.connect(self.list.addItem)
+
+		self.help_prefilter_btn = QPushButton()
+		self.help_prefilter_btn.setIcon(icon(MDI6.help_circle,color=self.help_color))
+		self.help_prefilter_btn.setIconSize(QSize(20, 20))
+		self.help_prefilter_btn.clicked.connect(self.help_prefilter)
+		self.help_prefilter_btn.setStyleSheet(self.button_select_all)
+		self.help_prefilter_btn.setToolTip("Help.")
+		
+		if self.apply_btn_option:
+			self.apply_btn = QPushButton("Apply")
+			self.apply_btn.setIcon(icon(MDI6.filter_cog_outline, color="white"))
+			self.apply_btn.setIconSize(QSize(20, 20))
+			self.apply_btn.setStyleSheet(self.button_style_sheet)
+			self.apply_btn.clicked.connect(self.parent_window.preprocess_image)
+
+	def help_prefilter(self):
+
+		"""
+		Helper for prefiltering strategy
+		"""
+
+		dict_path = os.sep.join([get_software_location(),'celldetective','gui','help','prefilter-for-segmentation.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 to {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
+
+
+class PreprocessingLayout2(PreprocessingLayout):
+
+	def __init__(self, fraction=75, *args, **kwargs):
+
+		self.fraction = fraction
+		super().__init__(apply_btn_option=False, *args, **kwargs)
+		self.preprocess_lbl.setText('Preprocessing: ')
+		self.preprocess_lbl.setStyleSheet("")
+		self.setContentsMargins(0,0,0,0)
+
+	def add_to_layout(self):
+		
+		main_layout = QHBoxLayout()
+		main_layout.setContentsMargins(0,0,0,0)
+		main_layout.setSpacing(5)
+		main_layout.addWidget(self.preprocess_lbl, self.fraction, alignment=Qt.AlignTop)
+
+		list_grid = QGridLayout()
+		list_grid.addWidget(self.list, 0, 0, 2, 2)
+		list_grid.addWidget(self.add_filter_btn, 0, 2, 1, 1)
+		list_grid.addWidget(self.delete_filter_btn, 1, 2, 1, 1)
+		main_layout.addLayout(list_grid, 100-self.fraction)
+		self.add_filter_btn.setFixedWidth(35)  # Ensure the button width is fixed
+		self.delete_filter_btn.setFixedWidth(35)
+		list_grid.setColumnStretch(2, 0)
+
+		self.addLayout(main_layout)
 
 
 class QCheckableComboBox(QComboBox):
@@ -427,7 +546,7 @@ class QHSeperationLine(QFrame):
 		self.setSizePolicy(QSizePolicy.Preferred, QSizePolicy.Minimum)
 
 
-class FeatureChoice(QWidget):
+class FeatureChoice(QWidget, Styles):
 
 	def __init__(self, parent_window):
 		super().__init__()
@@ -435,7 +554,6 @@ class FeatureChoice(QWidget):
 		self.setWindowTitle("Add feature")
 		# Create the QComboBox and add some items
 		self.combo_box = QComboBox(self)
-		center_window(self)
 
 		standard_measurements = ["area",
 								 "area_bbox",
@@ -465,12 +583,15 @@ class FeatureChoice(QWidget):
 		self.combo_box.addItems(standard_measurements)
 
 		self.add_btn = QPushButton("Add")
+		self.add_btn.setStyleSheet(self.button_style_sheet)
 		self.add_btn.clicked.connect(self.add_current_feature)
 
 		# Create the layout
 		layout = QVBoxLayout(self)
 		layout.addWidget(self.combo_box)
 		layout.addWidget(self.add_btn)
+		center_window(self)
+
 
 	def add_current_feature(self):
 		filtername = self.combo_box.currentText()
@@ -478,7 +599,7 @@ class FeatureChoice(QWidget):
 		self.close()
 
 
-class FilterChoice(QWidget):
+class FilterChoice(QWidget, Styles):
 
 	def __init__(self, parent_window):
 
@@ -499,9 +620,10 @@ class FilterChoice(QWidget):
 			'laplace_filter': None,
 			'abs_filter': None,
 			'ln_filter': None,
+			'invert_filter': {'value': 65535},
 			'subtract_filter': {'value': 1},
-			'dog_filter': {'sigma_low': 0.8, 'sigma_high': 1.6},
-			'log_filter': {'sigma': 2},
+			'dog_filter': {'blob_size': 30},
+			'log_filter': {'blob_size': 30},
 			'tophat_filter': {'size': 4, 'connectivity': 4},
 			'otsu_filter': None,
 			'local_filter': {'block_size': 73, 'method': 'mean', 'offset': 0},
@@ -523,16 +645,18 @@ class FilterChoice(QWidget):
 		self.arguments_labels = [QLabel('') for i in range(3)]
 		for i in range(2):
 			hbox = QHBoxLayout()
-			hbox.addWidget(self.arguments_labels[i], 20)
-			hbox.addWidget(self.arguments_le[i], 80)
+			hbox.addWidget(self.arguments_labels[i], 40)
+			hbox.addWidget(self.arguments_le[i], 60)
 			layout.addLayout(hbox)
 
 		self.add_btn = QPushButton("Add")
+		self.add_btn.setStyleSheet(self.button_style_sheet)
 		self.add_btn.clicked.connect(self.add_current_feature)
 		layout.addWidget(self.add_btn)
 
 		self.combo_box.setCurrentIndex(0)
 		self.update_arguments()
+		center_window(self)
 
 	def add_current_feature(self):
 
@@ -787,6 +911,9 @@ class ListWidget(QWidget):
 		self.addItemWindow = self.choiceWidget(self)
 		self.addItemWindow.show()
 
+	def addItemToList(self, item):
+		self.list_widget.addItems([item])
+
 	def getItems(self):
 
 		"""
@@ -814,6 +941,9 @@ class ListWidget(QWidget):
 				items.append(self.dtype(self.list_widget.item(x).text()))
 		return items
 
+	def clear(self):
+		self.items = []
+		self.list_widget.clear()
 
 	def removeSel(self):