celldetective 1.3.6.post1__tar.gz → 1.3.7__tar.gz

{celldetective-1.3.6.post1 → celldetective-1.3.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: celldetective
-Version: 1.3.6.post1
+Version: 1.3.7
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro

celldetective-1.3.7/celldetective/_version.py

@@ -0,0 +1 @@
+__version__ = "1.3.7"

{celldetective-1.3.6.post1 → celldetective-1.3.7}/celldetective/events.py

@@ -209,7 +209,11 @@ def compute_survival(df, class_of_interest, t_event, t_reference=None, FrameToMi
 		assert t_reference in cols,"The reference time cannot be found in the dataframe..."
 		first_detections = df.groupby(groupby_cols)[t_reference].max().values
 	
+
+	print(f"{classes=} {event_times=} {max_times=} {first_detections=}")
 	events, survival_times = switch_to_events(classes, event_times, max_times, origin_times=first_detections, left_censored=left_censored, FrameToMin=FrameToMin, cut_observation_time=cut_observation_time)
+	print(f"{events=} {survival_times=}")
+
 	ks = KaplanMeierFitter()
 	if len(events)>0:
 		ks.fit(survival_times, event_observed=events)

{celldetective-1.3.6.post1 → celldetective-1.3.7}/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):
@@ -115,13 +119,18 @@ 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)

{celldetective-1.3.6.post1 → celldetective-1.3.7}/celldetective/gui/InitWindow.py

@@ -1,7 +1,7 @@
 import os
 
 from PyQt5.QtWidgets import QApplication, QMainWindow
-from PyQt5.QtWidgets import QFileDialog, QWidget, QVBoxLayout, QCheckBox, QHBoxLayout, QLabel, QLineEdit, QPushButton, QMessageBox, QMenu, QAction
+from PyQt5.QtWidgets import QFileDialog, QDialog, QWidget, QVBoxLayout, QCheckBox, QHBoxLayout, QLabel, QLineEdit, QPushButton, QMessageBox, QMenu, QAction
 from PyQt5.QtCore import Qt, QUrl
 from PyQt5.QtGui import QIcon, QDesktopServices, QIntValidator
 
@@ -20,6 +20,9 @@ from subprocess import check_output, Popen
 from psutil import cpu_count
 import json
 
+from celldetective.gui.processes.downloader import DownloadProcess
+from celldetective.gui.workers import ProgressWindow
+
 class AppInitWindow(QMainWindow, Styles):
 
 	"""
@@ -42,11 +45,11 @@ class AppInitWindow(QMainWindow, Styles):
 		except Exception: # this command not being found can raise quite a few different errors depending on the configuration
 			print('No NVIDIA GPU detected...')
 			self.use_gpu = False
-		
+
 		self.soft_path = software_location
 		self.onlyInt = QIntValidator()
 		self.setWindowIcon(QIcon(os.sep.join([self.soft_path,'celldetective','icons','logo.png'])))
-		center_window(self)
+
 		self._createActions()
 		self._createMenuBar()
 
@@ -63,6 +66,8 @@ class AppInitWindow(QMainWindow, Styles):
 		self.create_buttons_hbox()
 		self.setCentralWidget(central_widget)
 		self.reload_previous_gpu_threads()
+		center_window(self)
+
 		self.show()
 	
 	def closeEvent(self, event):
@@ -188,18 +193,27 @@ class AppInitWindow(QMainWindow, Styles):
 		self.openCytotoxicityAssayDemo.triggered.connect(self.download_cytotoxicity_assay_demo)
 
 	def download_spreading_assay_demo(self):
-		
+
 		self.target_dir = str(QFileDialog.getExistingDirectory(self, 'Select Folder for Download'))
 		if self.target_dir=='':
 			return None
-		
+
 		if not os.path.exists(os.sep.join([self.target_dir,'demo_ricm'])):
-			download_zenodo_file('demo_ricm', self.target_dir)
+			self.output_dir = self.target_dir
+			self.file = 'demo_ricm'
+			process_args = {"output_dir": self.output_dir, "file": self.file}
+			self.job = ProgressWindow(DownloadProcess, parent_window=self, title="Download", position_info=False, process_args=process_args)
+			result = self.job.exec_()
+			if result == QDialog.Accepted:
+				pass
+			elif result == QDialog.Rejected:
+				return None
+			#download_zenodo_file('demo_ricm', self.target_dir)
 		self.experiment_path_selection.setText(os.sep.join([self.target_dir, 'demo_ricm']))
 		self.validate_button.click()
 
 	def download_cytotoxicity_assay_demo(self):
-		
+
 		self.target_dir = str(QFileDialog.getExistingDirectory(self, 'Select Folder for Download'))
 		if self.target_dir=='':
 			return None
@@ -290,7 +304,7 @@ class AppInitWindow(QMainWindow, Styles):
 
 
 	def open_experiment(self):
-		
+
 		self.browse_experiment_folder()
 		if self.experiment_path_selection.text()!='':
 			self.open_directory()
@@ -310,7 +324,7 @@ class AppInitWindow(QMainWindow, Styles):
 		QDesktopServices.openUrl(doc_url)
 
 	def open_models_folder(self):
-		
+
 		path = os.sep.join([self.soft_path,'celldetective','models',os.sep])
 		try:
 			Popen(f'explorer {os.path.realpath(path)}')

{celldetective-1.3.6.post1 → celldetective-1.3.7}/celldetective/gui/control_panel.py

@@ -31,7 +31,6 @@ class ControlPanel(QMainWindow, Styles):
 		self.setWindowTitle("celldetective")
 		self.setWindowIcon(self.celldetective_icon)
 		self.parent_window = parent_window
-		center_window(self)
 
 		self.init_wells_and_positions()
 		self.load_configuration()
@@ -92,6 +91,10 @@ class ControlPanel(QMainWindow, Styles):
 		self.screen_height = desktop.screenGeometry().height()
 		self.screen_width = desktop.screenGeometry().width()
 		self.scroll.setMinimumWidth(440)
+		
+		self.setAttribute(Qt.WA_DeleteOnClose)
+		center_window(self)
+
 
 		self.well_list.setCurrentIndex(0)
 		#self.position_list.setCurrentIndex(0)
@@ -536,14 +539,14 @@ class ControlPanel(QMainWindow, Styles):
 				# if os.path.exists(os.sep.join([self.pos,'labels_targets', os.sep])):
 				self.ProcessTargets.check_seg_btn.setEnabled(True)
 				
-				if os.path.exists(os.sep.join([self.pos,'output','tables','napari_target_trajectories.npy'])):
-					self.ProcessTargets.check_tracking_result_btn.setEnabled(True)
-				else:
-					self.ProcessTargets.check_tracking_result_btn.setEnabled(False)
-				if os.path.exists(os.sep.join([self.pos,'output','tables','napari_effector_trajectories.npy'])):
-					self.ProcessEffectors.check_tracking_result_btn.setEnabled(True)
-				else:
-					self.ProcessEffectors.check_tracking_result_btn.setEnabled(False)
+				# if os.path.exists(os.sep.join([self.pos,'output','tables','napari_target_trajectories.npy'])):
+				# 	self.ProcessTargets.check_tracking_result_btn.setEnabled(True)
+				# else:
+				# 	self.ProcessTargets.check_tracking_result_btn.setEnabled(False)
+				# if os.path.exists(os.sep.join([self.pos,'output','tables','napari_effector_trajectories.npy'])):
+				# 	self.ProcessEffectors.check_tracking_result_btn.setEnabled(True)
+				# else:
+				# 	self.ProcessEffectors.check_tracking_result_btn.setEnabled(False)
 
 				if os.path.exists(os.sep.join([self.pos,'output','tables','trajectories_effectors.csv'])):
 					df = pd.read_csv(os.sep.join([self.pos,'output','tables','trajectories_effectors.csv']), nrows=1)
@@ -553,8 +556,10 @@ class ControlPanel(QMainWindow, Styles):
 						self.ProcessEffectors.check_signals_btn.setEnabled(True)
 						self.ProcessEffectors.delete_tracks_btn.show()
 						self.ProcessEffectors.signal_analysis_action.setEnabled(True)
+						self.ProcessEffectors.check_tracking_result_btn.setEnabled(True)
 					else:
-						self.ProcessEffectors.signal_analysis_action.setEnabled(False)						
+						self.ProcessEffectors.signal_analysis_action.setEnabled(False)
+						self.ProcessEffectors.check_tracking_result_btn.setEnabled(False)			
 
 					#self.ProcessEffectors.signal_analysis_action.setEnabled(True)
 					self.ProcessEffectors.view_tab_btn.setEnabled(True)
@@ -575,9 +580,12 @@ class ControlPanel(QMainWindow, Styles):
 					if id_col=='TRACK_ID':
 						self.ProcessTargets.check_signals_btn.setEnabled(True)
 						self.ProcessTargets.signal_analysis_action.setEnabled(True)
+						self.ProcessTargets.check_tracking_result_btn.setEnabled(True)
 						self.ProcessTargets.delete_tracks_btn.show()
 					else:
-						self.ProcessTargets.signal_analysis_action.setEnabled(False)						
+						self.ProcessTargets.signal_analysis_action.setEnabled(False)
+						self.ProcessTargets.check_tracking_result_btn.setEnabled(False)
+
 					#self.ProcessTargets.signal_analysis_action.setEnabled(True)
 					self.ProcessTargets.view_tab_btn.setEnabled(True)
 					self.ProcessTargets.classify_btn.setEnabled(True)

{celldetective-1.3.6.post1 → celldetective-1.3.7}/celldetective/gui/generic_signal_plot.py

@@ -229,6 +229,11 @@ class GenericSignalPlotWidget(QWidget, Styles):
 										)
 		self.alpha_slider.valueChanged.connect(self.submit_alpha)
 		self.cell_lines_alpha_wdg.setLayout(alpha_hbox)
+
+		# self.submit_alpha_btn = QPushButton('submit')
+		# self.submit_alpha_btn.setStyleSheet(self.button_style_sheet_2)
+		# self.submit_alpha_btn.clicked.connect(self.submit_alpha)
+		# alpha_hbox.addWidget(self.submit_alpha_btn, 10)
 		self.layout.addWidget(self.cell_lines_alpha_wdg)
 
 		self.select_option = [QRadioButton() for i in range(2)]

{celldetective-1.3.6.post1 → celldetective-1.3.7}/celldetective/gui/gui_utils.py

@@ -622,8 +622,8 @@ class FilterChoice(QWidget, Styles):
 			'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},

celldetective-1.3.7/celldetective/gui/help/DL-segmentation-strategy.json

@@ -0,0 +1,41 @@
+{
+  "Are the cells in your image blob-like?": {
+    "yes": {
+      "Do you have a fluorescence image of the cells?": {
+        "yes": {
+          "Is there a mixture of different cell populations in the image?": {
+            "yes": "to train custom StarDist model",
+            "no": {
+              "Can the cells be identified using a single channel?": {
+                "yes": "to use the StarDist versatile fluorescence generalist model",
+                "no" : "to train a custom StarDist model using your multichannel data"
+              }
+            }
+          }
+        },
+        "no": "to train a custom StarDist model on your data"
+      }
+    },
+    "no": {
+      "Is there a mixture of different cell populations in your image?": {
+        "yes": "to train a custom cellpose model with your data, annotating one of the two populations selectively",
+        "no": {
+          "Is there significant variation in cell sizes?": {
+            "yes": "to train a custom cellpose model using your data",
+            "no": {
+              "Can the cells be identified using at most two channels (one for cytoplasm and one for nucleus)?": {
+                "yes": {
+                  "Is the cytoplasm channel a brightfield image?": {
+                    "yes": "to use the cellpose livecell generalist model",
+                    "no" : "to use cellpose cyto3 generalist model"
+                  }
+                },
+                "no": "to train a custom cellpose model using your multichannel data"
+              }
+            }
+          }
+        }
+      }
+    }
+  }
+}

celldetective-1.3.7/celldetective/gui/help/Threshold-vs-DL.json

@@ -0,0 +1,26 @@
+{
+  "Can cell masks be extracted from a single channel?": {
+    "yes": {
+      "Are cell-cell contacts rare?": {
+        "yes": {
+          "Are non-cell objects easy to separate from cells?": {
+            "yes": {
+              "Are there background heterogeneities in the images?": {
+                "yes": {
+                  "Can the heterogeneities be corrected?": {
+                    "yes": "to use a threshold-based pipeline for mask extraction.",
+                    "no": "to use a deep learning approach for better segmentation."
+                  }
+                },
+                "no": "to use a threshold-based pipeline for mask extraction."
+              }
+            },
+            "no": "to use a deep learning approach for segmentation."
+          }
+        },
+        "no": "to use a deep learning approach for segmentation."
+      }
+    },
+    "no": "to use a deep learning approach for segmentation."
+  }
+}

celldetective-1.3.7/celldetective/gui/help/cell-populations.json

@@ -0,0 +1,11 @@
+{
+  "Do you have multiple cell populations of interest in your images?": {
+    "yes": {
+      "Do you have more than two distinct cell populations of interest?": {
+        "yes": "Currently, celldetective does not support the analysis of interactions between more than two cell populations at once. We recommend studying interactions between two populations at a time, or grouping similar populations together (e.g., effector-like vs target-like cells). Later, you can use celldetective's classification tools to break down the results by individual cell population.",
+        "no": "Identify the effector-like population (which influences changes in the target population) and the target-like population. If you're unsure about the exact definitions, choose a convention and apply it consistently. Please note, the non-generalist deep learning models in celldetective may treat these populations slightly differently."
+      }
+    },
+    "no": "Assign your cell population as either `effectors` or `targets` and maintain consistency with this choice throughout your analysis. Keep in mind that the non-generalist deep learning models in celldetective may treat these populations differently."
+  }
+}

celldetective-1.3.7/celldetective/gui/help/exp-structure.json

@@ -0,0 +1,36 @@
+{
+  "Have you tested multiple biological conditions in your experiment?": {
+    "yes": {
+      "Did you capture images at multiple positions (tiles) for each biological condition?": {
+        "yes": {
+          "Did you record time-lapse sequences for your images?": {
+            "yes": "Set up N wells to represent your N biological conditions. Assign M positions for each well. Place each time-lapse sequence into its corresponding position folder.",
+            "no": "Set up N wells for your N biological conditions. Assign one position per well. Combine all tiles into a single image stack for each condition."
+          }
+        },
+        "no": {
+          "Did you record time-lapse sequences for your images?": {
+            "yes": "Set up N wells to represent your N biological conditions. Assign one position per well. Place each time-lapse sequence into its corresponding position folder.",
+            "no": "There isn’t enough data to create a valid stack. Consider combining data from multiple experiments to create stacks with more positions."
+          }
+        }
+      }
+    },
+    "no": {
+      "Did you capture images at multiple positions (tiles)?": {
+        "yes": {
+          "Did you record time-lapse sequences for your images?": {
+            "yes": "Set up a single well. Assign N positions. Place each time-lapse sequence into its corresponding position folder.",
+            "no": "Set up a single well. Assign one position. Combine all tiles into a single image stack and place it into the position folder."
+          }
+        },
+        "no": {
+          "Did you record time-lapse sequences for your images?": {
+            "yes": "Set up a single well and a single position. Place the time-lapse sequence into the position folder.",
+            "no": "There isn’t enough data to create a valid stack. Consider combining data from multiple experiments to increase the number of positions."
+          }
+        }
+      }
+    }
+  }
+}

celldetective-1.3.7/celldetective/gui/help/feature-btrack.json

@@ -0,0 +1,11 @@
+{
+  "Are morphological, tonal, or textural features important for identifying and tracking the cells of interest?": {
+    "yes": {
+      "Do these features remain constant or change gradually over time?": {
+        "yes": "You can include these features in bTrack. The tracker will combine motion data and feature information for improved tracking accuracy.",
+        "no": "Abrupt changes in these features could disrupt bTrack's performance and prematurely end trajectories. It's better to rely only on motion data and avoid using features."
+      }
+    },
+    "no": "There's no need to include features. The tracking will use only the positions of the cells. You can skip this step."
+  }
+}

celldetective-1.3.7/celldetective/gui/help/neighborhood.json

@@ -0,0 +1,16 @@
+{
+  "Do you want to establish relationships between the target and effector cell populations?": {
+    "yes": {
+      "Do you have the complete shape information for both populations?": {
+        "yes": "You can calculate a mask-contact neighborhood. Define the reference and neighbor populations. Adjust the tolerance parameter to control how sensitive the analysis is to contact between reference and neighbor cells.",
+        "no": "You can use an isotropic distance threshold. Define the reference and neighbor populations. Set a radius \( r > (R_{\text{ref}} + 0.5 \times R_{\text{neigh}}) \), where \( R_{\text{ref}} \) is the average radius of reference cells and \( R_{\text{neigh}} \) is the average radius of neighbor cells."
+      }
+    },
+    "no": {
+      "Do you have the complete shape information for the population of interest?": {
+        "yes": "You can calculate a mask-contact neighborhood. Use the same population as both the reference and neighbor. Adjust the tolerance parameter to control sensitivity to cell-cell contact.",
+        "no": "You can use an isotropic distance threshold. Use the same population as both the reference and neighbor. Set a radius \( r > 1.5 \times R \), where \( R \) is the average cell radius."
+      }
+    }
+  }
+}

celldetective-1.3.7/celldetective/gui/help/prefilter-for-segmentation.json

@@ -0,0 +1,16 @@
+{
+  "Are the cells brighter or darker than the background?": {
+    "yes": {
+      "Is the background heterogeneous (varying in intensity across the image)?": {
+        "yes": "Apply a prefilter to normalize the background before further processing.",
+        "no": "You can directly apply a threshold to segment the cells from the background."
+      }
+    },
+    "no": {
+      "Is the background perfectly homogeneous (constant intensity across the entire image)?": {
+        "yes": "Subtract the background value (subtract_filter) and compute the absolute value (abs_filter) for all pixels. Optionally, apply a slight Gaussian blur for smoother results.",
+        "no": "Use a Gaussian blur followed by a standard-deviation or variance filter to enhance cell features."
+      }
+    }
+  }
+}

celldetective-1.3.7/celldetective/gui/help/preprocessing.json

@@ -0,0 +1,51 @@
+{
+  "Is the background consistent across positions (spatially invariant within a well)?": {
+    "yes": {
+      "Are your image stacks time-series data?": {
+        "yes": {
+          "Does the background add to the signal (common in fluorescence imaging)?": {
+            "yes": "Perform a model-free background correction. Specify the channel(s) of interest and indicate that you have time-series data. Estimate the frame range where the background is best defined (e.g., before cell arrival). Adjust the threshold carefully to exclude non-background objects. If background intensity fluctuates slightly across frames or positions, enable the optimization option. Since the background is additive, subtract it from the images.",
+            "no": "Perform a model-free background correction. Specify the channel(s) of interest and indicate that you have time-series data. Estimate the frame range where the background is best defined (e.g., before cell arrival). Adjust the threshold carefully to exclude non-background objects. If background intensity fluctuates slightly across frames or positions, enable the optimization option. Since the background is not additive, divide the images by the background to express intensities relative to it."
+          }
+        },
+        "no": {
+          "Does the background add to the signal (common in fluorescence imaging)?": {
+            "yes": "Perform a model-free background correction. Specify the channel(s) of interest and indicate that you are working with tiles. Adjust the threshold carefully to exclude non-background objects. If background intensity fluctuates across positions, enable the optimization option. Since the background is additive, subtract it from the images.",
+            "no": "Perform a model-free background correction. Specify the channel(s) of interest and indicate that you are working with tiles. Adjust the threshold carefully to exclude non-background objects. If background intensity fluctuates across positions, enable the optimization option. Since the background is not additive, divide the images by the background to express intensities relative to it."
+          }
+        }
+      }
+    },
+    "no": {
+      "Is the background brighter at the center than at the edges?": {
+        "yes": {
+          "Is background correction critical for segmenting cells (common in traditional segmentation pipelines)?": {
+            "yes": {
+              "Does the background add to the signal (common in fluorescence imaging)?": {
+                "yes": "Perform a model-based correction using a paraboloid model. Specify the channel(s) of interest and adjust the threshold to exclude non-background objects. Subtract the background from the images.",
+                "no": "Perform a model-based correction using a paraboloid model. Specify the channel(s) of interest and adjust the threshold to exclude non-background objects. Divide the images by the background to express intensities relative to it."
+              }
+            },
+            "no": "Skip preprocessing to save storage. Preprocessing can be performed on-the-fly in the measurement module. See <a href='https://celldetective.readthedocs.io/en/latest/measure.html#background-correction'>the documentation</a>."
+          }
+        },
+        "no": {
+          "Is the background a constant value?": {
+            "yes": {
+              "Is background correction critical for segmenting cells (common in traditional segmentation pipelines)?": {
+                "yes": {
+                  "Does the background add to the signal (common in fluorescence imaging)?": {
+                    "yes": "Perform a model-based correction using a plane model. Specify the channel(s) of interest and adjust the threshold to exclude non-background objects. Subtract the background from the images.",
+                    "no": "Perform a model-based correction using a plane model. Specify the channel(s) of interest and adjust the threshold to exclude non-background objects. Divide the images by the background to express intensities relative to it."
+                  }
+                },
+                "no": "Skip preprocessing to save storage. Preprocessing can be performed on-the-fly in the measurement module. See <a href='https://celldetective.readthedocs.io/en/latest/measure.html#background-correction'>the documentation</a>."
+              }
+            },
+            "no": "For complex background patterns, avoid correction at this stage. Use the local cell correction available in the measurement module. See <a href='https://celldetective.readthedocs.io/en/latest/measure.html#background-correction'>the documentation</a>."
+          }
+        }
+      }
+    }
+  }
+}

celldetective-1.3.7/celldetective/gui/help/propagate-classification.json

@@ -0,0 +1,16 @@
+{
+  "Do you want to use instantaneous classification to interpret entire cell tracks?": {
+    "yes": {
+      "Do the cells undergo irreversible transitions between negative and positive states?": {
+        "yes": "Select the `irreversible event` option. This will classify cells as 0 (transition observed), 1 (no transition observed), or 2 (left-censored transition). In cases of uncertainty, transitioning cells (class 0) will be reassigned to class 2. If too many transitions are misidentified, consider lowering the R2 threshold.",
+        "no": {
+          "Do cells maintain a single state (positive or negative) throughout the movie?": {
+            "yes": "Select the 'unique state' option. Cells will be classified as 1 (always negative) or 2 (always positive).",
+            "no": "Currently, no propagation model in celldetective fits your data. Feel free to submit a <a href='https://github.com/remyeltorro/celldetective/issues/new?assignees=&labels=&projects=&template=%E2%AD%90-feature-request.md&title=%5BFEATURE%5D'>feature request</a>."
+          }
+        }
+      }
+    },
+    "no": "You do not need to enable the `Time correlated` option. Each cell will be classified independently at each time point."
+  }
+}

{celldetective-1.3.6.post1 → celldetective-1.3.7}/celldetective/gui/neighborhood_options.py

@@ -400,7 +400,7 @@ class ConfigNeighborhoods(QWidget, Styles):
 		
 		status_options = [self.reference_population_status_cb.currentText(), self.neighbor_population_status_cb.currentText()]
 		for k in range(2):
-			if status_options[k]=='--':
+			if status_options[k]=='--' or status_options[k]=='':
 				status_options[k] = None
 		if pop[0]!=pop[1]:
 			mode = 'two-pop'

{celldetective-1.3.6.post1 → celldetective-1.3.7}/celldetective/gui/plot_signals_ui.py

@@ -6,7 +6,7 @@ from PyQt5.QtGui import QIcon, QDoubleValidator
 from celldetective.gui.gui_utils import center_window
 from celldetective.gui.generic_signal_plot import GenericSignalPlotWidget
 from superqt import QLabeledSlider, QColormapComboBox, QSearchableComboBox
-from celldetective.utils import get_software_location, _extract_labels_from_config
+from celldetective.utils import get_software_location, _extract_labels_from_config, extract_cols_from_table_list
 from celldetective.io import load_experiment_tables
 from celldetective.signals import mean_signal
 import numpy as np
@@ -15,7 +15,6 @@ import matplotlib.pyplot as plt
 plt.rcParams['svg.fonttype'] = 'none'
 from glob import glob
 from natsort import natsorted
-import pandas as pd
 import math
 from celldetective.gui import Styles
 from matplotlib import colormaps
@@ -92,8 +91,14 @@ class ConfigSignalPlot(QWidget, Styles):
 			""")
 		main_layout.addWidget(panel_title, alignment=Qt.AlignCenter)
 
+		pops = []
+		for population in ['effectors','targets','pairs']:
+			tables = glob(self.exp_dir+os.sep.join(['W*','*','output','tables',f'trajectories_{population}.csv']))
+			if len(tables)>0:
+				pops.append(population)
+
 		labels = [QLabel('population: '), QLabel('class: '), QLabel('time of\ninterest: '), QLabel('cmap: ')]
-		self.cb_options = [['targets','effectors'],[], [], []]
+		self.cb_options = [pops,[], [], []]
 		self.cbs = [QComboBox() for i in range(len(labels))]
 		self.cbs[-1] = QColormapComboBox()
 		
@@ -161,12 +166,11 @@ class ConfigSignalPlot(QWidget, Styles):
 	def set_classes_and_times(self):
 
 		# Look for all classes and times
-		tables = natsorted(glob(self.exp_dir+os.sep.join(['W*','*','output','tables',f'trajectories_*.csv'])))
-		self.all_columns = []
-		for tab in tables:
-			cols = pd.read_csv(tab, nrows=1).columns.tolist()
-			self.all_columns.extend(cols)
-		self.all_columns = np.unique(self.all_columns)
+		population = self.cbs[0].currentText()
+		tables = natsorted(glob(self.exp_dir+os.sep.join(['W*','*','output','tables',f'trajectories_{population}.csv'])))
+		
+		self.all_columns = extract_cols_from_table_list(tables)
+
 		class_idx = np.array([s.startswith('class_') for s in self.all_columns])
 		time_idx = np.array([s.startswith('t_') for s in self.all_columns])