celldetective 1.3.9.post5__py3-none-any.whl → 1.4.1__py3-none-any.whl

celldetective/signals.py

@@ -156,6 +156,10 @@ def analyze_signals(trajectories, model, interpolate_na=True,
 	f = open(model_config_path)
 	config = json.load(f)
 	required_signals = config["channels"]
+	if 'selected_channels' in config:
+		selected_signals = config['selected_channels']
+		if np.any([s=='None' for s in selected_signals]):
+			trajectories['None'] = 0.
 	model_signal_length = config['model_signal_length']
 
 	try:
@@ -264,6 +268,8 @@ def analyze_signals(trajectories, model, interpolate_na=True,
 			plt.pause(3)
 			plt.close()
 
+	if "None" in list(trajectories.columns):
+		trajectories = trajectories.drop(columns=['None'])
 	return trajectories
 
 def analyze_signals_at_position(pos, model, mode, use_gpu=True, return_table=False):
@@ -324,7 +330,7 @@ def analyze_signals_at_position(pos, model, mode, use_gpu=True, return_table=Fal
 	else:
 		return None		
 
-def analyze_pair_signals_at_position(pos, model, use_gpu=True):
+def analyze_pair_signals_at_position(pos, model, use_gpu=True, populations=['targets','effectors']):
 	
 
 	pos = pos.replace('\\','/')
@@ -332,13 +338,10 @@ def analyze_pair_signals_at_position(pos, model, use_gpu=True):
 	assert os.path.exists(pos),f'Position {pos} is not a valid path.'
 	if not pos.endswith('/'):
 		pos += '/'
-					
-	df_targets = get_position_pickle(pos, population='targets')
-	df_effectors = get_position_pickle(pos, population='effectors')
-	dataframes = {
-		'targets': df_targets,
-		'effectors': df_effectors,
-	}
+
+	dataframes = {}
+	for pop in populations:
+		dataframes.update({pop: get_position_pickle(pos, population=pop)})
 	df_pairs = get_position_table(pos, population='pairs')
 
 	# Need to identify expected reference / neighbor tables
@@ -354,12 +357,19 @@ def analyze_pair_signals_at_position(pos, model, use_gpu=True):
 	reference_population = model_config_path['reference_population']
 	neighbor_population = model_config_path['neighbor_population']
 
+	if dataframes[reference_population] is None:
+		print(f"No tabulated data can be found for the reference population ({reference_population})... Abort...")
+		return None
+
+	if dataframes[neighbor_population] is None:
+		print(f"No tabulated data can be found for the neighbor population ({neighbor_population})... Abort...")
+		return None
+
 	df = analyze_pair_signals(df_pairs, dataframes[reference_population], dataframes[neighbor_population], model=model)
-	
 	table = pos + os.sep.join(["output","tables",f"trajectories_pairs.csv"])
 	df.to_csv(table, index=False)
 
-	return None		
+	return None
 
 
 def analyze_pair_signals(trajectories_pairs,trajectories_reference,trajectories_neighbors, model, interpolate_na=True, selected_signals=None,
@@ -2823,7 +2833,7 @@ def columnwise_mean(matrix, min_nbr_values = 1, projection='mean'):
 	return mean_line, mean_line_std
 
 
-def mean_signal(df, signal_name, class_col, time_col=None, class_value=[0], return_matrix=False, forced_max_duration=None, min_nbr_values=2,conflict_mode='mean', projection='mean'):
+def mean_signal(df, signal_name, class_col, time_col=None, class_value=[0], return_matrix=False, forced_max_duration=None, min_nbr_values=2,conflict_mode='mean', projection='mean',pairs=False):
 
 	"""
 	Calculate the mean and standard deviation of a specified signal for tracks of a given class in the input DataFrame.
@@ -2878,14 +2888,19 @@ def mean_signal(df, signal_name, class_col, time_col=None, class_value=[0], retu
 	if isinstance(time_col, (int,float)):
 		abs_time = True
 
-	n_tracks = len(df.groupby(['position','TRACK_ID']))
+	if not pairs:
+		groupby_cols = ['position','TRACK_ID']
+	else:
+		groupby_cols = ['position','REFERENCE_ID','NEIGHBOR_ID']
+
+	n_tracks = len(df.groupby(groupby_cols))
 	signal_matrix = np.zeros((n_tracks,int(max_duration)*2 + 1))
 	signal_matrix[:,:] = np.nan
 
-	df = df.sort_values(by=['position','TRACK_ID','FRAME'])
+	df = df.sort_values(by=groupby_cols+['FRAME'])
 
 	trackid=0
-	for track,track_group in df.loc[df[class_col].isin(class_value)].groupby(['position','TRACK_ID']):
+	for track,track_group in df.loc[df[class_col].isin(class_value)].groupby(groupby_cols):
 		cclass = track_group[class_col].to_numpy()[0]
 		if cclass != 0:
 			ref_time = 0

celldetective/tracking.py

@@ -189,7 +189,8 @@ def track(labels, configuration=None, stack=None, spatial_calibration=1, feature
 
 	if clean_trajectories_kwargs is not None:
 		df = clean_trajectories(df.copy(),**clean_trajectories_kwargs)
-
+	
+	df.loc[df["status_firstdetection"].isna(), "status_firstdetection"] = 0
 	df['ID'] = np.arange(len(df)).astype(int)
 
 	invalid_cols = [c for c in list(df.columns) if c.startswith('Unnamed')]
@@ -1003,10 +1004,14 @@ def write_first_detection_class(df, img_shape=None, edge_threshold=20, column_la
 		positions_y = track_group[column_labels['y']].values
 		dt = 1
 		
+		timeline = track_group['FRAME'].to_numpy()
+		status = np.ones_like(timeline)
+		
 		# Initialize
 		cclass = 2; t_first = np.nan;
 
 		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];
 
@@ -1015,19 +1020,25 @@ def write_first_detection_class(df, img_shape=None, edge_threshold=20, column_la
 				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 or edge_test:
+			if t_first<=0:
 				t_first = -1
 				cclass = 2
 			else:
 				t_first =  float(t_first) - float(dt)
 				if t_first==0:
 					t_first += 0.01
+			
+			if edge_test:
+				cclass = 2
+				# switch to class 2 but keep time/status information
 		else:
 			t_first = -1
 			cclass = 2
-
+		
+		status[timeline < t_first] = 0.
 		df.loc[indices, 'class_firstdetection'] = cclass
 		df.loc[indices, 't_firstdetection'] = t_first
+		df.loc[indices, 'status_firstdetection'] = status
 
 	return df
 

celldetective/utils.py

@@ -1,8 +1,6 @@
-
 import numpy as np
 import pandas as pd
 import matplotlib.pyplot as plt
-import re
 import os
 from scipy.ndimage import shift, zoom
 os.environ['TF_CPP_MIN_VLOG_LEVEL'] = '3'
@@ -31,9 +29,22 @@ from scipy.stats import ks_2samp
 from cliffs_delta import cliffs_delta
 from stardist.models import StarDist2D
 from cellpose.models import CellposeModel
-from pathlib import PosixPath, PurePosixPath, WindowsPath
+from pathlib import PosixPath, PurePath, PurePosixPath, WindowsPath, Path
+from prettytable import PrettyTable
+from typing import List, Dict, Union, Optional
+
+def is_integer_array(arr: np.ndarray) -> bool:
+
+	# Mask out NaNs
+	non_nan_values = arr[arr==arr].flatten()
+	test = np.all(np.mod(non_nan_values, 1) == 0)
+
+	if test:
+		return True
+	else:
+		return False
 
-def get_config(experiment):
+def get_config(experiment: Union[str,Path]) -> str:
 
 	"""
 	Retrieves the path to the configuration file for a given experiment.
@@ -81,7 +92,7 @@ def get_config(experiment):
 	return config
 
 
-def _remove_invalid_cols(df):
+def _remove_invalid_cols(df: pd.DataFrame) -> pd.DataFrame:
 
 	"""
 	Removes invalid columns from a DataFrame.
@@ -107,7 +118,7 @@ def _remove_invalid_cols(df):
 	df = df.dropna(axis=1, how='all')
 	return df
 
-def _extract_coordinates_from_features(df, timepoint):
+def _extract_coordinates_from_features(df: pd.DataFrame, timepoint: int) -> pd.DataFrame:
 
 	"""
 	Re-format coordinates from a regionprops table to tracking/measurement table format. 
@@ -148,7 +159,7 @@ def _extract_coordinates_from_features(df, timepoint):
 
 	return coords
 
-def _mask_intensity_measurements(df, mask_channels):
+def _mask_intensity_measurements(df: pd.DataFrame, mask_channels: Optional[List[str]]):
 
 	"""
 	Removes columns from a DataFrame that match specific channel name patterns.
@@ -197,7 +208,7 @@ def _mask_intensity_measurements(df, mask_channels):
 			df = df.drop(cols_to_drop, axis=1)
 	return df
 
-def _rearrange_multichannel_frame(frame, n_channels=None):
+def _rearrange_multichannel_frame(frame: np.ndarray, n_channels: Optional[int] = None) -> np.ndarray:
 
 	"""
 	Rearranges the axes of a multi-channel frame to ensure the channel axis is at the end.
@@ -258,7 +269,7 @@ def _rearrange_multichannel_frame(frame, n_channels=None):
 
 	return frame
 
-def _fix_no_contrast(frames, value=1):
+def _fix_no_contrast(frames: np.ndarray, value: Union[float,int] = 1):
 
 	"""
 	Ensures that frames with no contrast (i.e., containing only a single unique value) are adjusted.
@@ -297,7 +308,7 @@ def _fix_no_contrast(frames, value=1):
 			frames[0,0,k] += value
 	return frames
 
-def zoom_multiframes(frames, zoom_factor):
+def zoom_multiframes(frames: np.ndarray, zoom_factor: float) -> np.ndarray:
 
 	"""
 	Applies zooming to each frame (channel) in a multi-frame image.
@@ -370,7 +381,10 @@ def _prep_stardist_model(model_name, path, use_gpu=False, scale=1):
 	model = StarDist2D(None, name=model_name, basedir=path)
 	model.config.use_gpu = use_gpu
 	model.use_gpu = use_gpu
+
 	scale_model = scale
+
+
 	print(f"StarDist model {model_name} successfully loaded...")
 	return model, scale_model
 
@@ -424,7 +438,10 @@ def _prep_cellpose_model(model_name, path, use_gpu=False, n_channels=2, scale=No
 	else:
 		scale_model = scale * model.diam_mean / model.diam_labels
 
-	print(f"Diam mean: {model.diam_mean}; Diam labels: {model.diam_labels}; Final rescaling: {scale_model}...")
+	print(f'Cell size in model: {model.diam_mean} pixels...')
+	print(f'Cell size in training set: {model.diam_labels} pixels...')
+	print(f"Rescaling factor to apply: {scale_model}...")
+
 	print(f'Cellpose model {model_name} successfully loaded...')
 	return model, scale_model
 
@@ -1134,27 +1151,24 @@ def demangle_column_name(name):
 
 def extract_cols_from_query(query: str):
 	
-	# Track variables in a dictionary to be used as a dictionary of globals. From: https://stackoverflow.com/questions/64576913/extract-pandas-dataframe-column-names-from-query-string
-	
-	variables = {}
+	backtick_pattern = r'`([^`]+)`'
+	backticked = set(re.findall(backtick_pattern, query))
 
-	while True:
-		try:
-			# Try creating a Expr object with the query string and dictionary of globals.
-			# This will raise an error as long as the dictionary of globals is incomplete.
-			env = pd.core.computation.scope.ensure_scope(level=0, global_dict=variables)
-			pd.core.computation.eval.Expr(query, env=env)
+	# 2. Remove backtick sections so they don't get double-counted
+	cleaned_query = re.sub(backtick_pattern, "", query)
 
-			# Exit the loop when evaluation is successful.
-			break
-		except pd.errors.UndefinedVariableError as e:
-			# This relies on the format defined here: https://github.com/pandas-dev/pandas/blob/965ceca9fd796940050d6fc817707bba1c4f9bff/pandas/errors/__init__.py#L401
-			name = re.findall("name '(.+?)' is not defined", str(e))[0]
+	# 3. Extract bare identifiers from the remaining string
+	identifier_pattern = r'\b([A-Za-z_]\w*)\b'
+	bare = set(re.findall(identifier_pattern, cleaned_query))
 
-			# Add the name to the globals dictionary with a dummy value.
-			variables[name] = None
+	# 4. Remove Python keywords, operators, and pandas builtins
+	blacklist = set(dir(pd)) | set(dir(__builtins__)) | {
+		"and", "or", "not", "in", "True", "False"
+	}
+	bare = {c for c in bare if c not in blacklist}
+	cols = backticked | bare
 
-	return [demangle_column_name(name) for name in variables.keys()]
+	return list([demangle_column_name(c) for c in cols])
 
 def create_patch_mask(h, w, center=None, radius=None):
 
@@ -1261,7 +1275,7 @@ def rename_intensity_column(df, channels):
 		sections = np.array(re.split('-|_', intensity_cols[k]))
 		test_digit = np.array([False for s in sections])
 		for j,s in enumerate(sections):
-			if s.isdigit():
+			if str(s).isdigit():
 				if int(s)<len(channel_names):
 					test_digit[j] = True
 			
@@ -1794,8 +1808,8 @@ def _extract_channel_indices(channels, required_channels):
 
 	return channel_indices
 
-def ConfigSectionMap(path,section):
-
+def config_section_to_dict(path: Union[str,PurePath,Path], section: str) -> Union[Dict,None]:
+	
 	"""
 	Parse the config file to extract experiment parameters
 	following https://wiki.python.org/moin/ConfigParserExamples
@@ -1818,7 +1832,7 @@ def ConfigSectionMap(path,section):
 	--------
 	>>> config = "path/to/config_file.ini"
 	>>> section = "Channels"
-	>>> channel_dictionary = ConfigSectionMap(config,section)
+	>>> channel_dictionary = config_section_to_dict(config,section)
 	>>> print(channel_dictionary)
 	# {'brightfield_channel': '0',
 	#  'live_nuclei_channel': 'nan',
@@ -1842,7 +1856,7 @@ def ConfigSectionMap(path,section):
 		try:
 			dict1[option] = Config.get(section, option)
 			if dict1[option] == -1:
-				DebugPrint("skip: %s" % option)
+				print("skip: %s" % option)
 		except:
 			print("exception on %s!" % option)
 			dict1[option] = None
@@ -1896,10 +1910,10 @@ def _extract_channel_indices_from_config(config, channels_to_extract):
 	channels = []
 	for c in channels_to_extract:
 		try:
-			c1 = int(ConfigSectionMap(config,"Channels")[c])
+			c1 = int(config_section_to_dict(config, "Channels")[c])
 			channels.append(c1)
 		except Exception as e:
-			print(f"Warning... The channel {c} required by the model is not available in your data...")
+			print(f"Warning: The channel {c} required by the model is not available in your data...")
 			channels.append(None)
 	if np.all([c is None for c in channels]):
 		channels = None
@@ -1922,10 +1936,10 @@ def _extract_nbr_channels_from_config(config, return_names=False):
 	nbr_channels = 0
 	channels = []
 	try:
-		fields = ConfigSectionMap(config,"Channels")
+		fields = config_section_to_dict(config, "Channels")
 		for c in fields:
 			try:
-				channel = int(ConfigSectionMap(config, "Channels")[c])
+				channel = int(config_section_to_dict(config, "Channels")[c])
 				nbr_channels += 1
 				channels.append(c)
 			except:
@@ -1939,49 +1953,49 @@ def _extract_nbr_channels_from_config(config, return_names=False):
 		nbr_channels = 0
 		channels = []
 		try:
-			brightfield_channel = int(ConfigSectionMap(config,"MovieSettings")["brightfield_channel"])
+			brightfield_channel = int(config_section_to_dict(config, "MovieSettings")["brightfield_channel"])
 			nbr_channels += 1
 			channels.append('brightfield_channel')
 		except:
 			brightfield_channel = None
 
 		try:
-			live_nuclei_channel = int(ConfigSectionMap(config,"MovieSettings")["live_nuclei_channel"])
+			live_nuclei_channel = int(config_section_to_dict(config, "MovieSettings")["live_nuclei_channel"])
 			nbr_channels += 1
 			channels.append('live_nuclei_channel')
 		except:
 			live_nuclei_channel = None
 
 		try:
-			dead_nuclei_channel = int(ConfigSectionMap(config,"MovieSettings")["dead_nuclei_channel"])
+			dead_nuclei_channel = int(config_section_to_dict(config, "MovieSettings")["dead_nuclei_channel"])
 			nbr_channels +=1
 			channels.append('dead_nuclei_channel')
 		except:
 			dead_nuclei_channel = None
 
 		try:
-			effector_fluo_channel = int(ConfigSectionMap(config,"MovieSettings")["effector_fluo_channel"])
+			effector_fluo_channel = int(config_section_to_dict(config, "MovieSettings")["effector_fluo_channel"])
 			nbr_channels +=1
 			channels.append('effector_fluo_channel')
 		except:
 			effector_fluo_channel = None
 
 		try:
-			adhesion_channel = int(ConfigSectionMap(config,"MovieSettings")["adhesion_channel"])
+			adhesion_channel = int(config_section_to_dict(config, "MovieSettings")["adhesion_channel"])
 			nbr_channels += 1
 			channels.append('adhesion_channel')
 		except:
 			adhesion_channel = None
 
 		try:
-			fluo_channel_1 = int(ConfigSectionMap(config,"MovieSettings")["fluo_channel_1"])
+			fluo_channel_1 = int(config_section_to_dict(config, "MovieSettings")["fluo_channel_1"])
 			nbr_channels += 1
 			channels.append('fluo_channel_1')
 		except:
 			fluo_channel_1 = None	
 
 		try:
-			fluo_channel_2 = int(ConfigSectionMap(config,"MovieSettings")["fluo_channel_2"])
+			fluo_channel_2 = int(config_section_to_dict(config, "MovieSettings")["fluo_channel_2"])
 			nbr_channels += 1
 			channels.append('fluo_channel_2')
 		except:
@@ -2087,10 +2101,10 @@ def _extract_labels_from_config(config,number_of_wells):
 
 	
 	try:
-		concentrations = ConfigSectionMap(config,"Labels")["concentrations"].split(",")
-		cell_types = ConfigSectionMap(config,"Labels")["cell_types"].split(",")
-		antibodies = ConfigSectionMap(config,"Labels")["antibodies"].split(",")
-		pharmaceutical_agents = ConfigSectionMap(config,"Labels")["pharmaceutical_agents"].split(",")
+		concentrations = config_section_to_dict(config, "Labels")["concentrations"].split(",")
+		cell_types = config_section_to_dict(config, "Labels")["cell_types"].split(",")
+		antibodies = config_section_to_dict(config, "Labels")["antibodies"].split(",")
+		pharmaceutical_agents = config_section_to_dict(config, "Labels")["pharmaceutical_agents"].split(",")
 		index = np.arange(len(concentrations)).astype(int) + 1
 		if not np.all(pharmaceutical_agents=="None"):
 			labels = [f"W{idx}: [CT] "+a+"; [Ab] "+b+" @ "+c+" pM "+d for idx,a,b,c,d in zip(index,cell_types,antibodies,concentrations,pharmaceutical_agents)]
@@ -2136,10 +2150,10 @@ def _extract_channels_from_config(config):
 	channel_names = []
 	channel_indices = []
 	try:
-		fields = ConfigSectionMap(config,"Channels")
+		fields = config_section_to_dict(config, "Channels")
 		for c in fields:
 			try:
-				idx = int(ConfigSectionMap(config, "Channels")[c])
+				idx = int(config_section_to_dict(config, "Channels")[c])
 				channel_names.append(c)
 				channel_indices.append(idx)
 			except:
@@ -2188,7 +2202,7 @@ def extract_experiment_channels(experiment):
 	return _extract_channels_from_config(config)
 
 
-def get_software_location():
+def get_software_location() -> str:
 
 	"""
 	Get the installation folder of celldetective.
@@ -2241,7 +2255,7 @@ def remove_trajectory_measurements(trajectories, column_labels={'track': "TRACK_
 	tracks = trajectories.copy()
 
 	columns_to_keep = [column_labels['track'], column_labels['time'], column_labels['x'], column_labels['y'],column_labels['x']+'_um', column_labels['y']+'_um', 'class_id', 
-					  't', 'state', 'generation', 'root', 'parent', 'ID', 't0', 'class', 'status', 'class_color', 'status_color', 'class_firstdetection', 't_firstdetection', 'velocity']
+					  't', 'state', 'generation', 'root', 'parent', 'ID', 't0', 'class', 'status', 'class_color', 'status_color', 'class_firstdetection', 't_firstdetection', 'status_firstdetection','velocity']
 	cols = list(tracks.columns)
 	for c in columns_to_keep:
 		if c not in cols:
@@ -2833,8 +2847,7 @@ def download_url_to_file(url, dst, progress=True):
 		shutil.move(f.name, dst)
 	finally:
 		f.close()
-		if os.path.exists(f.name):
-			os.remove(f.name)
+		remove_file_if_exists(f.name)
 
 def get_zenodo_files(cat=None):
 
@@ -2864,11 +2877,13 @@ def get_zenodo_files(cat=None):
 		categories.append(category)
 	
 	if cat is not None:
-		assert cat in [os.sep.join(['models','segmentation_generic']), os.sep.join(['models','segmentation_targets']), os.sep.join(['models','segmentation_effectors']), \
-						   'demos', os.sep.join(['datasets','signal_annotations']), os.sep.join(['datasets','segmentation_annotations']),  os.sep.join(['models','signal_detection'])]
-		categories = np.array(categories)
-		all_files_short = np.array(all_files_short)
-		return list(all_files_short[np.where(categories==cat)[0]])
+		if cat in [os.sep.join(['models','segmentation_generic']), os.sep.join(['models','segmentation_targets']), os.sep.join(['models','segmentation_effectors']), \
+						   'demos', os.sep.join(['datasets','signal_annotations']), os.sep.join(['datasets','segmentation_annotations']),  os.sep.join(['models','signal_detection'])]:
+			categories = np.array(categories)
+			all_files_short = np.array(all_files_short)
+			return list(all_files_short[np.where(categories==cat)[0]])
+		else:
+			return []
 	else:
 		return all_files_short,categories
 
@@ -2964,7 +2979,7 @@ def collapse_trajectories_by_status(df, status=None, projection='mean', populati
 
 	return group_table
 
-def step_function(t, t_shift, dt):
+def step_function(t: Union[np.ndarray,List], t_shift: float, dt: float) -> np.ndarray:
 
 	"""
 	Computes a step function using the logistic sigmoid function.
@@ -3006,7 +3021,7 @@ def step_function(t, t_shift, dt):
 	return 1/(1+np.exp(-(t-t_shift)/dt))
 
 
-def test_2samp_generic(data, feature=None, groupby_cols=None, method="ks_2samp", *args, **kwargs):
+def test_2samp_generic(data: pd.DataFrame, feature: Optional[str] = None, groupby_cols: Optional[Union[str,List[str]]] = None, method="ks_2samp", *args, **kwargs) -> pd.DataFrame:
 
 	"""
 	Performs pairwise statistical tests between groups of data, comparing a specified feature using a chosen method.
@@ -3076,4 +3091,18 @@ def test_2samp_generic(data, feature=None, groupby_cols=None, method="ks_2samp",
 	pivot.set_index("cdt1",drop=True, inplace=True)
 	pivot.index.name = None
 
-	return pivot
+	return pivot
+
+def pretty_table(dct: dict):
+	table = PrettyTable()
+	for c in dct.keys():
+		table.add_column(str(c), [])
+	table.add_row([dct.get(c, "") for c in dct.keys()])
+	print(table)
+
+def remove_file_if_exists(file: Union[str,Path]):
+	if os.path.exists(file):
+		try:
+			os.remove(file)
+		except Exception as e:
+			print(e)

{celldetective-1.3.9.post5.dist-info → celldetective-1.4.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: celldetective
-Version: 1.3.9.post5
+Version: 1.4.1
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro
@@ -44,12 +44,17 @@ Requires-Dist: h5py
 Requires-Dist: cliffs_delta
 Requires-Dist: requests
 Requires-Dist: trackpy
+Requires-Dist: prettyprint
+Requires-Dist: pandas
+Requires-Dist: matplotlib
+Requires-Dist: prettytable
 Dynamic: author
 Dynamic: author-email
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page
 Dynamic: license
+Dynamic: license-file
 Dynamic: requires-dist
 Dynamic: summary
 
@@ -183,26 +188,29 @@ 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/10.1101/2024.03.15.585250v3)
-paper (currently preprint):
+[Celldetective](https://elifesciences.org/reviewed-preprints/105302)
+paper (currently a reviewed preprint at eLife):
 
 ``` raw
-@article {Torro2024.03.15.585250,
-    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 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}
+@article{torroCelldetectiveAIenhancedImage2025,
+  title = {Celldetective: An {{AI-enhanced}} Image Analysis Tool for Unraveling Dynamic Cell Interactions},
+  shorttitle = {Celldetective},
+  author = {Torro, Rémy and Díaz-Bello, Beatriz and Arawi, Dalia El and Dervanova, Ksenija and Ammer, Lorna and Dupuy, Florian and Chames, Patrick and Sengupta, Kheya and Limozin, Laurent},
+  date = {2025-03-10},
+  journaltitle = {eLife},
+  volume = {14},
+  publisher = {eLife Sciences Publications Limited},
+  doi = {10.7554/eLife.105302.1},
+  url = {https://elifesciences.org/reviewed-preprints/105302},
+  urldate = {2025-03-20},
+  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.},
+  langid = {english},
+  file = {/home/torro/Zotero/storage/VFYBBMQF/Torro et al. - 2025 - Celldetective an AI-enhanced image analysis tool .pdf;/home/torro/Zotero/storage/UGMCKKST/105302.html}
 }
 ```
 
 Make sure you to cite the papers of any segmentation model (StarDist,
-Cellpose) or tracker (bTrack) you used through Celldetective.
+Cellpose) or tracker (bTrack, TrackPy) you used through Celldetective.
 
 # Bibliography