celldetective 1.3.4.post1__py3-none-any.whl → 1.3.6.post1__py3-none-any.whl

celldetective/tracking.py

@@ -8,17 +8,18 @@ from btrack import BayesianTracker
 
 from celldetective.measure import measure_features
 from celldetective.utils import rename_intensity_column, velocity_per_track
-from celldetective.io import view_on_napari_btrack, interpret_tracking_configuration
+from celldetective.io import interpret_tracking_configuration
 
 import os
 import subprocess
+import trackpy as tp
 
 abs_path = os.sep.join([os.path.split(os.path.dirname(os.path.realpath(__file__)))[0],'celldetective'])
 
 def track(labels, configuration=None, stack=None, spatial_calibration=1, features=None, channel_names=None,
 		  haralick_options=None, return_napari_data=False, view_on_napari=False, mask_timepoints=None, mask_channels=None, volume=(2048,2048),
 		  optimizer_options = {'tm_lim': int(12e4)}, track_kwargs={'step_size': 100}, objects=None,
-		  clean_trajectories_kwargs=None, column_labels={'track': "TRACK_ID", 'time': 'FRAME', 'x': 'POSITION_X', 'y': 'POSITION_Y'},
+		  clean_trajectories_kwargs=None, btrack_option=True, search_range=None, memory=None,column_labels={'track': "TRACK_ID", 'time': 'FRAME', 'x': 'POSITION_X', 'y': 'POSITION_Y'},
 		  ):
 
 	"""
@@ -90,6 +91,12 @@ def track(labels, configuration=None, stack=None, spatial_calibration=1, feature
 	configuration = interpret_tracking_configuration(configuration)
 
 	if objects is None:
+		
+		if not btrack_option:
+			features = []
+			channel_names = None
+			haralick_options = None
+
 		objects = extract_objects_and_features(labels, stack, features, 
 										   channel_names=channel_names,
 										   haralick_options=haralick_options,
@@ -97,78 +104,100 @@ def track(labels, configuration=None, stack=None, spatial_calibration=1, feature
 										   mask_channels=mask_channels,
 										   )
 
-	columns = list(objects.columns)
-	to_remove = ['x','y','class_id','t']
-	for tr in to_remove:
-		try:
-			columns.remove(tr)
-		except:
-			print(f'column {tr} could not be found...')
-
-	scaler = StandardScaler()
-	if columns:
-		x = objects[columns].values
-		x_scaled = scaler.fit_transform(x)
-		df_temp = pd.DataFrame(x_scaled, columns=columns, index = objects.index)
-		objects[columns] = df_temp
-	else:
-		print('Warning: no features were passed to bTrack...')
+	if btrack_option:
+		columns = list(objects.columns)
+		to_remove = ['x','y','class_id','t']
+		for tr in to_remove:
+			try:
+				columns.remove(tr)
+			except:
+				print(f'column {tr} could not be found...')
 
-	# 2) track the objects
-	new_btrack_objects = localizations_to_objects(objects)
+		scaler = StandardScaler()
+		if columns:
+			x = objects[columns].values
+			x_scaled = scaler.fit_transform(x)
+			df_temp = pd.DataFrame(x_scaled, columns=columns, index = objects.index)
+			objects[columns] = df_temp
+		else:
+			print('Warning: no features were passed to bTrack...')
 
-	with BayesianTracker() as tracker:
+		# 2) track the objects
+		new_btrack_objects = localizations_to_objects(objects)
 
-		tracker.configure(configuration)
+		with BayesianTracker() as tracker:
 
-		if columns:
-			tracking_updates = ["motion","visual"]
-			#tracker.tracking_updates = ["motion","visual"]
-			tracker.features = columns
+			tracker.configure(configuration)
+
+			if columns:
+				tracking_updates = ["motion","visual"]
+				#tracker.tracking_updates = ["motion","visual"]
+				tracker.features = columns
+			else:
+				tracking_updates = ["motion"]
+			
+			tracker.append(new_btrack_objects)
+			tracker.volume = ((0,volume[0]), (0,volume[1]), (-1e5, 1e5)) #(-1e5, 1e5)
+			#print(tracker.volume)
+			tracker.track(tracking_updates=tracking_updates, **track_kwargs)
+			tracker.optimize(options=optimizer_options)
+
+			data, properties, graph = tracker.to_napari() #ndim=2
+		# do the table post processing and napari options
+		if data.shape[1]==4:
+			df = pd.DataFrame(data, columns=[column_labels['track'],column_labels['time'],column_labels['y'],column_labels['x']])
+		elif data.shape[1]==5:
+			df = pd.DataFrame(data, columns=[column_labels['track'],column_labels['time'],"z",column_labels['y'],column_labels['x']])
+			df = df.drop(columns=['z'])	
+		df[column_labels['x']+'_um'] = df[column_labels['x']]*spatial_calibration
+		df[column_labels['y']+'_um'] = df[column_labels['y']]*spatial_calibration
+
+	else:
+		properties = None
+		graph = {}
+		print(f"{objects=} {objects.columns=}")
+		objects = objects.rename(columns={"t": "frame"})
+		if search_range is not None and memory is not None:
+			data = tp.link(objects, search_range, memory=memory,link_strategy='auto')
 		else:
-			tracking_updates = ["motion"]
-		
-		tracker.append(new_btrack_objects)
-		tracker.volume = ((0,volume[0]), (0,volume[1]), (-1e5, 1e5)) #(-1e5, 1e5)
-		#print(tracker.volume)
-		tracker.track(tracking_updates=tracking_updates, **track_kwargs)
-		tracker.optimize(options=optimizer_options)
-
-		data, properties, graph = tracker.to_napari() #ndim=2
-
-	# do the table post processing and napari options
-	if data.shape[1]==4:
-		df = pd.DataFrame(data, columns=[column_labels['track'],column_labels['time'],column_labels['y'],column_labels['x']])
-	elif data.shape[1]==5:
-		df = pd.DataFrame(data, columns=[column_labels['track'],column_labels['time'],"z",column_labels['y'],column_labels['x']])
-		df = df.drop(columns=['z'])	
-	df[column_labels['x']+'_um'] = df[column_labels['x']]*spatial_calibration
-	df[column_labels['y']+'_um'] = df[column_labels['y']]*spatial_calibration
-
-	df = df.merge(pd.DataFrame(properties),left_index=True, right_index=True)
-	if columns:
-		x = df[columns].values
-		x_scaled = scaler.inverse_transform(x)
-		df_temp = pd.DataFrame(x_scaled, columns=columns, index = df.index)
-		df[columns] = df_temp
-
-	# set dummy features to NaN
-	df.loc[df['dummy'],['class_id']+columns] = np.nan 
+			print('Please provide a valid search range and memory value...')
+			return None
+		data['particle'] = data['particle'] + 1 # force track id to start at 1
+		df = data.rename(columns={'frame': column_labels['time'], 'x': column_labels['x'], 'y': column_labels['y'], 'particle': column_labels['track']})
+		df['state'] = 5.0; df['generation'] = 0.0; df['root'] = 1.0; df['parent'] = 1.0; df['dummy'] = False; df['z'] = 0.0;
+		data = df[[column_labels['track'],column_labels['time'],"z",column_labels['y'],column_labels['x']]].to_numpy()
+		print(f"{df=}")
+
+	if btrack_option:
+		df = df.merge(pd.DataFrame(properties),left_index=True, right_index=True)
+		if columns:
+			x = df[columns].values
+			x_scaled = scaler.inverse_transform(x)
+			df_temp = pd.DataFrame(x_scaled, columns=columns, index = df.index)
+			df[columns] = df_temp
+
+		# set dummy features to NaN
+		df.loc[df['dummy'],['class_id']+columns] = np.nan
+
 	df = df.sort_values(by=[column_labels['track'],column_labels['time']])
 	df = velocity_per_track(df, window_size=3, mode='bi')
 
 	if channel_names is not None:
 		df = rename_intensity_column(df, channel_names)
 
-	df = write_first_detection_class(df, column_labels=column_labels)
+	df = write_first_detection_class(df, img_shape=volume, column_labels=column_labels)
 
 	if clean_trajectories_kwargs is not None:
 		df = clean_trajectories(df.copy(),**clean_trajectories_kwargs)
 
 	df['ID'] = np.arange(len(df)).astype(int)
 
-	if view_on_napari:
-		view_on_napari_btrack(data,properties,graph,stack=stack,labels=labels,relabel=True)
+	invalid_cols = [c for c in list(df.columns) if c.startswith('Unnamed')]
+	if len(invalid_cols)>0:
+		df = df.drop(invalid_cols, axis=1)	
+
+	# if view_on_napari:
+	# 	view_on_napari_btrack(data,properties,graph,stack=stack,labels=labels,relabel=True)
 
 	if return_napari_data:
 		napari_data = {"data": data, "properties": properties, "graph": graph}
@@ -921,44 +950,58 @@ def track_at_position(pos, mode, return_tracks=False, view_on_napari=False, thre
 	# # else:
 	# return None
 
-def write_first_detection_class(tab, column_labels={'track': "TRACK_ID", 'time': 'FRAME', 'x': 'POSITION_X', 'y': 'POSITION_Y'}):
+def write_first_detection_class(df, img_shape=None, edge_threshold=20, column_labels={'track': "TRACK_ID", 'time': 'FRAME', 'x': 'POSITION_X', 'y': 'POSITION_Y'}):
 	
 	"""
-	Annotates a dataframe with the time of the first detection and classifies tracks based on their detection status.
+	Assigns a classification and first detection time to tracks in the given DataFrame. This function must be called
+	before any track post-processing.
 
-	This function processes a dataframe containing tracking data, identifying the first point of detection for each
-	track based on the x-coordinate values. It annotates the dataframe with the time of the first detection and
-	assigns a class to each track indicating whether the first detection occurs at the start, during, or if there's
-	no detection within the tracking data.
+	This function computes the first detection time and a detection class (`class_firstdetection`) for each track in the data. 
+	Tracks that start on or near the image edge, or those detected at the initial frame, are marked with special classes.
 
 	Parameters
 	----------
-	tab : pandas.DataFrame
-		The dataframe containing tracking data, expected to have columns for track ID, time, and spatial coordinates.
+	df : pandas.DataFrame
+		A DataFrame containing track data. Expected to have at least the columns specified in `column_labels` and `class_id` (mask value).
+
+	img_shape : tuple of int, optional
+		The shape of the image as `(height, width)`. Used to determine whether the first detection occurs near the image edge.
+
+	edge_threshold : int, optional, default=20
+		The distance in pixels from the image edge to consider a detection as near the edge.
+
 	column_labels : dict, optional
-		A dictionary mapping standard column names ('track', 'time', 'x', 'y') to the corresponding column names in
-		`tab`. Default column names are 'TRACK_ID', 'FRAME', 'POSITION_X', 'POSITION_Y'.
+		A dictionary mapping logical column names to actual column names in `tab`. Keys include:
+		- `'track'`: The column indicating the track ID (default: `"TRACK_ID"`).
+		- `'time'`: The column indicating the frame/time (default: `"FRAME"`).
+		- `'x'`: The column indicating the X-coordinate (default: `"POSITION_X"`).
+		- `'y'`: The column indicating the Y-coordinate (default: `"POSITION_Y"`).
 
 	Returns
 	-------
 	pandas.DataFrame
-		The input dataframe `tab` with two additional columns: 'class_firstdetection' indicating the detection class,
-		and 't_firstdetection' indicating the time of the first detection.
+		The input DataFrame `df` with two additional columns:
+		- `'class_firstdetection'`: A class assigned based on detection status:
+			- `0`: Valid detection not near the edge and not at the initial frame.
+			- `2`: Detection near the edge, at the initial frame, or no detection available.
+		- `'t_firstdetection'`: The adjusted first detection time (in frame units):
+			- `-1`: Indicates no valid detection or detection near the edge.
+			- A float value representing the adjusted first detection time otherwise.
 
 	Notes
 	-----
-	- Detection is based on the presence of non-NaN values in the 'x' column for each track.
-	- Tracks with their first detection at the first time point are classified differently (`cclass=2`) and assigned
-	  a `t_first` of -1, indicating no prior detection.
-	- The function assumes uniform time steps between each frame in the tracking data.
-
+	- The function assumes that tracks are grouped and sorted by track ID and frame.
+	- Detections near the edge or at the initial frame (frame 0) are considered invalid and assigned special values.
+	- If `img_shape` is not provided, edge checks are skipped.
 	"""
 
-	tab = tab.sort_values(by=[column_labels['track'],column_labels['time']])
-	for tid,track_group in tab.groupby(column_labels['track']):
+	df = df.sort_values(by=[column_labels['track'],column_labels['time']])
+	for tid,track_group in df.groupby(column_labels['track']):
 		indices = track_group.index
-		detection = track_group[column_labels['x']].values
+		detection = track_group['class_id'].values
 		timeline = track_group[column_labels['time']].values
+		positions_x = track_group[column_labels['x']].values
+		positions_y = track_group[column_labels['y']].values
 		dt = 1
 		
 		# Initialize
@@ -966,8 +1009,14 @@ def write_first_detection_class(tab, column_labels={'track': "TRACK_ID", 'time':
 
 		if np.any(detection==detection):
 			t_first = timeline[detection==detection][0]
+			x_first = positions_x[detection==detection][0]; y_first = positions_y[detection==detection][0];
+
+			edge_test = False
+			if img_shape is not None:
+				edge_test = (x_first < edge_threshold) or (y_first < edge_threshold) or (y_first > (img_shape[0] - edge_threshold)) or (x_first > (img_shape[1] - edge_threshold))
+
 			cclass = 0
-			if t_first<=0:
+			if t_first<=0 or edge_test:
 				t_first = -1
 				cclass = 2
 			else:
@@ -978,10 +1027,10 @@ def write_first_detection_class(tab, column_labels={'track': "TRACK_ID", 'time':
 			t_first = -1
 			cclass = 2
 
-		tab.loc[indices, 'class_firstdetection'] = cclass
-		tab.loc[indices, 't_firstdetection'] = t_first
+		df.loc[indices, 'class_firstdetection'] = cclass
+		df.loc[indices, 't_firstdetection'] = t_first
 
-	return tab
+	return df
 
 
 

celldetective/utils.py

@@ -30,6 +30,15 @@ from skimage.morphology import disk
 from scipy.stats import ks_2samp
 from cliffs_delta import cliffs_delta
 
+
+def extract_cols_from_table_list(tables, nrows=1):
+	all_columns = []
+	for tab in tables:
+		cols = pd.read_csv(tab, nrows=1).columns.tolist()
+		all_columns.extend(cols)
+	all_columns = np.unique(all_columns)
+	return all_columns
+
 def safe_log(array):
 
 	if isinstance(array,int) or isinstance(array,float):
@@ -415,7 +424,7 @@ def estimate_unreliable_edge(activation_protocol=[['gauss',2],['std',4]]):
 	else:
 		edge=0
 		for fct in activation_protocol:
-			if isinstance(fct[1],(int,np.int_)):
+			if isinstance(fct[1],(int,np.int_)) and not fct[0]=='invert':
 				edge+=fct[1]
 		return edge
 
@@ -547,8 +556,14 @@ def extract_cols_from_query(query: str):
 			# Add the name to the globals dictionary with a dummy value.
 			variables[name] = None
 
-	return list(variables.keys())
+	# Reverse mangling for special characters in column names.
+	def demangle_column_name(name):
+		if name.startswith("BACKTICK_QUOTED_STRING_"):
+			# Unquote backtick-quoted string.
+			return name[len("BACKTICK_QUOTED_STRING_"):].replace("_DOT_", ".").replace("_SLASH_", "/")
+		return name
 
+	return [demangle_column_name(name) for name in variables.keys()]
 
 def create_patch_mask(h, w, center=None, radius=None):
 
@@ -646,15 +661,14 @@ def rename_intensity_column(df, channels):
 	channel_names = np.array(channels)
 	channel_indices = np.arange(len(channel_names),dtype=int)
 
-	if np.any(['intensity' in c for c in df.columns]):
+	if np.any(['intensity' in c for c in list(df.columns)]):
 
 		intensity_indices = [s.startswith('intensity') for s in df.columns]
 		intensity_columns = df.columns[intensity_indices]
 
-		if len(channel_names) > 1:
+		if len(channel_names) >= 1:
 			to_rename = {}
 			for k in range(len(intensity_columns)):
-				#print(intensity_columns[k])
 
 				sections = np.array(re.split('-|_', intensity_columns[k]))
 				test_digit = np.array([s.isdigit() for s in sections])
@@ -664,7 +678,11 @@ def rename_intensity_column(df, channels):
 				new_name = np.delete(sections, np.where(test_digit)[0]) #np.where(test_digit)[0]
 				new_name = '_'.join(list(new_name))
 				new_name = new_name.replace('intensity', channel_name)
-				to_rename.update({intensity_columns[k]: new_name.replace('-','_')})
+				new_name = new_name.replace('-','_')
+				new_name = new_name.replace('_nanmean','_mean')
+
+				to_rename.update({intensity_columns[k]: new_name})
+
 				if 'centre' in intensity_columns[k]:
 					# sections = np.array(re.split('-|_', intensity_columns[k]))
 					measure = np.array(re.split('-|_', new_name))
@@ -1232,7 +1250,10 @@ def ConfigSectionMap(path,section):
 	Config = configparser.ConfigParser()
 	Config.read(path)
 	dict1 = {}
-	options = Config.options(section)
+	try:
+		options = Config.options(section)
+	except:
+		return None
 	for option in options:
 		try:
 			dict1[option] = Config.get(section, option)

{celldetective-1.3.4.post1.dist-info → celldetective-1.3.6.post1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: celldetective
-Version: 1.3.4.post1
+Version: 1.3.6.post1
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro
@@ -20,7 +20,7 @@ Requires-Dist: cellpose<3
 Requires-Dist: scikit-learn
 Requires-Dist: btrack
 Requires-Dist: tensorflow~=2.15.0
-Requires-Dist: napari
+Requires-Dist: napari<0.6.0
 Requires-Dist: tqdm
 Requires-Dist: mahotas
 Requires-Dist: fonticon-materialdesignicons6
@@ -42,6 +42,7 @@ Requires-Dist: pytest-qt
 Requires-Dist: h5py
 Requires-Dist: cliffs_delta
 Requires-Dist: requests
+Requires-Dist: trackpy
 
 # Celldetective
 

{celldetective-1.3.4.post1.dist-info → celldetective-1.3.6.post1.dist-info}/RECORD

@@ -1,48 +1,48 @@
 celldetective/__init__.py,sha256=bi3SGTMo6s2qQBsJAaKy-a4xaGcTQVW8zsqaiX5XKeY,139
 celldetective/__main__.py,sha256=bxTlSvbKhqn3LW_azd2baDCnDsgb37PAP9DfuAJ1_5M,1844
-celldetective/_version.py,sha256=O9z4W-emw0sUnueuXoMBlkVWoLZBTUjF8-PzKP_tSiI,28
-celldetective/events.py,sha256=R6GDtiH0ZuEbad0R-nrlTHmho0Hly3QyyVYx2dD__P0,8051
+celldetective/_version.py,sha256=bW6H44PSm7DIqPxnn6PKr6QzSOJZU8d_cyKDCh6Mv18,28
+celldetective/events.py,sha256=GtlFgfSQD8F7FBFCptWU0R8R3BL_UoMBzmGJ7IyAgeE,8143
 celldetective/extra_properties.py,sha256=y556D6EMjLGhtjDqRoOTRGa85XxTIe0K1Asb26VZXmo,5643
-celldetective/filters.py,sha256=9w4JyPH2cISRu7gtUDVsm9whiMMWxuc1vwhfaq3zWkY,3683
-celldetective/io.py,sha256=_SO32G5Sc60vHQhQj7gXvDNTXjVd1uZ8x1HnFxCYU0g,90833
-celldetective/measure.py,sha256=PXi13O6wjXbgj53o-C8DEWLVkmy9qb4vocmq1irPVV0,57450
+celldetective/filters.py,sha256=-UuS_aH_JxEPMWlb7VAaIsNQUXlARhfZ1DL_qypGFA0,3892
+celldetective/io.py,sha256=cNr7pg8MWGL9V28pfDjZsiriYnU19oFLnhC5P6JqT9k,122535
+celldetective/measure.py,sha256=b0pZckV9dMJEUoLqvUfLmUWo7z0xPc0Xe4qnvaoq_KY,60066
 celldetective/neighborhood.py,sha256=s-zVsfGnPlqs6HlDJCXRh21lLiPKbA_S1JC6uZvfG_0,56712
-celldetective/preprocessing.py,sha256=WmetQCgmHK6fo8AuwESPLab05WgeIy8ElBs-9KM-Cco,44081
-celldetective/relative_measurements.py,sha256=av5DiGlGsbILPav8aVcFlhbmbPLPZPxCB5qQejzhiRY,30400
+celldetective/preprocessing.py,sha256=Wlt_PJua97CpMuWe_M65znUmz_yjYPqWIcs2ZK_RLgk,44109
+celldetective/relative_measurements.py,sha256=ZviXp6-z_SB60e7z3GznqfEngv70waOK0sMxm_q-JJA,30546
 celldetective/segmentation.py,sha256=NjAVaVpZufpJ-LIvBx5UFH6j5kjRKE6EVLjttDrqaqs,30826
-celldetective/signals.py,sha256=ueRZmmMuVSNFpFAHhF06xE8zr4qjuN8i-jxJj_qyfVI,121475
-celldetective/tracking.py,sha256=e6XMunjVRhBnv1cRF66hkK-Hbti5KyPrs2mnR6qKpvU,38027
-celldetective/utils.py,sha256=oP_GHPdJJHK9s8sIlzKEXfTjCvzxAifdYYynkSMfu7A,89145
+celldetective/signals.py,sha256=mrQjHA7xDgL6EUVk9U359sUwSgSvSCsdNJDt0truCA4,121574
+celldetective/tracking.py,sha256=babNFkxtYDwoAl_WJcZC-GYItafKShV2PLSWimxM6oA,40361
+celldetective/utils.py,sha256=5nxfYnl0xsfocPg6BH2SmZ4n1jKMUUWXVZW3-xabXbk,89802
 celldetective/datasets/segmentation_annotations/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 celldetective/datasets/signal_annotations/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 celldetective/gui/InitWindow.py,sha256=sQSwfZ6SIQeZDQ_3KZoMO2MH9Fs9rhWeqxzEf9PFjEM,14534
 celldetective/gui/__init__.py,sha256=2_r2xfOj4_2xj0yBkCTIfzlF94AHKm-j6Pvpd7DddQc,989
 celldetective/gui/about.py,sha256=FJZrj6C-p6uqp_3UaprKosuW-Sw9_HPNQAvFbis9Gdk,1749
 celldetective/gui/analyze_block.py,sha256=h0sp7Tk3hZFM8w0yTidwIjZX4WRI-lQF3JCFObrLCPo,2761
-celldetective/gui/btrack_options.py,sha256=OrvbG5coZhLRk5jtXiLFJu34z1hWHN9kHkBiZ7XMZoI,39269
-celldetective/gui/classifier_widget.py,sha256=mo7Gel3DKhFTUt184WvF0AOsw4HQ7kC8qrkSf8jr3hY,18412
-celldetective/gui/configure_new_exp.py,sha256=Eyr-M4FH-4xrUJbIGNdKXAtXb_ULr8lCol26JSzXEww,20125
-celldetective/gui/control_panel.py,sha256=Xr8W37KkRoR2R4ILsZbclnU6-g3WP1WjjTz6k39PN_8,21645
-celldetective/gui/generic_signal_plot.py,sha256=cfPvNcLtsVp3xvKyOg1ekMKXcomN6fEnlowUnXrYK2c,36293
-celldetective/gui/gui_utils.py,sha256=b6L4mThjN8upgXx4YeNRrfSSCF2l1epb_uEU8cc31F8,34171
+celldetective/gui/btrack_options.py,sha256=tY0XiDcsI4KDgwZtcaP7HWLJ_isxamM-7sFX-m5Dcwk,44662
+celldetective/gui/classifier_widget.py,sha256=UyElqL9Rq5cKcM6i8ZLGCqkMqqnSDaw6i_hRoV_7WSE,19817
+celldetective/gui/configure_new_exp.py,sha256=sRBGhMoQUP8-XchmfV6VvuFHceS4Q8qPY2ua7DQOaHI,20754
+celldetective/gui/control_panel.py,sha256=CKbn6K7_s_K6r-hJMAJmWhDjj8mrYhk_ycr8x_8DIDQ,21710
+celldetective/gui/generic_signal_plot.py,sha256=iINeKvItGL4X8ONDRM7yv1zovEX1hhLreeOXbxiKTy0,36078
+celldetective/gui/gui_utils.py,sha256=1-B5f1sij-3jM-Y9IuhoLH7Skcua3r6V0w8yNdX-Nr0,39358
 celldetective/gui/json_readers.py,sha256=Su3angSobroeGrrumGgQcs3Cr_9l9p52-Hfm3qneVcI,3664
 celldetective/gui/layouts.py,sha256=XsqiHR58DXsG5SSD5S8KOtUv4yw-y-s2_wZx_XsHeJs,52013
-celldetective/gui/measurement_options.py,sha256=MnJ9dToJb-_UppqHEyFoIvqY8M2cneTGmqxMToeTJ48,39579
-celldetective/gui/neighborhood_options.py,sha256=BvWwsIX1KWogUgHWRZptqY3ZRmH1aj7r8tiLmbRFhW4,19783
+celldetective/gui/measurement_options.py,sha256=cfiC4lq-XqY4Sa4Vkw5mys7JKaa9tE2BgeN8_k-SIDY,40355
+celldetective/gui/neighborhood_options.py,sha256=IUzcE8RrnNbDuLebvIyUxN0-mL05SexlWPzqAWZDPuQ,19814
 celldetective/gui/plot_measurements.py,sha256=n0pDUcYcsKlSMaUaBSVplGziuWp_7jKaeXdREs-MqyI,50848
-celldetective/gui/plot_signals_ui.py,sha256=dLClQYdQcs98Dq6RWixWXM7_iS67CicOe695bA9LM-w,16447
-celldetective/gui/process_block.py,sha256=tk3zhhXhutszmFP3T7zbXnoCOZRbFUHPBR4cNNaHQOk,68683
+celldetective/gui/plot_signals_ui.py,sha256=ASHXrFr5ctCs5ppWmC7KqU1EtzqbvI8D1FKtvd2dAiQ,16495
+celldetective/gui/process_block.py,sha256=OCEYCRd8s3rT9x4Rs9ut3s7cM4bv9spKjhvASRPyOgY,68746
 celldetective/gui/retrain_segmentation_model_options.py,sha256=ACeQ_DdSLy1EK0z_S_9v-0HOiLXjUmrz4sdvHWZT6FI,23330
 celldetective/gui/retrain_signal_model_options.py,sha256=XigNdGlNu3KWB_MYBcKQhfXjcWwVZNMmu0qmxNoo14E,21919
 celldetective/gui/seg_model_loader.py,sha256=vWvPMU6nkTiQfI-x2WjQHrdJGFdV4a4Ne-4YIOq_YZ8,18153
-celldetective/gui/signal_annotator.py,sha256=gZtuWoVWjaIzxy5SL1Cg2rBrsH9-s-oYSxJe7CQeEiY,88656
-celldetective/gui/signal_annotator2.py,sha256=fAgkNexxvcnY4KvIxtgHKF3B9K-wsgfA8KbkALq4UPY,108945
+celldetective/gui/signal_annotator.py,sha256=xJh69pzOFGbM3V2ySXL2BSav6Tp2mhF0LyPBpFWgp7w,88892
+celldetective/gui/signal_annotator2.py,sha256=0h7WUFnOEHXoyLobDDRcDcTIC-DIF9q2ykx6aI-5g1c,106339
 celldetective/gui/signal_annotator_options.py,sha256=ztFFgA70SJ0QkntxYGsgDNCvSuSR5GjF7_J6pYVYc1g,11020
 celldetective/gui/styles.py,sha256=awg5NfGWUoM4V_LpVlmPP7JorpofiLVNqLBv4zRy89E,5058
-celldetective/gui/survival_ui.py,sha256=7qUenqEIaWEwdf-nKE1gN0LAdybgQbRLb3OJMTI9bfk,10193
-celldetective/gui/tableUI.py,sha256=2tBZN3X1nrBD_t58yaCY4NENWeHtgvaN0IcKzZn18SM,50500
-celldetective/gui/thresholds_gui.py,sha256=6Lgr_CK2LBn_gMsWf0gIQvQIQSMg3oIhFfknFeg8Fh4,50721
-celldetective/gui/viewers.py,sha256=0KmtAKZUNY5xpKFcFajgc1Jbnf_86rw_ooX6UrMmEHc,46328
+celldetective/gui/survival_ui.py,sha256=J4ZYjX8ne0wT0ruQu9WL3WfLnRIAQalkaAR8ngb7PkI,14170
+celldetective/gui/tableUI.py,sha256=0bWEECh6BCRV5K2jFaZe9c3H78vBUxYFppplKQiLteU,51022
+celldetective/gui/thresholds_gui.py,sha256=VjCVBCDsNh_LoXfEqUn32nsYQwO9-Elh3Gl1RBv7acc,48756
+celldetective/gui/viewers.py,sha256=mne5GLFAjv-vxMABXP7I9VhrJGtPnZj560HLdlwDZSU,47806
 celldetective/gui/help/DL-segmentation-strategy.json,sha256=59jVtn8pECbCqPQwJifgViVYTF1AxLQDIkNJMS7CJuk,1143
 celldetective/gui/help/Threshold-vs-DL.json,sha256=SELQk3qF8xcwmkX686Bqrr7i5KiXqN7r4jbUydCLRDU,603
 celldetective/gui/help/cell-populations.json,sha256=wP0ekhokb9oHE3XqOQrC5ARewNgOlv0GJrQeVQyMJzg,1075
@@ -80,11 +80,11 @@ celldetective/models/tracking_configs/no_z_motion.json,sha256=b4RWOJ0w6Y2e0vJYwK
 celldetective/models/tracking_configs/ricm.json,sha256=L-vmwCR1f89U-qnH2Ms0cBfPFR_dxIWoe2ccH8V-QBA,2727
 celldetective/models/tracking_configs/ricm2.json,sha256=DDjJ6ScYcDWvlsy7ujPID8v8H28vcNcMuZmNR8XmGxo,2718
 celldetective/scripts/analyze_signals.py,sha256=YE05wZujl2hQFWkvqATBcCx-cAd_V3RxnvKoh0SB7To,2194
-celldetective/scripts/measure_cells.py,sha256=jUwPSjIzR4sCvjer_K5vSlRQX3e8AhJE3xhUbevES7c,12143
+celldetective/scripts/measure_cells.py,sha256=szZ79zWPWbr-13zU3RPIYnsUwW4xAx-YwKKbvhulTK4,12606
 celldetective/scripts/measure_relative.py,sha256=L_NjIUfHSGupkAKLZkubBHJdZh0ugPhCTJem80b0zMM,4261
-celldetective/scripts/segment_cells.py,sha256=bnNacgp_6qpb1fvwPizxVctsUNiFBegKalo-PSpXPEU,8262
+celldetective/scripts/segment_cells.py,sha256=CxAuqmSslDoq1zFlZrgt4-ZORVCv-bF-kdXHWQgf8MY,8216
 celldetective/scripts/segment_cells_thresholds.py,sha256=6ERg-hxdHMSgXPQSBPtYt2lccTlkz9ZLktYgb57Avmw,5168
-celldetective/scripts/track_cells.py,sha256=ezNpenAYBz010iMZNRIk0qwGAceiXRLvY7ZxoQcT2IM,8052
+celldetective/scripts/track_cells.py,sha256=r_EaOIPgwGewHsvcbLaqTkxp4PQ4uDLq-E0bbUDZ1p4,8581
 celldetective/scripts/train_segmentation_model.py,sha256=XExaGg8kkdirgN206J0mwiWtqeRE076-Ld2b89tReAI,9229
 celldetective/scripts/train_signal_model.py,sha256=D643wKVYg-LWHF2VU9FWKSuazXrpCpQK0YjGqoIimD0,3167
 tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -99,9 +99,9 @@ tests/test_segmentation.py,sha256=k1b_zIZdlytEdJcHjAUQEO3gTBAHtv5WvrwQN2xD4kc,34
 tests/test_signals.py,sha256=No4cah6KxplhDcKXnU8RrA7eDla4hWw6ccf7xGnBokU,3599
 tests/test_tracking.py,sha256=8hebWSqEIuttD1ABn-6dKCT7EXKRR7-4RwyFWi1WPFo,8800
 tests/test_utils.py,sha256=NKRCAC1d89aBK5cWjTb7-pInYow901RrT-uBlIdz4KI,3692
-celldetective-1.3.4.post1.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-celldetective-1.3.4.post1.dist-info/METADATA,sha256=-fcPPLCWNqV8h4WdVm1bceP9_ujji_v52WeylF4tdZ8,10534
-celldetective-1.3.4.post1.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-celldetective-1.3.4.post1.dist-info/entry_points.txt,sha256=2NU6_EOByvPxqBbCvjwxlVlvnQreqZ3BKRCVIKEv3dg,62
-celldetective-1.3.4.post1.dist-info/top_level.txt,sha256=6rsIKKfGMKgud7HPuATcpq6EhdXwcg_yknBVWn9x4C4,20
-celldetective-1.3.4.post1.dist-info/RECORD,,
+celldetective-1.3.6.post1.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+celldetective-1.3.6.post1.dist-info/METADATA,sha256=wbiMcVjmdJpkTzkpfmGiWwS5sgeRZ4H5dEHPIWUBCqM,10563
+celldetective-1.3.6.post1.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+celldetective-1.3.6.post1.dist-info/entry_points.txt,sha256=2NU6_EOByvPxqBbCvjwxlVlvnQreqZ3BKRCVIKEv3dg,62
+celldetective-1.3.6.post1.dist-info/top_level.txt,sha256=6rsIKKfGMKgud7HPuATcpq6EhdXwcg_yknBVWn9x4C4,20
+celldetective-1.3.6.post1.dist-info/RECORD,,