celldetective 1.3.2__tar.gz → 1.3.3.post1__tar.gz

{celldetective-1.3.2 → celldetective-1.3.3.post1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: celldetective
-Version: 1.3.2
+Version: 1.3.3.post1
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro
@@ -172,20 +172,20 @@ For more information about how to get started, please check the [documentation](
 # How to cite?
 
 If you use this software in your research, please cite the
-[Celldetective](https://www.biorxiv.org/content/10.1101/2024.03.15.585250v1)
+[Celldetective](https://www.biorxiv.org/content/10.1101/2024.03.15.585250v3)
 paper (currently preprint):
 
 ``` raw
 @article {Torro2024.03.15.585250,
-    author = {R{\'e}my Torro and Beatriz D{\`\i}az-Bello and Dalia El Arawi and Lorna Ammer and Patrick Chames and Kheya Sengupta and Laurent Limozin},
+    author = {Torro, R{\'e}my and D{\'\i}az-Bello, Beatriz and Arawi, Dalia El and Dervanova, Ksenija and Ammer, Lorna and Dupuy, Florian and Chames, Patrick and Sengupta, Kheya and Limozin, Laurent},
     title = {Celldetective: an AI-enhanced image analysis tool for unraveling dynamic cell interactions},
     elocation-id = {2024.03.15.585250},
     year = {2024},
     doi = {10.1101/2024.03.15.585250},
     publisher = {Cold Spring Harbor Laboratory},
-    abstract = {A current key challenge in bioimaging is the analysis of multimodal and multidimensional data reporting dynamic interactions between diverse cell populations. We developed Celldetective, a software that integrates AI-based segmentation and tracking algorithms and automated signal analysis into a user-friendly graphical interface. It offers complete interactive visualization, annotation, and training capabilities. We demonstrate it by analyzing original experimental data of spreading immune effector cells as well as antibody-dependent cell cytotoxicity events using multimodal fluorescence microscopy.Competing Interest StatementThe authors have declared no competing interest.},
-    URL = {https://www.biorxiv.org/content/early/2024/03/17/2024.03.15.585250},
-    eprint = {https://www.biorxiv.org/content/early/2024/03/17/2024.03.15.585250.full.pdf},
+    abstract = {A current challenge in bioimaging for immunology and immunotherapy research lies in analyzing multimodal and multidimensional data that capture dynamic interactions between diverse cell populations. Here, we introduce Celldetective, an open-source Python-based software designed for high-performance, end-to-end analysis of image-based in vitro immune and immunotherapy assays. Purpose-built for multicondition, 2D multichannel time-lapse microscopy of mixed cell populations, Celldetective is optimized for the needs of immunology assays. The software seamlessly integrates AI-based segmentation, Bayesian tracking, and automated single-cell event detection, all within an intuitive graphical interface that supports interactive visualization, annotation, and training capabilities. We demonstrate its utility with original data on immune effector cell interactions with an activating surface, mediated by bispecific antibodies, and further showcase its potential for analyzing extensive sets of pairwise interactions in antibody-dependent cell cytotoxicity events.Competing Interest StatementThe authors have declared no competing interest.},
+    URL = {https://www.biorxiv.org/content/early/2024/11/13/2024.03.15.585250},
+    eprint = {https://www.biorxiv.org/content/early/2024/11/13/2024.03.15.585250.full.pdf},
     journal = {bioRxiv}
 }
 ```

{celldetective-1.3.2 → celldetective-1.3.3.post1}/README.md

@@ -128,20 +128,20 @@ For more information about how to get started, please check the [documentation](
 # How to cite?
 
 If you use this software in your research, please cite the
-[Celldetective](https://www.biorxiv.org/content/10.1101/2024.03.15.585250v1)
+[Celldetective](https://www.biorxiv.org/content/10.1101/2024.03.15.585250v3)
 paper (currently preprint):
 
 ``` raw
 @article {Torro2024.03.15.585250,
-    author = {R{\'e}my Torro and Beatriz D{\`\i}az-Bello and Dalia El Arawi and Lorna Ammer and Patrick Chames and Kheya Sengupta and Laurent Limozin},
+    author = {Torro, R{\'e}my and D{\'\i}az-Bello, Beatriz and Arawi, Dalia El and Dervanova, Ksenija and Ammer, Lorna and Dupuy, Florian and Chames, Patrick and Sengupta, Kheya and Limozin, Laurent},
     title = {Celldetective: an AI-enhanced image analysis tool for unraveling dynamic cell interactions},
     elocation-id = {2024.03.15.585250},
     year = {2024},
     doi = {10.1101/2024.03.15.585250},
     publisher = {Cold Spring Harbor Laboratory},
-    abstract = {A current key challenge in bioimaging is the analysis of multimodal and multidimensional data reporting dynamic interactions between diverse cell populations. We developed Celldetective, a software that integrates AI-based segmentation and tracking algorithms and automated signal analysis into a user-friendly graphical interface. It offers complete interactive visualization, annotation, and training capabilities. We demonstrate it by analyzing original experimental data of spreading immune effector cells as well as antibody-dependent cell cytotoxicity events using multimodal fluorescence microscopy.Competing Interest StatementThe authors have declared no competing interest.},
-    URL = {https://www.biorxiv.org/content/early/2024/03/17/2024.03.15.585250},
-    eprint = {https://www.biorxiv.org/content/early/2024/03/17/2024.03.15.585250.full.pdf},
+    abstract = {A current challenge in bioimaging for immunology and immunotherapy research lies in analyzing multimodal and multidimensional data that capture dynamic interactions between diverse cell populations. Here, we introduce Celldetective, an open-source Python-based software designed for high-performance, end-to-end analysis of image-based in vitro immune and immunotherapy assays. Purpose-built for multicondition, 2D multichannel time-lapse microscopy of mixed cell populations, Celldetective is optimized for the needs of immunology assays. The software seamlessly integrates AI-based segmentation, Bayesian tracking, and automated single-cell event detection, all within an intuitive graphical interface that supports interactive visualization, annotation, and training capabilities. We demonstrate its utility with original data on immune effector cell interactions with an activating surface, mediated by bispecific antibodies, and further showcase its potential for analyzing extensive sets of pairwise interactions in antibody-dependent cell cytotoxicity events.Competing Interest StatementThe authors have declared no competing interest.},
+    URL = {https://www.biorxiv.org/content/early/2024/11/13/2024.03.15.585250},
+    eprint = {https://www.biorxiv.org/content/early/2024/11/13/2024.03.15.585250.full.pdf},
     journal = {bioRxiv}
 }
 ```

celldetective-1.3.3.post1/celldetective/_version.py

@@ -0,0 +1 @@
+__version__ = "1.3.3.post1"

{celldetective-1.3.2 → celldetective-1.3.3.post1}/celldetective/gui/control_panel.py

@@ -450,8 +450,8 @@ class ControlPanel(QMainWindow, Styles):
 			self.view_stack_btn.setEnabled(False)
 			self.ProcessEffectors.signal_analysis_action.setEnabled(True)
 			self.ProcessTargets.signal_analysis_action.setEnabled(True)
-
-			self.delete_tracks_btn.hide()
+			if hasattr(self,'delete_tracks_btn'):
+				self.delete_tracks_btn.hide()
 			self.ProcessTargets.delete_tracks_btn.hide()
 			self.ProcessEffectors.delete_tracks_btn.hide()
 		else:

{celldetective-1.3.2 → celldetective-1.3.3.post1}/celldetective/gui/measurement_options.py

@@ -10,7 +10,7 @@ from superqt import QLabeledDoubleSlider
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
 
-from celldetective.gui.thresholds_gui import ThresholdSpot
+#from celldetective.gui.thresholds_gui import ThresholdSpot
 from celldetective.utils import extract_experiment_channels, get_software_location
 from celldetective.io import load_frames, auto_load_number_of_frames
 from celldetective.measure import compute_haralick_features
@@ -26,7 +26,7 @@ from tifffile import imread
 from pathlib import Path
 import gc
 
-from celldetective.gui.viewers import CellEdgeVisualizer
+from celldetective.gui.viewers import CellEdgeVisualizer, SpotDetectionVisualizer
 from celldetective.gui.layouts import ProtocolDesignerLayout, BackgroundFitCorrectionLayout, LocalCorrectionLayout
 from celldetective.gui.gui_utils import ThresholdLineEdit
 from celldetective.gui import Styles
@@ -951,51 +951,54 @@ class ConfigMeasurements(QMainWindow, Styles):
 
 		layout.addWidget(self.threshold_lbl, 4, 0)
 		layout.addWidget(self.threshold_value, 4, 1)
-		self.preview_spot = QPushButton('Preview')
-		self.preview_spot.clicked.connect(self.spot_preview)
-		self.preview_spot.setStyleSheet(self.button_style_sheet_2)
-		layout.addWidget(self.preview_spot, 5, 0, 1, 2)
-		self.spot_channel.setEnabled(False)
-		self.spot_channel_lbl.setEnabled(False)
-		self.diameter_value.setEnabled(False)
-		self.diameter_lbl.setEnabled(False)
-		self.threshold_value.setEnabled(False)
-		self.threshold_lbl.setEnabled(False)
-		self.preview_spot.setEnabled(False)
 
+		self.spot_viewer_btn = QPushButton()
+		self.spot_viewer_btn.clicked.connect(self.spot_preview)
+		self.spot_viewer_btn.setIcon(icon(MDI6.image_check, color="k"))
+		self.spot_viewer_btn.setStyleSheet(self.button_select_all)
+		self.spot_viewer_btn.setToolTip('Set detection parameters visually.')
+		layout.addWidget(self.spot_viewer_btn, 1, 1, 1, 1, alignment=Qt.AlignRight)
+
+		self.spot_detection_widgets = [self.spot_channel, self.spot_channel_lbl, self.diameter_value, self.diameter_lbl, self.threshold_value, self.threshold_lbl, self.spot_viewer_btn]
+		for wg in self.spot_detection_widgets:
+			wg.setEnabled(False)
 
 	def enable_spot_preview(self):
 
 		diam = self.diameter_value.text().replace(',','').replace('.','')
 		thresh = self.threshold_value.text().replace(',','').replace('.','')
 		if diam.isnumeric() and thresh.isnumeric():
-			self.preview_spot.setEnabled(True)
+			self.spot_viewer_btn.setEnabled(True)
 		else:
-			self.preview_spot.setEnabled(False)
+			self.spot_viewer_btn.setEnabled(False)
 
 	def spot_preview(self):
 		self.locate_image()
 		if self.test_frame is not None:
 			self.locate_mask()
 			if self.test_mask is not None:
-				self.spot_visual = ThresholdSpot(current_channel=self.spot_channel.currentIndex(), img=self.test_frame,
-												 mask=self.test_mask, parent_window=self)
+				self.spot_visual = SpotDetectionVisualizer(frame_slider=True,
+														   contrast_slider=True,
+														   cell_type=self.mode,
+														   channel_cb=True,
+														   channel_names = self.channel_names,
+														   stack_path=self.current_stack,
+														   n_channels=len(self.channel_names),
+														   target_channel=self.spot_channel.currentIndex(),
+														   window_title='Detect spots',
+														   parent_channel_cb=self.spot_channel,
+														   parent_diameter_le=self.diameter_value,
+														   parent_threshold_le=self.threshold_value,
+														   PxToUm = 1,)
+				self.spot_visual.show()
+				#self.spot_visual = ThresholdSpot(current_channel=self.spot_channel.currentIndex(), img=self.test_frame,
+				#								 mask=self.test_mask, parent_window=self)
 
 	def enable_spot_detection(self):
-		if self.spot_check.isChecked():
-			self.spot_channel.setEnabled(True)
-			self.spot_channel_lbl.setEnabled(True)
-			self.diameter_value.setEnabled(True)
-			self.diameter_lbl.setEnabled(True)
-			self.threshold_value.setEnabled(True)
-			self.threshold_lbl.setEnabled(True)
-			self.preview_spot.setEnabled(True)
 
+		if self.spot_check.isChecked():
+			for wg in self.spot_detection_widgets:
+				wg.setEnabled(True)
 		else:
-			self.spot_channel.setEnabled(False)
-			self.spot_channel_lbl.setEnabled(False)
-			self.diameter_value.setEnabled(False)
-			self.diameter_lbl.setEnabled(False)
-			self.threshold_value.setEnabled(False)
-			self.threshold_lbl.setEnabled(False)
-			self.preview_spot.setEnabled(False)
+			for wg in self.spot_detection_widgets:
+				wg.setEnabled(False)

{celldetective-1.3.2 → celldetective-1.3.3.post1}/celldetective/gui/process_block.py

@@ -291,6 +291,7 @@ class ProcessPanel(QFrame, Styles):
 		self.signal_models_list.addItems(signal_models)
 
 	def generate_tracking_options(self):
+		
 		grid_track = QHBoxLayout()
 
 		self.track_action = QCheckBox("TRACK")
@@ -303,16 +304,6 @@ class ProcessPanel(QFrame, Styles):
 			padding-top: 5px;
 			""")
 		grid_track.addWidget(self.track_action, 75)
-		#self.to_disable.append(self.track_action_tc)
-
-		# self.show_track_table_btn = QPushButton()
-		# self.show_track_table_btn.setIcon(icon(MDI6.table,color="black"))
-		# self.show_track_table_btn.setIconSize(QSize(20, 20))
-		# self.show_track_table_btn.setToolTip("Show trajectories table.")
-		# self.show_track_table_btn.setStyleSheet(self.button_select_all)
-		# #self.show_track_table_btn.clicked.connect(self.display_trajectory_table)
-		# self.show_track_table_btn.setEnabled(False)
-		# grid_track.addWidget(self.show_track_table_btn, 6)  #4,3,1,1, alignment=Qt.AlignLeft
 
 		self.delete_tracks_btn = QPushButton()
 		self.delete_tracks_btn.setIcon(icon(MDI6.trash_can,color="black"))
@@ -640,25 +631,6 @@ class ProcessPanel(QFrame, Styles):
 
 		self.seg_model_list.insertSeparator(len(self.models_truncated))
 
-
-		#if ("live_nuclei_channel" in self.exp_channels)*("dead_nuclei_channel" in self.exp_channels):
-		# 	print("both channels found")
-		# 	index = self.tc_seg_model_list.findText("MCF7_Hoescht_PI_w_primary_NK", Qt.MatchFixedString)
-		# 	if index >= 0:
-		# 		self.tc_seg_model_list.setCurrentIndex(index)
-		# elif ("live_nuclei_channel" in self.exp_channels)*("dead_nuclei_channel" not in self.exp_channels):
-		# 	index = self.tc_seg_model_list.findText("MCF7_Hoescht_w_primary_NK", Qt.MatchFixedString)
-		# 	if index >= 0:
-		# 		self.tc_seg_model_list.setCurrentIndex(index)
-		# elif ("live_nuclei_channel" not in self.exp_channels)*("dead_nuclei_channel" in self.exp_channels):
-		# 	index = self.tc_seg_model_list.findText("MCF7_PI_w_primary_NK", Qt.MatchFixedString)
-		# 	if index >= 0:
-		# 		self.tc_seg_model_list.setCurrentIndex(index)
-		# elif ("live_nuclei_channel" not in self.exp_channels)*("dead_nuclei_channel" not in self.exp_channels)*("adhesion_channel" in self.exp_channels):
-		# 	index = self.tc_seg_model_list.findText("RICM", Qt.MatchFixedString)
-		# 	if index >= 0:
-		# 		self.tc_seg_model_list.setCurrentIndex(index)
-
 	def tick_all_actions(self):
 		self.switch_all_ticks_option()
 		if self.all_ticked:
@@ -884,28 +856,7 @@ class ProcessPanel(QFrame, Styles):
 		if self.segment_action.isChecked():
 			self.segment_action.setChecked(False)
 
-		# QApplication.restoreOverrideCursor()
-		# self.unfreeze()
-
-	# 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.cellpose_calibrated = False
 
 	def open_napari_tracking(self):
 		print(f'View the tracks before post-processing for position {self.parent_window.pos} in napari...')
@@ -933,24 +884,6 @@ class ProcessPanel(QFrame, Styles):
 			if returnValue == QMessageBox.Ok:
 				return None
 
-	# def interpret_pos_location(self):
-
-	# 	"""
-	# 	Read the well/position selection from the control panel to decide which data to load
-	# 	Set position_indices to None if all positions must be taken
-
-	# 	"""
-
-	# 	if self.well_option==len(self.wells):
-	# 		self.well_indices = np.arange(len(self.wells))
-	# 	else:
-	# 		self.well_indices = np.array([self.well_option],dtype=int)
-
-	# 	if self.position_option==0:
-	# 		self.position_indices = None
-	# 	else:
-	# 		self.position_indices = np.array([self.position_option],dtype=int)
-
 	def load_available_tables(self):
 
 		"""
@@ -1016,6 +949,7 @@ class ProcessPanel(QFrame, Styles):
 		self.process_population()
 
 
+
 class NeighPanel(QFrame, Styles):
 	def __init__(self, parent_window):
 
@@ -1523,35 +1457,12 @@ class NeighPanel(QFrame, Styles):
 					rel_measure_at_position(self.pos)
 
 				if self.signal_analysis_action.isChecked():
-					
-					# df_targets = get_position_pickle(self.pos, population='targets')
-					# df_effectors = get_position_pickle(self.pos, population='effectors')
-					# self.dataframes = {
-					# 	'targets': df_targets,
-					# 	'effectors': df_effectors,
-					# }
-
-					# df_pairs = get_position_table(self.pos, population='pairs')
-
-					# # Need to identify expected reference / neighbor tables
-					# model_path = locate_signal_model(self.pair_signal_models_list.currentText(), pairs=True)
-					# print(f'Looking for model in {model_path}...')
-					# complete_path = model_path
-					# complete_path = rf"{complete_path}"
-					# model_config_path = os.sep.join([complete_path, 'config_input.json'])
-					# model_config_path = rf"{model_config_path}"
-					# f = open(model_config_path)
-					# model_config_path = json.load(f)
-
-					# reference_population = model_config_path['reference_population']
-					# neighbor_population = model_config_path['neighbor_population']
-
-					# analyze_pair_signals(df_pairs, self.dataframes[reference_population], self.dataframes[neighbor_population], model=self.pair_signal_models_list.currentText())
+
 					analyze_pair_signals_at_position(self.pos, self.pair_signal_models_list.currentText(), use_gpu=self.parent_window.parent_window.use_gpu)
+
 		self.parent_window.update_position_options()
 		print('Done.')
 
-
 	def check_signals2(self):
 
 		test = self.parent_window.locate_selected_position()

{celldetective-1.3.2 → celldetective-1.3.3.post1}/celldetective/gui/retrain_segmentation_model_options.py

@@ -616,4 +616,6 @@ class ConfigSegmentationModelTraining(QMainWindow, Styles):
 		
 		train_segmentation_model(model_folder+"training_instructions.json", use_gpu=self.parent_window.parent_window.parent_window.use_gpu)
 
-		# self.parent.refresh_signal_models()
+		self.parent_window.init_seg_model_list()
+		idx = self.parent_window.seg_model_list.findText(model_name)
+		self.parent_window.seg_model_list.setCurrentIndex(idx)