celldetective 1.4.2__py3-none-any.whl → 1.5.0b1__py3-none-any.whl

celldetective/neighborhood.py

@@ -3,1462 +3,1917 @@ import pandas as pd
 from tqdm import tqdm
 from skimage.graph import pixel_graph
 import os
-from celldetective.utils import contour_of_instance_segmentation, extract_identity_col
+from celldetective.utils.masks import contour_of_instance_segmentation
+from celldetective.utils.data_cleaning import extract_identity_col
 from scipy.spatial.distance import cdist
-from celldetective.io import locate_labels, get_position_pickle, get_position_table
-
-abs_path = os.sep.join([os.path.split(os.path.dirname(os.path.realpath(__file__)))[0], 'celldetective'])
-
-def _fill_distance_neighborhood_at_t(time_index, setA, setB, dist_map, attention_weight=None, include_dead_weight=False, symmetrize=False, compute_cum_sum=False,
-							   weights=None, closest_A=None, neigh_col="", column_labelsA=None, column_labelsB=None, statusA=None, statusB=None, distance=10):
-
-	index_A = list(setA.loc[setA[column_labelsA['time']] == time_index].index)
-	index_B = list(setB.loc[setB[column_labelsB['time']] == time_index].index)
-
-	dataA = setA.loc[setA[column_labelsA['time']] == time_index, [column_labelsA['x'], column_labelsA['y'], column_labelsA['track'],statusA]].to_numpy()
-
-	ids_A = dataA[:, 2]
-	status_A = dataA[:, 3]
-
-	dataB = setB.loc[setB[column_labelsB['time']] == time_index, [column_labelsB['x'], column_labelsB['y'], column_labelsB['track'],statusB]].to_numpy()
-	ids_B = dataB[:, 2]
-	status_B = dataB[:, 3]
-
-	for k in range(dist_map.shape[0]):
-		
-		col = dist_map[k, :]
-		col[col == 0.] = 1.0E06
-		
-		neighs_B = np.array([ids_B[i] for i in np.where((col <= distance))[0]])
-		status_neigh_B = np.array([status_B[i] for i in np.where((col <= distance))[0]])
-		dist_B = [round(col[i], 2) for i in np.where((col <= distance))[0]]
-		if len(dist_B) > 0:
-			closest_B_cell = neighs_B[np.argmin(dist_B)]
-		
-		if symmetrize and attention_weight:
-			n_neighs = float(len(neighs_B))
-			if not include_dead_weight:
-				n_neighs_alive = len(np.where(status_neigh_B == 1)[0])
-				neigh_count = n_neighs_alive
-			else:
-				neigh_count = n_neighs
-			if neigh_count > 0:
-				weight_A = 1. / neigh_count
-			else:
-				weight_A = np.nan
-			
-			if not include_dead_weight and status_A[k] == 0:
-				weight_A = 0
-		
-		neighs = []
-		setA.at[index_A[k], neigh_col] = []
-		for n in range(len(neighs_B)):
-			
-			# index in setB
-			n_index = np.where(ids_B == neighs_B[n])[0][0]
-			# Assess if neigh B is closest to A
-			if attention_weight:
-				if closest_A[n_index] == ids_A[k]:
-					closest = True
-				else:
-					closest = False
-			
-			if symmetrize:
-				# Load neighborhood previous data
-				sym_neigh = setB.loc[index_B[n_index], neigh_col]
-				if neighs_B[n] == closest_B_cell:
-					closest_b = True
-				else:
-					closest_b = False
-				if isinstance(sym_neigh, list):
-					sym_neigh.append({'id': ids_A[k], 'distance': dist_B[n], 'status': status_A[k]})
-				else:
-					sym_neigh = [{'id': ids_A[k], 'distance': dist_B[n], 'status': status_A[k]}]
-				if attention_weight:
-					sym_neigh[-1].update({'weight': weight_A, 'closest': closest_b})
-			
-			# Write the minimum info about neighborhing cell B
-			neigh_dico = {'id': neighs_B[n], 'distance': dist_B[n], 'status': status_neigh_B[n]}
-			if attention_weight:
-				neigh_dico.update({'weight': weights[n_index], 'closest': closest})
-			
-			if compute_cum_sum:
-				# Compute the integrated presence of the neighboring cell B
-				assert column_labelsB[
-						   'track'] == 'TRACK_ID', 'The set B does not seem to contain tracked data. The cumulative time will be meaningless.'
-				past_neighs = [[ll['id'] for ll in l] if len(l) > 0 else [None] for l in setA.loc[
-					(setA[column_labelsA['track']] == ids_A[k]) & (setA[column_labelsA['time']] <= time_index), neigh_col].to_numpy()]
-				past_neighs = [item for sublist in past_neighs for item in sublist]
-				
-				if attention_weight:
-					past_weights = [[ll['weight'] for ll in l] if len(l) > 0 else [None] for l in setA.loc[
-						(setA[column_labelsA['track']] == ids_A[k]) & (
-								setA[column_labelsA['time']] <= time_index), neigh_col].to_numpy()]
-					past_weights = [item for sublist in past_weights for item in sublist]
-				
-				cum_sum = len(np.where(past_neighs == neighs_B[n])[0])
-				neigh_dico.update({'cumulated_presence': cum_sum + 1})
-				
-				if attention_weight:
-					cum_sum_weighted = np.sum(
-						[w if l == neighs_B[n] else 0 for l, w in zip(past_neighs, past_weights)])
-					neigh_dico.update({'cumulated_presence_weighted': cum_sum_weighted + weights[n_index]})
-			
-			if symmetrize:
-				setB.at[index_B[n_index], neigh_col] = sym_neigh
-			
-			neighs.append(neigh_dico)
-		
-		setA.at[index_A[k], neigh_col] = neighs
-
-def _fill_contact_neighborhood_at_t(time_index, setA, setB, dist_map, intersection_map=None, attention_weight=None, include_dead_weight=False, symmetrize=False, compute_cum_sum=False,
-							   weights=None, closest_A=None, neigh_col="", column_labelsA=None, column_labelsB=None, statusA=None, statusB=None, d_filter=10):
-
-	index_A = list(setA.loc[setA[column_labelsA['time']] == time_index].index)
-	index_B = list(setB.loc[setB[column_labelsB['time']] == time_index].index)
-
-	dataA = setA.loc[setA[column_labelsA['time']] == time_index, [column_labelsA['x'], column_labelsA['y'], column_labelsA['track'], column_labelsA['mask_id'],
-	statusA]].to_numpy()
-
-	ids_A = dataA[:, 2]
-	status_A = dataA[:, 4]
-
-	dataB = setB.loc[setB[column_labelsB['time']] == time_index, [column_labelsB['x'], column_labelsB['y'], column_labelsB['track'], column_labelsB['mask_id'],
-	statusB]].to_numpy()
-	ids_B = dataB[:, 2]
-	status_B = dataB[:, 4]
-
-	for k in range(dist_map.shape[0]):
-
-		col = dist_map[k, :]
-		col_inter = intersection_map[k, :]
-		col[col == 0.] = 1.0E06
-
-		neighs_B = np.array([ids_B[i] for i in np.where((col <= d_filter))[0]])
-		status_neigh_B = np.array([status_B[i] for i in np.where((col <= d_filter))[0]])
-		dist_B = [round(col[i], 2) for i in np.where((col <= d_filter))[0]]
-		intersect_B = [round(col_inter[i], 2) for i in np.where((col <= d_filter))[0]]
-
-		if len(dist_B) > 0:
-			closest_B_cell = neighs_B[np.argmin(dist_B)]
-
-		if symmetrize and attention_weight:
-			n_neighs = float(len(neighs_B))
-			if not include_dead_weight:
-				n_neighs_alive = len(np.where(status_neigh_B == 1)[0])
-				neigh_count = n_neighs_alive
-			else:
-				neigh_count = n_neighs
-			if neigh_count > 0:
-				weight_A = 1. / neigh_count
-			else:
-				weight_A = np.nan
-
-			if not include_dead_weight and status_A[k] == 0:
-				weight_A = 0
-
-		neighs = []
-		setA.at[index_A[k], neigh_col] = []
-		for n in range(len(neighs_B)):
-
-			# index in setB
-			n_index = np.where(ids_B == neighs_B[n])[0][0]
-			# Assess if neigh B is closest to A
-			if attention_weight:
-				if closest_A[n_index] == ids_A[k]:
-					closest = True
-				else:
-					closest = False
-
-			if symmetrize:
-				# Load neighborhood previous data
-				sym_neigh = setB.loc[index_B[n_index], neigh_col]
-				if neighs_B[n] == closest_B_cell:
-					closest_b = True
-				else:
-					closest_b = False
-				if isinstance(sym_neigh, list):
-					sym_neigh.append({'id': ids_A[k], 'distance': dist_B[n], 'status': status_A[k],
-									  'intersection': intersect_B[n]})
-				else:
-					sym_neigh = [{'id': ids_A[k], 'distance': dist_B[n], 'status': status_A[k],
-								  'intersection': intersect_B[n]}]
-				if attention_weight:
-					sym_neigh[-1].update({'weight': weight_A, 'closest': closest_b})
-
-			# Write the minimum info about neighborhing cell B
-			neigh_dico = {'id': neighs_B[n], 'distance': dist_B[n], 'status': status_neigh_B[n],
-						  'intersection': intersect_B[n]}
-			if attention_weight:
-				neigh_dico.update({'weight': weights[n_index], 'closest': closest})
-
-			if compute_cum_sum:
-				# Compute the integrated presence of the neighboring cell B
-				assert column_labelsB[
-						   'track'] == 'TRACK_ID', 'The set B does not seem to contain tracked data. The cumulative time will be meaningless.'
-				past_neighs = [[ll['id'] for ll in l] if len(l) > 0 else [None] for l in setA.loc[
-					(setA[column_labelsA['track']] == ids_A[k]) & (
-							setA[column_labelsA['time']] <= time_index), neigh_col].to_numpy()]
-				past_neighs = [item for sublist in past_neighs for item in sublist]
-
-				if attention_weight:
-					past_weights = [[ll['weight'] for ll in l] if len(l) > 0 else [None] for l in
-									setA.loc[
-										(setA[column_labelsA['track']] == ids_A[k]) & (
-												setA[column_labelsA['time']] <= time_index), neigh_col].to_numpy()]
-					past_weights = [item for sublist in past_weights for item in sublist]
-
-				cum_sum = len(np.where(past_neighs == neighs_B[n])[0])
-				neigh_dico.update({'cumulated_presence': cum_sum + 1})
-
-				if attention_weight:
-					cum_sum_weighted = np.sum(
-						[w if l == neighs_B[n] else 0 for l, w in zip(past_neighs, past_weights)])
-					neigh_dico.update(
-						{'cumulated_presence_weighted': cum_sum_weighted + weights[n_index]})
-
-			if symmetrize:
-				setB.at[index_B[n_index], neigh_col] = sym_neigh
-
-			neighs.append(neigh_dico)
-
-		setA.at[index_A[k], neigh_col] = neighs
-
-
-def _compute_mask_contact_dist_map(setA, setB, labelsA, labelsB=None, distance=10, mode="self", column_labelsA=None, column_labelsB=None):
-
-	coordinates_A = setA.loc[:, [column_labelsA['x'], column_labelsA['y']]].to_numpy()
-	coordinates_B = setB.loc[:, [column_labelsB['x'], column_labelsB['y']]].to_numpy()
-	ids_A = setA.loc[:, column_labelsA["track"]].to_numpy()
-	ids_B = setB.loc[:, column_labelsB["track"]].to_numpy()
-	mask_ids_A = setA.loc[:, column_labelsA["mask_id"]].to_numpy()
-	mask_ids_B = setB.loc[:, column_labelsB["mask_id"]].to_numpy()
-
-	# compute distance matrix
-	dist_map = cdist(coordinates_A, coordinates_B, metric="euclidean")
-	intersection_map = np.zeros_like(dist_map).astype(float)
-
-	# Do the mask contact computation
-	labelsA = np.where(np.isin(labelsA, mask_ids_A), labelsA.copy(), 0.)
-
-	if labelsB is not None:
-		labelsB = np.where(np.isin(labelsB, mask_ids_B), labelsB.copy(), 0.)
-
-	contact_pairs = contact_neighborhood(labelsA, labelsB=labelsB, border=distance, connectivity=2)
-
-	# Put infinite distance to all non-contact pairs (something like this)
-	flatA = labelsA.flatten()
-	if labelsB is not None:
-		flatB = labelsB.flatten()
-
-	if len(contact_pairs) > 0:
-		mask = np.ones_like(dist_map).astype(bool)
-
-		indices_to_keep = []
-		for cp in contact_pairs:
-
-			cp = np.abs(cp)
-			mask_A, mask_B = cp
-			idx_A = np.where(mask_ids_A == int(mask_A))[0][0]
-			idx_B = np.where(mask_ids_B == int(mask_B))[0][0]
-
-			intersection = 0
-			if labelsB is not None:
-				intersection = len(flatA[(flatA == int(mask_A)) & (flatB == int(mask_B))])
-
-			indices_to_keep.append([idx_A, idx_B, intersection])
-			print(f'Ref cell #{ids_A[idx_A]} matched with neigh. cell #{ids_B[idx_B]}...')
-			print(f'Computed intersection: {intersection} px...')
-
-		if len(indices_to_keep) > 0:
-			indices_to_keep = np.array(indices_to_keep)
-			mask[indices_to_keep[:, 0], indices_to_keep[:, 1]] = False
-			if mode == 'self':
-				mask[indices_to_keep[:, 1], indices_to_keep[:, 0]] = False
-			dist_map[mask] = 1.0E06
-			intersection_map[indices_to_keep[:, 0], indices_to_keep[:, 1]] = indices_to_keep[:, 2]
-		else:
-			dist_map[:, :] = 1.0E06
-	else:
-		dist_map[:, :] = 1.0E06
-
-	return dist_map, intersection_map
+from celldetective.utils.image_loaders import locate_labels
+from celldetective.utils.data_loaders import get_position_table, get_position_pickle
+
+abs_path = os.sep.join(
+    [os.path.split(os.path.dirname(os.path.realpath(__file__)))[0], "celldetective"]
+)
+
+
+def _fill_distance_neighborhood_at_t(
+    time_index,
+    setA,
+    setB,
+    dist_map,
+    attention_weight=None,
+    include_dead_weight=False,
+    symmetrize=False,
+    compute_cum_sum=False,
+    weights=None,
+    closest_A=None,
+    neigh_col="",
+    column_labelsA=None,
+    column_labelsB=None,
+    statusA=None,
+    statusB=None,
+    distance=10,
+):
+
+    index_A = list(setA.loc[setA[column_labelsA["time"]] == time_index].index)
+    index_B = list(setB.loc[setB[column_labelsB["time"]] == time_index].index)
+
+    dataA = setA.loc[
+        setA[column_labelsA["time"]] == time_index,
+        [column_labelsA["x"], column_labelsA["y"], column_labelsA["track"], statusA],
+    ].to_numpy()
+
+    ids_A = dataA[:, 2]
+    status_A = dataA[:, 3]
+
+    dataB = setB.loc[
+        setB[column_labelsB["time"]] == time_index,
+        [column_labelsB["x"], column_labelsB["y"], column_labelsB["track"], statusB],
+    ].to_numpy()
+    ids_B = dataB[:, 2]
+    status_B = dataB[:, 3]
+
+    for k in range(dist_map.shape[0]):
+
+        col = dist_map[k, :]
+        col[col == 0.0] = 1.0e06
+
+        neighs_B = np.array([ids_B[i] for i in np.where((col <= distance))[0]])
+        status_neigh_B = np.array([status_B[i] for i in np.where((col <= distance))[0]])
+        dist_B = [round(col[i], 2) for i in np.where((col <= distance))[0]]
+        if len(dist_B) > 0:
+            closest_B_cell = neighs_B[np.argmin(dist_B)]
+
+        if symmetrize and attention_weight:
+            n_neighs = float(len(neighs_B))
+            if not include_dead_weight:
+                n_neighs_alive = len(np.where(status_neigh_B == 1)[0])
+                neigh_count = n_neighs_alive
+            else:
+                neigh_count = n_neighs
+            if neigh_count > 0:
+                weight_A = 1.0 / neigh_count
+            else:
+                weight_A = np.nan
+
+            if not include_dead_weight and status_A[k] == 0:
+                weight_A = 0
+
+        neighs = []
+        setA.at[index_A[k], neigh_col] = []
+        for n in range(len(neighs_B)):
+
+            # index in setB
+            n_index = np.where(ids_B == neighs_B[n])[0][0]
+            # Assess if neigh B is closest to A
+            if attention_weight:
+                if closest_A[n_index] == ids_A[k]:
+                    closest = True
+                else:
+                    closest = False
+
+            if symmetrize:
+                # Load neighborhood previous data
+                sym_neigh = setB.loc[index_B[n_index], neigh_col]
+                if neighs_B[n] == closest_B_cell:
+                    closest_b = True
+                else:
+                    closest_b = False
+                if isinstance(sym_neigh, list):
+                    sym_neigh.append(
+                        {"id": ids_A[k], "distance": dist_B[n], "status": status_A[k]}
+                    )
+                else:
+                    sym_neigh = [
+                        {"id": ids_A[k], "distance": dist_B[n], "status": status_A[k]}
+                    ]
+                if attention_weight:
+                    sym_neigh[-1].update({"weight": weight_A, "closest": closest_b})
+
+            # Write the minimum info about neighborhing cell B
+            neigh_dico = {
+                "id": neighs_B[n],
+                "distance": dist_B[n],
+                "status": status_neigh_B[n],
+            }
+            if attention_weight:
+                neigh_dico.update({"weight": weights[n_index], "closest": closest})
+
+            if compute_cum_sum:
+                # Compute the integrated presence of the neighboring cell B
+                assert (
+                    column_labelsB["track"] == "TRACK_ID"
+                ), "The set B does not seem to contain tracked data. The cumulative time will be meaningless."
+                past_neighs = [
+                    [ll["id"] for ll in l] if len(l) > 0 else [None]
+                    for l in setA.loc[
+                        (setA[column_labelsA["track"]] == ids_A[k])
+                        & (setA[column_labelsA["time"]] <= time_index),
+                        neigh_col,
+                    ].to_numpy()
+                ]
+                past_neighs = [item for sublist in past_neighs for item in sublist]
+
+                if attention_weight:
+                    past_weights = [
+                        [ll["weight"] for ll in l] if len(l) > 0 else [None]
+                        for l in setA.loc[
+                            (setA[column_labelsA["track"]] == ids_A[k])
+                            & (setA[column_labelsA["time"]] <= time_index),
+                            neigh_col,
+                        ].to_numpy()
+                    ]
+                    past_weights = [
+                        item for sublist in past_weights for item in sublist
+                    ]
+
+                cum_sum = len(np.where(past_neighs == neighs_B[n])[0])
+                neigh_dico.update({"cumulated_presence": cum_sum + 1})
+
+                if attention_weight:
+                    cum_sum_weighted = np.sum(
+                        [
+                            w if l == neighs_B[n] else 0
+                            for l, w in zip(past_neighs, past_weights)
+                        ]
+                    )
+                    neigh_dico.update(
+                        {
+                            "cumulated_presence_weighted": cum_sum_weighted
+                            + weights[n_index]
+                        }
+                    )
+
+            if symmetrize:
+                setB.at[index_B[n_index], neigh_col] = sym_neigh
+
+            neighs.append(neigh_dico)
+
+        setA.at[index_A[k], neigh_col] = neighs
+
+
+def _fill_contact_neighborhood_at_t(
+    time_index,
+    setA,
+    setB,
+    dist_map,
+    intersection_map=None,
+    attention_weight=None,
+    include_dead_weight=False,
+    symmetrize=False,
+    compute_cum_sum=False,
+    weights=None,
+    closest_A=None,
+    neigh_col="",
+    column_labelsA=None,
+    column_labelsB=None,
+    statusA=None,
+    statusB=None,
+    d_filter=10,
+):
+
+    index_A = list(setA.loc[setA[column_labelsA["time"]] == time_index].index)
+    index_B = list(setB.loc[setB[column_labelsB["time"]] == time_index].index)
+
+    dataA = setA.loc[
+        setA[column_labelsA["time"]] == time_index,
+        [
+            column_labelsA["x"],
+            column_labelsA["y"],
+            column_labelsA["track"],
+            column_labelsA["mask_id"],
+            statusA,
+        ],
+    ].to_numpy()
+
+    ids_A = dataA[:, 2]
+    status_A = dataA[:, 4]
+
+    dataB = setB.loc[
+        setB[column_labelsB["time"]] == time_index,
+        [
+            column_labelsB["x"],
+            column_labelsB["y"],
+            column_labelsB["track"],
+            column_labelsB["mask_id"],
+            statusB,
+        ],
+    ].to_numpy()
+    ids_B = dataB[:, 2]
+    status_B = dataB[:, 4]
+
+    for k in range(dist_map.shape[0]):
+
+        col = dist_map[k, :]
+        col_inter = intersection_map[k, :]
+        col[col == 0.0] = 1.0e06
+
+        neighs_B = np.array([ids_B[i] for i in np.where((col <= d_filter))[0]])
+        status_neigh_B = np.array([status_B[i] for i in np.where((col <= d_filter))[0]])
+        dist_B = [round(col[i], 2) for i in np.where((col <= d_filter))[0]]
+        intersect_B = [round(col_inter[i], 2) for i in np.where((col <= d_filter))[0]]
+
+        if len(dist_B) > 0:
+            closest_B_cell = neighs_B[np.argmin(dist_B)]
+
+        if symmetrize and attention_weight:
+            n_neighs = float(len(neighs_B))
+            if not include_dead_weight:
+                n_neighs_alive = len(np.where(status_neigh_B == 1)[0])
+                neigh_count = n_neighs_alive
+            else:
+                neigh_count = n_neighs
+            if neigh_count > 0:
+                weight_A = 1.0 / neigh_count
+            else:
+                weight_A = np.nan
+
+            if not include_dead_weight and status_A[k] == 0:
+                weight_A = 0
+
+        neighs = []
+        setA.at[index_A[k], neigh_col] = []
+        for n in range(len(neighs_B)):
+
+            # index in setB
+            n_index = np.where(ids_B == neighs_B[n])[0][0]
+            # Assess if neigh B is closest to A
+            if attention_weight:
+                if closest_A[n_index] == ids_A[k]:
+                    closest = True
+                else:
+                    closest = False
+
+            if symmetrize:
+                # Load neighborhood previous data
+                sym_neigh = setB.loc[index_B[n_index], neigh_col]
+                if neighs_B[n] == closest_B_cell:
+                    closest_b = True
+                else:
+                    closest_b = False
+                if isinstance(sym_neigh, list):
+                    sym_neigh.append(
+                        {
+                            "id": ids_A[k],
+                            "distance": dist_B[n],
+                            "status": status_A[k],
+                            "intersection": intersect_B[n],
+                        }
+                    )
+                else:
+                    sym_neigh = [
+                        {
+                            "id": ids_A[k],
+                            "distance": dist_B[n],
+                            "status": status_A[k],
+                            "intersection": intersect_B[n],
+                        }
+                    ]
+                if attention_weight:
+                    sym_neigh[-1].update({"weight": weight_A, "closest": closest_b})
+
+            # Write the minimum info about neighborhing cell B
+            neigh_dico = {
+                "id": neighs_B[n],
+                "distance": dist_B[n],
+                "status": status_neigh_B[n],
+                "intersection": intersect_B[n],
+            }
+            if attention_weight:
+                neigh_dico.update({"weight": weights[n_index], "closest": closest})
+
+            if compute_cum_sum:
+                # Compute the integrated presence of the neighboring cell B
+                assert (
+                    column_labelsB["track"] == "TRACK_ID"
+                ), "The set B does not seem to contain tracked data. The cumulative time will be meaningless."
+                past_neighs = [
+                    [ll["id"] for ll in l] if len(l) > 0 else [None]
+                    for l in setA.loc[
+                        (setA[column_labelsA["track"]] == ids_A[k])
+                        & (setA[column_labelsA["time"]] <= time_index),
+                        neigh_col,
+                    ].to_numpy()
+                ]
+                past_neighs = [item for sublist in past_neighs for item in sublist]
+
+                if attention_weight:
+                    past_weights = [
+                        [ll["weight"] for ll in l] if len(l) > 0 else [None]
+                        for l in setA.loc[
+                            (setA[column_labelsA["track"]] == ids_A[k])
+                            & (setA[column_labelsA["time"]] <= time_index),
+                            neigh_col,
+                        ].to_numpy()
+                    ]
+                    past_weights = [
+                        item for sublist in past_weights for item in sublist
+                    ]
+
+                cum_sum = len(np.where(past_neighs == neighs_B[n])[0])
+                neigh_dico.update({"cumulated_presence": cum_sum + 1})
+
+                if attention_weight:
+                    cum_sum_weighted = np.sum(
+                        [
+                            w if l == neighs_B[n] else 0
+                            for l, w in zip(past_neighs, past_weights)
+                        ]
+                    )
+                    neigh_dico.update(
+                        {
+                            "cumulated_presence_weighted": cum_sum_weighted
+                            + weights[n_index]
+                        }
+                    )
+
+            if symmetrize:
+                setB.at[index_B[n_index], neigh_col] = sym_neigh
+
+            neighs.append(neigh_dico)
+
+        setA.at[index_A[k], neigh_col] = neighs
+
+
+def _compute_mask_contact_dist_map(
+    setA,
+    setB,
+    labelsA,
+    labelsB=None,
+    distance=10,
+    mode="self",
+    column_labelsA=None,
+    column_labelsB=None,
+):
+
+    coordinates_A = setA.loc[:, [column_labelsA["x"], column_labelsA["y"]]].to_numpy()
+    coordinates_B = setB.loc[:, [column_labelsB["x"], column_labelsB["y"]]].to_numpy()
+    ids_A = setA.loc[:, column_labelsA["track"]].to_numpy()
+    ids_B = setB.loc[:, column_labelsB["track"]].to_numpy()
+    mask_ids_A = setA.loc[:, column_labelsA["mask_id"]].to_numpy()
+    mask_ids_B = setB.loc[:, column_labelsB["mask_id"]].to_numpy()
+
+    # compute distance matrix
+    dist_map = cdist(coordinates_A, coordinates_B, metric="euclidean")
+    intersection_map = np.zeros_like(dist_map).astype(float)
+
+    # Do the mask contact computation
+    labelsA = np.where(np.isin(labelsA, mask_ids_A), labelsA.copy(), 0.0)
+
+    if labelsB is not None:
+        labelsB = np.where(np.isin(labelsB, mask_ids_B), labelsB.copy(), 0.0)
+
+    contact_pairs = contact_neighborhood(
+        labelsA, labelsB=labelsB, border=distance, connectivity=2
+    )
+
+    # Put infinite distance to all non-contact pairs (something like this)
+    flatA = labelsA.flatten()
+    if labelsB is not None:
+        flatB = labelsB.flatten()
+
+    if len(contact_pairs) > 0:
+        mask = np.ones_like(dist_map).astype(bool)
+
+        indices_to_keep = []
+        for cp in contact_pairs:
+
+            cp = np.abs(cp)
+            mask_A, mask_B = cp
+            idx_A = np.where(mask_ids_A == int(mask_A))[0][0]
+            idx_B = np.where(mask_ids_B == int(mask_B))[0][0]
+
+            intersection = 0
+            if labelsB is not None:
+                intersection = len(
+                    flatA[(flatA == int(mask_A)) & (flatB == int(mask_B))]
+                )
+
+            indices_to_keep.append([idx_A, idx_B, intersection])
+            print(
+                f"Ref cell #{ids_A[idx_A]} matched with neigh. cell #{ids_B[idx_B]}..."
+            )
+            print(f"Computed intersection: {intersection} px...")
+
+        if len(indices_to_keep) > 0:
+            indices_to_keep = np.array(indices_to_keep)
+            mask[indices_to_keep[:, 0], indices_to_keep[:, 1]] = False
+            if mode == "self":
+                mask[indices_to_keep[:, 1], indices_to_keep[:, 0]] = False
+            dist_map[mask] = 1.0e06
+            intersection_map[indices_to_keep[:, 0], indices_to_keep[:, 1]] = (
+                indices_to_keep[:, 2]
+            )
+        else:
+            dist_map[:, :] = 1.0e06
+    else:
+        dist_map[:, :] = 1.0e06
+
+    return dist_map, intersection_map
 
 
 def set_live_status(setA, setB, status, not_status_option):
-	"""
-	Updates the live status for cells in two datasets based on specified status columns and options.
-
-	This function assigns a live status to cells in two datasets (setA and setB) based on the provided
-	status columns and options. If no status column is provided, all cells are marked as live. Otherwise,
-	the function updates the datasets based on the status criteria, potentially inverting the status
-	based on the `not_status_option`.
-
-	Parameters
-	----------
-	setA : pandas.DataFrame
-		The first dataset containing trajectory or position information for cells.
-	setB : pandas.DataFrame
-		The second dataset containing trajectory or position information for cells.
-	status : list or None
-		A list containing the names of the columns in setA and setB that classify cells as alive (1) or dead (0).
-		If None, all cells are considered alive. The list should contain exactly two elements.
-	not_status_option : list
-		A list containing boolean values indicating whether to invert the status for setA and setB, respectively.
-		True means the status should be inverted; False means it should not.
-
-	Returns
-	-------
-	tuple
-		A tuple containing the updated setA and setB DataFrames, along with the final status column names
-		used to classify cells in each set.
-
-	"""
-
-	print(f"Provided statuses: {status}...")
-	if status is None or status==["live_status","live_status"] or status==[None,None]:
-		setA.loc[:,'live_status'] = 1
-		setB.loc[:,'live_status'] = 1
-		status = ['live_status', 'live_status']
-	elif isinstance(status,list):
-		assert len(status)==2,'Please provide only two columns to classify cells as alive or dead.'
-		if status[0] is None or status[0]=='live_status':
-			setA.loc[:,'live_status'] = 1
-			status[0] = 'live_status'
-		elif status[0] is not None and isinstance(not_status_option, list):
-			setA.loc[setA[status[0]] == 2, status[0]] = 1  # already happened events become event
-			if not_status_option[0]:
-				setA.loc[:,'not_'+status[0]] = [not a if a==0 or a==1 else np.nan for a in setA.loc[:,status[0]].values]
-				status[0] = 'not_'+status[0]
-		if status[1] is None or status[1]=='live_status':
-			setB.loc[:,'live_status'] = 1
-			status[1] = 'live_status'
-		elif status[1] is not None and isinstance(not_status_option, list):
-			setB.loc[setB[status[1]] == 2, status[1]] = 1  # already happened events become event
-			if not_status_option[1]:
-				setB.loc[:, 'not_' + status[1]] = [not a if a == 0 or a == 1 else np.nan for a in
-												   setB.loc[:, status[1]].values]
-				status[1] = 'not_' + status[1]
-
-		assert status[0] in list(setA.columns)
-		assert status[1] in list(setB.columns)
-
-	setA = setA.reset_index(drop=True)
-	setB = setB.reset_index(drop=True)
-
-	return setA, setB, status
-
-
-def compute_attention_weight(dist_matrix, cut_distance, opposite_cell_status, opposite_cell_ids, axis=1,
-							 include_dead_weight=True):
-	"""
-	Computes the attention weight for each cell based on its proximity to cells of an opposite type within a specified distance.
-
-	This function calculates the attention weight for cells by considering the distance to the cells of an opposite type
-	within a given cutoff distance. It optionally considers only the 'live' opposite cells based on their status. The function
-	returns two arrays: one containing the attention weights and another containing the IDs of the closest opposite cells.
-
-	Parameters
-	----------
-	dist_matrix : ndarray
-		A 2D array representing the distance matrix between cells of two types.
-	cut_distance : float
-		The cutoff distance within which opposite cells will influence the attention weight.
-	opposite_cell_status : ndarray
-		An array indicating the status (e.g., live or dead) of each opposite cell. Only used when `include_dead_weight` is False.
-	opposite_cell_ids : ndarray
-		An array containing the IDs of the opposite cells.
-	axis : int, optional
-		The axis along which to compute the weights (default is 1). Axis 0 corresponds to rows, and axis 1 corresponds to columns.
-	include_dead_weight : bool, optional
-		If True, includes all opposite cells within the cutoff distance in the weight calculation, regardless of their status.
-		If False, only considers opposite cells that are 'live' (default is True).
-
-	Returns
-	-------
-	tuple of ndarrays
-		A tuple containing two arrays: `weights` and `closest_opposite`. `weights` is an array of attention weights for each cell,
-		and `closest_opposite` is an array of the IDs of the closest opposite cells within the cutoff distance.
-
-	"""
-
-	weights = np.empty(dist_matrix.shape[axis])
-	closest_opposite = np.empty(dist_matrix.shape[axis])
-
-	for i in range(dist_matrix.shape[axis]):
-		if axis == 1:
-			row = dist_matrix[:, i]
-		elif axis == 0:
-			row = dist_matrix[i, :]
-		row[row == 0.] = 1.0E06
-		nbr_opposite = len(row[row <= cut_distance])
-
-		if not include_dead_weight:
-			stat = opposite_cell_status[np.where(row <= cut_distance)[0]]
-			nbr_opposite = len(stat[stat == 1])
-			index_subpop = np.argmin(row[opposite_cell_status == 1])
-			closest_opposite[i] = opposite_cell_ids[opposite_cell_status == 1][index_subpop]
-		else:
-			closest_opposite[i] = opposite_cell_ids[np.argmin(row)]
-
-		if nbr_opposite > 0:
-			weight = 1. / float(nbr_opposite)
-			weights[i] = weight
-
-	return weights, closest_opposite
-
-
-def distance_cut_neighborhood(setA, setB, distance, mode='two-pop', status=None, not_status_option=None,
-							  compute_cum_sum=True,
-							  attention_weight=True, symmetrize=True, include_dead_weight=True,
-							  column_labels={'track': "TRACK_ID", 'time': 'FRAME', 'x': 'POSITION_X',
-											 'y': 'POSITION_Y'}):
-	"""
-
-	Match neighbors in set A and B within a circle of radius d.
-
-	Parameters
-	----------
-	setA,setB : pandas DataFrame
-		Trajectory or position sets A and B.
-	distance : float
-		Cut-distance in pixels to match neighboring pairs.
-	mode: str
-		neighboring mode, between 'two-pop' (e.g. target-effector) and 'self' (target-target or effector-effector).
-	status: None or status
-		name to look for cells to ignore (because they are dead). By default all cells are kept.
-	compute_cum_sum: bool,
-		compute cumulated time of presence of neighbours (only if trajectories available for both sets)
-	attention_weight: bool,
-		compute the attention weight (how much a cell of set B is shared across cells of set A)
-	symmetrize: bool,
-		write in set B the neighborhood of set A
-	include_dead_weight: bool
-		do not count dead cells when establishing attention weight
-	"""
-
-	# Check live_status option
-	if setA is not None and setB is not None:
-		setA, setB, status = set_live_status(setA, setB, status, not_status_option)
-	else:
-		return None, None
-
-	# Check distance option
-	if not isinstance(distance, list):
-		distance = [distance]
-
-	for d in distance:
-		# loop over each provided distance
-
-		if mode == 'two-pop':
-			neigh_col = f'neighborhood_2_circle_{d}_px'
-		elif mode == 'self':
-			neigh_col = f'neighborhood_self_circle_{d}_px'
-
-		cl = []
-		for s in [setA, setB]:
-
-			# Check whether data can be tracked
-			temp_column_labels = column_labels.copy()
-
-			id_col = extract_identity_col(s)
-			temp_column_labels.update({'track': id_col})
-			if id_col=='ID':
-				compute_cum_sum = False  # if no tracking data then cum_sum is not relevant
-			cl.append(temp_column_labels)
-
-			# Remove nan tracks (cells that do not belong to a track)
-			s[neigh_col] = np.nan
-			s[neigh_col] = s[neigh_col].astype(object)
-			s.dropna(subset=[cl[-1]['track']], inplace=True)
-
-		# Loop over each available timestep
-		timeline = np.unique(np.concatenate([setA[cl[0]['time']].to_numpy(), setB[cl[1]['time']].to_numpy()])).astype(
-			int)
-		for t in tqdm(timeline):
-
-			coordinates_A = setA.loc[setA[cl[0]['time']] == t, [cl[0]['x'], cl[0]['y']]].to_numpy()
-			ids_A = setA.loc[setA[cl[0]['time']] == t, cl[0]['track']].to_numpy()
-			status_A = setA.loc[setA[cl[0]['time']] == t, status[0]].to_numpy()
-
-			coordinates_B = setB.loc[setB[cl[1]['time']] == t, [cl[1]['x'], cl[1]['y']]].to_numpy()
-			ids_B = setB.loc[setB[cl[1]['time']] == t, cl[1]['track']].to_numpy()
-
-			if len(ids_A) > 0 and len(ids_B) > 0:
-
-				# compute distance matrix
-				dist_map = cdist(coordinates_A, coordinates_B, metric="euclidean")
-
-				if attention_weight:
-					weights, closest_A = compute_attention_weight(dist_map, d, status_A, ids_A, axis=1, include_dead_weight=include_dead_weight)
-
-				_fill_distance_neighborhood_at_t(t, setA, setB, dist_map,
-												attention_weight=attention_weight,
-												include_dead_weight=include_dead_weight, symmetrize=symmetrize,
-												compute_cum_sum=compute_cum_sum, weights=weights, closest_A=closest_A,
-												neigh_col=neigh_col, column_labelsA=cl[0], column_labelsB=cl[1],
-												statusA=status[0], statusB=status[1], distance=d)
-
-	return setA, setB
-
-
-def compute_neighborhood_at_position(pos, distance, population=['targets', 'effectors'], theta_dist=None,
-									 img_shape=(2048, 2048), return_tables=False, clear_neigh=False,
-									 event_time_col=None,
-									 neighborhood_kwargs={'mode': 'two-pop', 'status': None, 'not_status_option': None,
-														  'include_dead_weight': True, "compute_cum_sum": False,
-														  "attention_weight": True, 'symmetrize': True}):
-	"""
-	Computes neighborhood metrics for specified cell populations within a given position, based on distance criteria and additional parameters.
-
-	This function assesses the neighborhood interactions between two specified cell populations (or within a single population) at a given position.
-	It computes various neighborhood metrics based on specified distances, considering the entire image or excluding edge regions.
-	The results are optionally cleared of previous neighborhood calculations and can be returned as updated tables.
-
-	Parameters
-	----------
-	pos : str
-		The path to the position directory where the analysis is to be performed.
-	distance : float or list of float
-		The distance(s) in pixels to define neighborhoods.
-	population : list of str, optional
-		Names of the cell populations to analyze. If a single population is provided, it is used for both populations in the analysis (default is ['targets', 'effectors']).
-	theta_dist : float or list of float, optional
-		Edge threshold(s) in pixels to exclude cells close to the image boundaries from the analysis. If not provided, defaults to 90% of each specified distance.
-	img_shape : tuple of int, optional
-		The dimensions (height, width) of the images in pixels (default is (2048, 2048)).
-	return_tables : bool, optional
-		If True, returns the updated data tables for both populations (default is False).
-	clear_neigh : bool, optional
-		If True, clears existing neighborhood columns from the data tables before computing new metrics (default is False).
-	event_time_col : str, optional
-		The column name indicating the event time for each cell, required if mean neighborhood metrics are to be computed before events.
-	neighborhood_kwargs : dict, optional
-		Additional keyword arguments for neighborhood computation, including mode, status options, and metrics (default includes mode 'two-pop', and symmetrization).
-
-	Returns
-	-------
-	pandas.DataFrame or (pandas.DataFrame, pandas.DataFrame)
-		If `return_tables` is True, returns the updated data tables for the specified populations. If only one population is analyzed, both returned data frames will be identical.
-
-	Raises
-	------
-	AssertionError
-		If the specified position path does not exist or if the number of distances and edge thresholds do not match.
-
-	"""
-
-	pos = pos.replace('\\', '/')
-	pos = rf"{pos}"
-	assert os.path.exists(pos), f'Position {pos} is not a valid path.'
-
-	if isinstance(population, str):
-		population = [population, population]
-
-	if not isinstance(distance, list):
-		distance = [distance]
-	if not theta_dist is None and not isinstance(theta_dist, list):
-		theta_dist = [theta_dist]
-
-	if theta_dist is None:
-		theta_dist = [0.9 * d for d in distance]
-	assert len(theta_dist) == len(distance), 'Incompatible number of distances and number of edge thresholds.'
-
-	if population[0] == population[1]:
-		neighborhood_kwargs.update({'mode': 'self'})
-	if population[1] != population[0]:
-		neighborhood_kwargs.update({'mode': 'two-pop'})
-
-	df_A, path_A = get_position_table(pos, population=population[0], return_path=True)
-	df_B, path_B = get_position_table(pos, population=population[1], return_path=True)
-	if df_A is None or df_B is None:
-		return None
-
-	if clear_neigh:
-		if os.path.exists(path_A.replace('.csv','.pkl')):
-			os.remove(path_A.replace('.csv','.pkl'))
-		if os.path.exists(path_B.replace('.csv','.pkl')):
-			os.remove(path_B.replace('.csv','.pkl'))
-		df_pair, pair_path = get_position_table(pos, population='pairs', return_path=True)
-		if df_pair is not None:
-			os.remove(pair_path)
-
-
-	df_A_pkl = get_position_pickle(pos, population=population[0], return_path=False)
-	df_B_pkl = get_position_pickle(pos, population=population[1], return_path=False)
-
-	if df_A_pkl is not None:
-		pkl_columns = np.array(df_A_pkl.columns)
-		neigh_columns = np.array([c.startswith('neighborhood') for c in pkl_columns])
-		cols = list(pkl_columns[neigh_columns]) + ['FRAME']
-
-		id_col = extract_identity_col(df_A_pkl)
-		cols.append(id_col)
-		on_cols = [id_col, 'FRAME']
-
-		print(f'Recover {cols} from the pickle file...')
-		try:
-			df_A = pd.merge(df_A, df_A_pkl.loc[:,cols], how="outer", on=on_cols)
-			print(df_A.columns)
-		except Exception as e:
-			print(f'Failure to merge pickle and csv files: {e}')
-
-	if df_B_pkl is not None and df_B is not None:
-		pkl_columns = np.array(df_B_pkl.columns)
-		neigh_columns = np.array([c.startswith('neighborhood') for c in pkl_columns])
-		cols = list(pkl_columns[neigh_columns]) + ['FRAME']
-
-		id_col = extract_identity_col(df_B_pkl)
-		cols.append(id_col)
-		on_cols = [id_col, 'FRAME']
-
-		print(f'Recover {cols} from the pickle file...')
-		try:
-			df_B = pd.merge(df_B, df_B_pkl.loc[:,cols], how="outer", on=on_cols)
-		except Exception as e:
-			print(f'Failure to merge pickle and csv files: {e}')
-
-	if clear_neigh:
-		unwanted = df_A.columns[df_A.columns.str.contains('neighborhood')]
-		df_A = df_A.drop(columns=unwanted)
-		unwanted = df_B.columns[df_B.columns.str.contains('neighborhood')]
-		df_B = df_B.drop(columns=unwanted)
-
-	df_A, df_B = distance_cut_neighborhood(df_A, df_B, distance, **neighborhood_kwargs)
-
-	if df_A is None or df_B is None or len(df_A)==0:
-		return None
-
-	for td, d in zip(theta_dist, distance):
-
-		if neighborhood_kwargs['mode'] == 'two-pop':
-			neigh_col = f'neighborhood_2_circle_{d}_px'
-
-		elif neighborhood_kwargs['mode'] == 'self':
-			neigh_col = f'neighborhood_self_circle_{d}_px'
-
-		# edge_filter_A = (df_A['POSITION_X'] > td)&(df_A['POSITION_Y'] > td)&(df_A['POSITION_Y'] < (img_shape[0] - td))&(df_A['POSITION_X'] < (img_shape[1] - td))
-		# edge_filter_B = (df_B['POSITION_X'] > td)&(df_B['POSITION_Y'] > td)&(df_B['POSITION_Y'] < (img_shape[0] - td))&(df_B['POSITION_X'] < (img_shape[1] - td))
-		# df_A.loc[~edge_filter_A, neigh_col] = np.nan
-		# df_B.loc[~edge_filter_B, neigh_col] = np.nan
-
-		print('Count neighborhood...')
-		df_A = compute_neighborhood_metrics(df_A, neigh_col, metrics=['inclusive','exclusive','intermediate'], decompose_by_status=True)
-		# if neighborhood_kwargs['symmetrize']:
-		# 	df_B = compute_neighborhood_metrics(df_B, neigh_col, metrics=['inclusive','exclusive','intermediate'], decompose_by_status=True)
-		print('Done...')
-
-		if 'TRACK_ID' in list(df_A.columns):
-			if not np.all(df_A['TRACK_ID'].isnull()):
-				print('Estimate average neighborhood before/after event...')
-				df_A = mean_neighborhood_before_event(df_A, neigh_col, event_time_col)
-				if event_time_col is not None:
-					df_A = mean_neighborhood_after_event(df_A, neigh_col, event_time_col)
-				print('Done...')
-
-	if not population[0] == population[1]:
-		# Remove neighborhood column from neighbor table, rename with actual population name
-		for td, d in zip(theta_dist, distance):
-			if neighborhood_kwargs['mode'] == 'two-pop':
-				neigh_col = f'neighborhood_2_circle_{d}_px'
-				new_neigh_col = neigh_col.replace('_2_',f'_({population[0]}-{population[1]})_')
-				df_A = df_A.rename(columns={neigh_col: new_neigh_col})
-			elif neighborhood_kwargs['mode'] == 'self':
-				neigh_col = f'neighborhood_self_circle_{d}_px'
-			df_B = df_B.drop(columns=[neigh_col])
-		df_B.to_pickle(path_B.replace('.csv', '.pkl'))
-
-	cols_to_rename = [c for c in list(df_A.columns) if c.startswith('intermediate_count_') or c.startswith('inclusive_count_') or c.startswith('exclusive_count_') or c.startswith('mean_count_')]
-	new_col_names = [c.replace('_2_',f'_({population[0]}-{population[1]})_') for c in cols_to_rename]
-	new_name_map = {}
-	for k,c in enumerate(cols_to_rename):
-		new_name_map.update({c: new_col_names[k]})
-	df_A = df_A.rename(columns=new_name_map)
-	
-	df_A.to_pickle(path_A.replace('.csv', '.pkl'))
-
-	unwanted = df_A.columns[df_A.columns.str.startswith('neighborhood_')]
-	df_A2 = df_A.drop(columns=unwanted)
-	df_A2.to_csv(path_A, index=False)
-
-	if not population[0] == population[1]:
-		unwanted = df_B.columns[df_B.columns.str.startswith('neighborhood_')]
-		df_B_csv = df_B.drop(unwanted, axis=1, inplace=False)
-		df_B_csv.to_csv(path_B, index=False)
-
-	if return_tables:
-		return df_A, df_B
-
-def compute_neighborhood_metrics(neigh_table, neigh_col, metrics=['inclusive','exclusive','intermediate'], decompose_by_status=False):
-
-	"""
-	Computes and appends neighborhood metrics to a dataframe based on specified neighborhood characteristics.
-
-	This function iterates through a dataframe grouped by either 'TRACK_ID' or ['position', 'TRACK_ID'] (if 'position' column exists)
-	and computes various neighborhood metrics (inclusive, exclusive, intermediate counts) for each cell. It can also decompose these
-	metrics by cell status (e.g., live or dead) if specified.
-
-	Parameters
-	----------
-	neigh_table : pandas.DataFrame
-		A dataframe containing neighborhood information for each cell, including position, track ID, frame, and a specified neighborhood column.
-	neigh_col : str
-		The column name in `neigh_table` that contains neighborhood information (e.g., a list of neighbors with their attributes).
-	metrics : list of str, optional
-		The metrics to be computed from the neighborhood information. Possible values include 'inclusive', 'exclusive', and 'intermediate'.
-		Default is ['inclusive', 'exclusive', 'intermediate'].
-	decompose_by_status : bool, optional
-		If True, the metrics are computed separately for different statuses (e.g., live or dead) of the neighboring cells. Default is False.
-
-	Returns
-	-------
-	pandas.DataFrame
-		The input dataframe with additional columns for each of the specified metrics, and, if `decompose_by_status` is True, separate
-		metrics for each status.
-
-	Notes
-	-----
-	- 'inclusive' count refers to the total number of neighbors.
-	- 'exclusive' count refers to the number of neighbors that are closest.
-	- 'intermediate' count refers to the sum of weights attributed to neighbors, representing a weighted count.
-	- If `decompose_by_status` is True, metrics are appended with '_s0' or '_s1' to indicate the status they correspond to.
-
-	Examples
-	--------
-	>>> neigh_table = pd.DataFrame({
-	...     'TRACK_ID': [1, 1, 2, 2],
-	...     'FRAME': [1, 2, 1, 2],
-	...     'neighborhood_info': [{'weight': 1, 'status': 1, 'closest': 1}, ...]  # example neighborhood info
-	... })
-	>>> neigh_col = 'neighborhood_info'
-	>>> updated_neigh_table = compute_neighborhood_metrics(neigh_table, neigh_col, metrics=['inclusive'], decompose_by_status=True)
-	# Computes the inclusive count of neighbors for each cell, decomposed by cell status.
-
-	"""
-
-	neigh_table = neigh_table.reset_index(drop=True)
-	if 'position' in list(neigh_table.columns):
-		groupbycols = ['position']
-	else:
-		groupbycols = []
-
-	id_col = extract_identity_col(neigh_table)
-	groupbycols.append(id_col)
-
-	neigh_table.sort_values(by=groupbycols+['FRAME'],inplace=True)
-
-	for tid, group in neigh_table.groupby(groupbycols):
-		group = group.dropna(subset=neigh_col)
-		indices = list(group.index)
-		neighbors = group[neigh_col].to_numpy()
-
-		if 'inclusive' in metrics:
-			n_inclusive = [len(n) for n in neighbors]
-
-		if 'intermediate' in metrics:
-			n_intermediate = np.zeros(len(neighbors))
-			n_intermediate[:] = np.nan
-
-		if 'exclusive' in metrics:
-			n_exclusive = np.zeros(len(neighbors))
-			n_exclusive[:] = np.nan
-
-		if decompose_by_status:
-
-			if 'inclusive' in metrics:
-				n_inclusive_status_0 = np.zeros(len(neighbors))
-				n_inclusive_status_0[:] = np.nan
-				n_inclusive_status_1 = np.zeros(len(neighbors))
-				n_inclusive_status_1[:] = np.nan
-
-			if 'intermediate' in metrics:
-				n_intermediate_status_0 = np.zeros(len(neighbors))
-				n_intermediate_status_0[:] = np.nan
-				n_intermediate_status_1 = np.zeros(len(neighbors))
-				n_intermediate_status_1[:] = np.nan
-
-			if 'exclusive' in metrics:
-				n_exclusive_status_0 = np.zeros(len(neighbors))
-				n_exclusive_status_0[:] = np.nan
-				n_exclusive_status_1 = np.zeros(len(neighbors))
-				n_exclusive_status_1[:] = np.nan
-
-		for t in range(len(neighbors)):
-
-			neighs_at_t = neighbors[t]
-			weights_at_t = [n['weight'] for n in neighs_at_t]
-			status_at_t = [n['status'] for n in neighs_at_t]
-			closest_at_t = [n['closest'] for n in neighs_at_t]
-
-			if 'intermediate' in metrics:
-				n_intermediate[t] = np.sum(weights_at_t)
-			if 'exclusive' in metrics:
-				n_exclusive[t] = sum([c == 1.0 for c in closest_at_t])
-
-			if decompose_by_status:
-
-				if 'inclusive' in metrics:
-					n_inclusive_status_0[t] = sum([s == 0.0 for s in status_at_t])
-					n_inclusive_status_1[t] = sum([s == 1.0 for s in status_at_t])
-
-				if 'intermediate' in metrics:
-					weights_at_t = np.array(weights_at_t)
-
-					# intermediate
-					weights_status_1 = weights_at_t[np.array([s == 1.0 for s in status_at_t], dtype=bool)]
-					weights_status_0 = weights_at_t[np.array([s == 0.0 for s in status_at_t], dtype=bool)]
-					n_intermediate_status_1[t] = np.sum(weights_status_1)
-					n_intermediate_status_0[t] = np.sum(weights_status_0)
-
-				if 'exclusive' in metrics:
-					n_exclusive_status_0[t] = sum(
-						[c == 1.0 if s == 0.0 else False for c, s in zip(closest_at_t, status_at_t)])
-					n_exclusive_status_1[t] = sum(
-						[c == 1.0 if s == 1.0 else False for c, s in zip(closest_at_t, status_at_t)])
-
-		if 'inclusive' in metrics:
-			neigh_table.loc[indices, 'inclusive_count_' + neigh_col] = n_inclusive
-		if 'intermediate' in metrics:
-			neigh_table.loc[indices, 'intermediate_count_' + neigh_col] = n_intermediate
-		if 'exclusive' in metrics:
-			neigh_table.loc[indices, 'exclusive_count_' + neigh_col] = n_exclusive
-
-		if decompose_by_status:
-			if 'inclusive' in metrics:
-				neigh_table.loc[indices, 'inclusive_count_s0_' + neigh_col] = n_inclusive_status_0
-				neigh_table.loc[indices, 'inclusive_count_s1_' + neigh_col] = n_inclusive_status_1
-			if 'intermediate' in metrics:
-				neigh_table.loc[indices, 'intermediate_count_s0_' + neigh_col] = n_intermediate_status_0
-				neigh_table.loc[indices, 'intermediate_count_s1_' + neigh_col] = n_intermediate_status_1
-			if 'exclusive' in metrics:
-				neigh_table.loc[indices, 'exclusive_count_s0_' + neigh_col] = n_exclusive_status_0
-				neigh_table.loc[indices, 'exclusive_count_s1_' + neigh_col] = n_exclusive_status_1
-
-	return neigh_table
-
-
-def mean_neighborhood_before_event(neigh_table, neigh_col, event_time_col,
-								   metrics=['inclusive', 'exclusive', 'intermediate']):
-	"""
-	Computes the mean neighborhood metrics for each cell track before a specified event time.
-
-	This function calculates the mean values of specified neighborhood metrics (inclusive, exclusive, intermediate)
-	for each cell track up to and including the frame of an event. The function requires the neighborhood metrics to
-	have been previously computed and appended to the input dataframe. It operates on grouped data based on position
-	and track ID, handling cases with or without position information.
-
-	Parameters
-	----------
-	neigh_table : pandas.DataFrame
-		A dataframe containing cell track data with precomputed neighborhood metrics and event time information.
-	neigh_col : str
-		The base name of the neighborhood metric columns in `neigh_table`.
-	event_time_col : str or None
-		The column name indicating the event time for each cell track. If None, the maximum frame number in the
-		dataframe is used as the event time for all tracks.
-
-	Returns
-	-------
-	pandas.DataFrame
-		The input dataframe with added columns for the mean neighborhood metrics before the event for each cell track.
-		The new columns are named as 'mean_count_{metric}_{neigh_col}_before_event', where {metric} is one of
-		'inclusive', 'exclusive', 'intermediate'.
-
-	"""
-
-
-	neigh_table = neigh_table.reset_index(drop=True)
-	if 'position' in list(neigh_table.columns):
-		groupbycols = ['position']
-	else:
-		groupbycols = []
-
-	id_col = extract_identity_col(neigh_table)
-	groupbycols.append(id_col)
-
-	neigh_table.sort_values(by=groupbycols+['FRAME'],inplace=True)
-	suffix = '_before_event'
-
-	if event_time_col is None:
-		print('No event time was provided... Estimating the mean neighborhood over the whole observation time...')
-		neigh_table.loc[:, 'event_time_temp'] = neigh_table['FRAME'].max()
-		event_time_col = 'event_time_temp'
-		suffix = ''
-
-	for tid, group in neigh_table.groupby(groupbycols):
-
-		group = group.dropna(subset=neigh_col)
-		indices = list(group.index)
-
-		event_time_values = group[event_time_col].to_numpy()
-		if len(event_time_values) > 0:
-			event_time = event_time_values[0]
-		else:
-			continue
-
-		if event_time < 0.:
-			event_time = group['FRAME'].max()
-
-		if 'intermediate' in metrics:
-			valid_counts_intermediate = group.loc[
-				group['FRAME'] <= event_time, 'intermediate_count_s1_' + neigh_col].to_numpy()
-			if len(valid_counts_intermediate[valid_counts_intermediate == valid_counts_intermediate]) > 0:
-				neigh_table.loc[indices, f'mean_count_intermediate_{neigh_col}{suffix}'] = np.nanmean(
-					valid_counts_intermediate)
-		if 'inclusive' in metrics:
-			valid_counts_inclusive = group.loc[
-				group['FRAME'] <= event_time, 'inclusive_count_s1_' + neigh_col].to_numpy()
-			if len(valid_counts_inclusive[valid_counts_inclusive == valid_counts_inclusive]) > 0:
-				neigh_table.loc[indices, f'mean_count_inclusive_{neigh_col}{suffix}'] = np.nanmean(
-					valid_counts_inclusive)
-		if 'exclusive' in metrics:
-			valid_counts_exclusive = group.loc[
-				group['FRAME'] <= event_time, 'exclusive_count_s1_' + neigh_col].to_numpy()
-			if len(valid_counts_exclusive[valid_counts_exclusive == valid_counts_exclusive]) > 0:
-				neigh_table.loc[indices, f'mean_count_exclusive_{neigh_col}{suffix}'] = np.nanmean(
-					valid_counts_exclusive)
-
-	if event_time_col == 'event_time_temp':
-		neigh_table = neigh_table.drop(columns='event_time_temp')
-	return neigh_table
-
-
-def mean_neighborhood_after_event(neigh_table, neigh_col, event_time_col,
-								  metrics=['inclusive', 'exclusive', 'intermediate']):
-	"""
-	Computes the mean neighborhood metrics for each cell track after a specified event time.
-
-	This function calculates the mean values of specified neighborhood metrics (inclusive, exclusive, intermediate)
-	for each cell track after the event time. The function requires the neighborhood metrics to
-	have been previously computed and appended to the input dataframe. It operates on grouped data based on position
-	and track ID, handling cases with or without position information.
-
-	Parameters
-	----------
-	neigh_table : pandas.DataFrame
-		A dataframe containing cell track data with precomputed neighborhood metrics and event time information.
-	neigh_col : str
-		The base name of the neighborhood metric columns in `neigh_table`.
-	event_time_col : str or None
-		The column name indicating the event time for each cell track. If None, the maximum frame number in the
-		dataframe is used as the event time for all tracks.
-
-	Returns
-	-------
-	pandas.DataFrame
-		The input dataframe with added columns for the mean neighborhood metrics before the event for each cell track.
-		The new columns are named as 'mean_count_{metric}_{neigh_col}_before_event', where {metric} is one of
-		'inclusive', 'exclusive', 'intermediate'.
-
-	"""
-
-
-	neigh_table = neigh_table.reset_index(drop=True)
-	if 'position' in list(neigh_table.columns):
-		groupbycols = ['position']
-	else:
-		groupbycols = []
-
-	id_col = extract_identity_col(neigh_table)
-	groupbycols.append(id_col)
-
-	neigh_table.sort_values(by=groupbycols+['FRAME'],inplace=True)
-	suffix = '_after_event'
-
-	if event_time_col is None:
-		neigh_table.loc[:, 'event_time_temp'] = None  # neigh_table['FRAME'].max()
-		event_time_col = 'event_time_temp'
-		suffix = ''
-
-	for tid, group in neigh_table.groupby(groupbycols):
-
-		group = group.dropna(subset=neigh_col)
-		indices = list(group.index)
-
-		event_time_values = group[event_time_col].to_numpy()
-		if len(event_time_values) > 0:
-			event_time = event_time_values[0]
-		else:
-			continue
-
-		if event_time is not None and (event_time >= 0.):
-
-			if 'intermediate' in metrics:
-				valid_counts_intermediate = group.loc[
-					group['FRAME'] > event_time, 'intermediate_count_s1_' + neigh_col].to_numpy()
-				if len(valid_counts_intermediate[valid_counts_intermediate == valid_counts_intermediate]) > 0:
-					neigh_table.loc[indices, f'mean_count_intermediate_{neigh_col}{suffix}'] = np.nanmean(
-						valid_counts_intermediate)
-			if 'inclusive' in metrics:
-				valid_counts_inclusive = group.loc[
-					group['FRAME'] > event_time, 'inclusive_count_s1_' + neigh_col].to_numpy()
-				if len(valid_counts_inclusive[valid_counts_inclusive == valid_counts_inclusive]) > 0:
-					neigh_table.loc[indices, f'mean_count_inclusive_{neigh_col}{suffix}'] = np.nanmean(
-						valid_counts_inclusive)
-			if 'exclusive' in metrics:
-				valid_counts_exclusive = group.loc[
-					group['FRAME'] > event_time, 'exclusive_count_s1_' + neigh_col].to_numpy()
-				if len(valid_counts_exclusive[valid_counts_exclusive == valid_counts_exclusive]) > 0:
-					neigh_table.loc[indices, f'mean_count_exclusive_{neigh_col}{suffix}'] = np.nanmean(
-						valid_counts_exclusive)
-
-	if event_time_col == 'event_time_temp':
-		neigh_table = neigh_table.drop(columns='event_time_temp')
-
-	return neigh_table
+    """
+    Updates the live status for cells in two datasets based on specified status columns and options.
+
+    This function assigns a live status to cells in two datasets (setA and setB) based on the provided
+    status columns and options. If no status column is provided, all cells are marked as live. Otherwise,
+    the function updates the datasets based on the status criteria, potentially inverting the status
+    based on the `not_status_option`.
+
+    Parameters
+    ----------
+    setA : pandas.DataFrame
+            The first dataset containing trajectory or position information for cells.
+    setB : pandas.DataFrame
+            The second dataset containing trajectory or position information for cells.
+    status : list or None
+            A list containing the names of the columns in setA and setB that classify cells as alive (1) or dead (0).
+            If None, all cells are considered alive. The list should contain exactly two elements.
+    not_status_option : list
+            A list containing boolean values indicating whether to invert the status for setA and setB, respectively.
+            True means the status should be inverted; False means it should not.
+
+    Returns
+    -------
+    tuple
+            A tuple containing the updated setA and setB DataFrames, along with the final status column names
+            used to classify cells in each set.
+
+    """
+
+    print(f"Provided statuses: {status}...")
+    if (
+        status is None
+        or status == ["live_status", "live_status"]
+        or status == [None, None]
+    ):
+        setA.loc[:, "live_status"] = 1
+        setB.loc[:, "live_status"] = 1
+        status = ["live_status", "live_status"]
+    elif isinstance(status, list):
+        assert (
+            len(status) == 2
+        ), "Please provide only two columns to classify cells as alive or dead."
+        if status[0] is None or status[0] == "live_status":
+            setA.loc[:, "live_status"] = 1
+            status[0] = "live_status"
+        elif status[0] is not None and isinstance(not_status_option, list):
+            setA.loc[setA[status[0]] == 2, status[0]] = (
+                1  # already happened events become event
+            )
+            if not_status_option[0]:
+                setA.loc[:, "not_" + status[0]] = [
+                    not a if a == 0 or a == 1 else np.nan
+                    for a in setA.loc[:, status[0]].values
+                ]
+                status[0] = "not_" + status[0]
+        if status[1] is None or status[1] == "live_status":
+            setB.loc[:, "live_status"] = 1
+            status[1] = "live_status"
+        elif status[1] is not None and isinstance(not_status_option, list):
+            setB.loc[setB[status[1]] == 2, status[1]] = (
+                1  # already happened events become event
+            )
+            if not_status_option[1]:
+                setB.loc[:, "not_" + status[1]] = [
+                    not a if a == 0 or a == 1 else np.nan
+                    for a in setB.loc[:, status[1]].values
+                ]
+                status[1] = "not_" + status[1]
+
+        assert status[0] in list(setA.columns)
+        assert status[1] in list(setB.columns)
+
+    setA = setA.reset_index(drop=True)
+    setB = setB.reset_index(drop=True)
+
+    return setA, setB, status
+
+
+def compute_attention_weight(
+    dist_matrix,
+    cut_distance,
+    opposite_cell_status,
+    opposite_cell_ids,
+    axis=1,
+    include_dead_weight=True,
+):
+    """
+    Computes the attention weight for each cell based on its proximity to cells of an opposite type within a specified distance.
+
+    This function calculates the attention weight for cells by considering the distance to the cells of an opposite type
+    within a given cutoff distance. It optionally considers only the 'live' opposite cells based on their status. The function
+    returns two arrays: one containing the attention weights and another containing the IDs of the closest opposite cells.
+
+    Parameters
+    ----------
+    dist_matrix : ndarray
+            A 2D array representing the distance matrix between cells of two types.
+    cut_distance : float
+            The cutoff distance within which opposite cells will influence the attention weight.
+    opposite_cell_status : ndarray
+            An array indicating the status (e.g., live or dead) of each opposite cell. Only used when `include_dead_weight` is False.
+    opposite_cell_ids : ndarray
+            An array containing the IDs of the opposite cells.
+    axis : int, optional
+            The axis along which to compute the weights (default is 1). Axis 0 corresponds to rows, and axis 1 corresponds to columns.
+    include_dead_weight : bool, optional
+            If True, includes all opposite cells within the cutoff distance in the weight calculation, regardless of their status.
+            If False, only considers opposite cells that are 'live' (default is True).
+
+    Returns
+    -------
+    tuple of ndarrays
+            A tuple containing two arrays: `weights` and `closest_opposite`. `weights` is an array of attention weights for each cell,
+            and `closest_opposite` is an array of the IDs of the closest opposite cells within the cutoff distance.
+
+    """
+
+    weights = np.empty(dist_matrix.shape[axis])
+    closest_opposite = np.empty(dist_matrix.shape[axis])
+
+    for i in range(dist_matrix.shape[axis]):
+        if axis == 1:
+            row = dist_matrix[:, i]
+        elif axis == 0:
+            row = dist_matrix[i, :]
+        row[row == 0.0] = 1.0e06
+        nbr_opposite = len(row[row <= cut_distance])
+
+        if not include_dead_weight:
+            stat = opposite_cell_status[np.where(row <= cut_distance)[0]]
+            nbr_opposite = len(stat[stat == 1])
+            index_subpop = np.argmin(row[opposite_cell_status == 1])
+            closest_opposite[i] = opposite_cell_ids[opposite_cell_status == 1][
+                index_subpop
+            ]
+        else:
+            closest_opposite[i] = opposite_cell_ids[np.argmin(row)]
+
+        if nbr_opposite > 0:
+            weight = 1.0 / float(nbr_opposite)
+            weights[i] = weight
+
+    return weights, closest_opposite
+
+
+def distance_cut_neighborhood(
+    setA,
+    setB,
+    distance,
+    mode="two-pop",
+    status=None,
+    not_status_option=None,
+    compute_cum_sum=True,
+    attention_weight=True,
+    symmetrize=True,
+    include_dead_weight=True,
+    column_labels={
+        "track": "TRACK_ID",
+        "time": "FRAME",
+        "x": "POSITION_X",
+        "y": "POSITION_Y",
+    },
+):
+    """
+
+    Match neighbors in set A and B within a circle of radius d.
+
+    Parameters
+    ----------
+    setA,setB : pandas DataFrame
+            Trajectory or position sets A and B.
+    distance : float
+            Cut-distance in pixels to match neighboring pairs.
+    mode: str
+            neighboring mode, between 'two-pop' (e.g. target-effector) and 'self' (target-target or effector-effector).
+    status: None or status
+            name to look for cells to ignore (because they are dead). By default all cells are kept.
+    compute_cum_sum: bool,
+            compute cumulated time of presence of neighbours (only if trajectories available for both sets)
+    attention_weight: bool,
+            compute the attention weight (how much a cell of set B is shared across cells of set A)
+    symmetrize: bool,
+            write in set B the neighborhood of set A
+    include_dead_weight: bool
+            do not count dead cells when establishing attention weight
+    """
+
+    # Check live_status option
+    if setA is not None and setB is not None:
+        setA, setB, status = set_live_status(setA, setB, status, not_status_option)
+    else:
+        return None, None
+
+    # Check distance option
+    if not isinstance(distance, list):
+        distance = [distance]
+
+    for d in distance:
+        # loop over each provided distance
+
+        if mode == "two-pop":
+            neigh_col = f"neighborhood_2_circle_{d}_px"
+        elif mode == "self":
+            neigh_col = f"neighborhood_self_circle_{d}_px"
+
+        cl = []
+        for s in [setA, setB]:
+
+            # Check whether data can be tracked
+            temp_column_labels = column_labels.copy()
+
+            id_col = extract_identity_col(s)
+            temp_column_labels.update({"track": id_col})
+            if id_col == "ID":
+                compute_cum_sum = (
+                    False  # if no tracking data then cum_sum is not relevant
+                )
+            cl.append(temp_column_labels)
+
+            # Remove nan tracks (cells that do not belong to a track)
+            s[neigh_col] = np.nan
+            s[neigh_col] = s[neigh_col].astype(object)
+            s.dropna(subset=[cl[-1]["track"]], inplace=True)
+
+        # Loop over each available timestep
+        timeline = np.unique(
+            np.concatenate(
+                [setA[cl[0]["time"]].to_numpy(), setB[cl[1]["time"]].to_numpy()]
+            )
+        ).astype(int)
+        for t in tqdm(timeline):
+
+            coordinates_A = setA.loc[
+                setA[cl[0]["time"]] == t, [cl[0]["x"], cl[0]["y"]]
+            ].to_numpy()
+            ids_A = setA.loc[setA[cl[0]["time"]] == t, cl[0]["track"]].to_numpy()
+            status_A = setA.loc[setA[cl[0]["time"]] == t, status[0]].to_numpy()
+
+            coordinates_B = setB.loc[
+                setB[cl[1]["time"]] == t, [cl[1]["x"], cl[1]["y"]]
+            ].to_numpy()
+            ids_B = setB.loc[setB[cl[1]["time"]] == t, cl[1]["track"]].to_numpy()
+
+            if len(ids_A) > 0 and len(ids_B) > 0:
+
+                # compute distance matrix
+                dist_map = cdist(coordinates_A, coordinates_B, metric="euclidean")
+
+                if attention_weight:
+                    weights, closest_A = compute_attention_weight(
+                        dist_map,
+                        d,
+                        status_A,
+                        ids_A,
+                        axis=1,
+                        include_dead_weight=include_dead_weight,
+                    )
+
+                _fill_distance_neighborhood_at_t(
+                    t,
+                    setA,
+                    setB,
+                    dist_map,
+                    attention_weight=attention_weight,
+                    include_dead_weight=include_dead_weight,
+                    symmetrize=symmetrize,
+                    compute_cum_sum=compute_cum_sum,
+                    weights=weights,
+                    closest_A=closest_A,
+                    neigh_col=neigh_col,
+                    column_labelsA=cl[0],
+                    column_labelsB=cl[1],
+                    statusA=status[0],
+                    statusB=status[1],
+                    distance=d,
+                )
+
+    return setA, setB
+
+
+def compute_neighborhood_at_position(
+    pos,
+    distance,
+    population=["targets", "effectors"],
+    theta_dist=None,
+    img_shape=(2048, 2048),
+    return_tables=False,
+    clear_neigh=False,
+    event_time_col=None,
+    neighborhood_kwargs={
+        "mode": "two-pop",
+        "status": None,
+        "not_status_option": None,
+        "include_dead_weight": True,
+        "compute_cum_sum": False,
+        "attention_weight": True,
+        "symmetrize": True,
+    },
+):
+    """
+    Computes neighborhood metrics for specified cell populations within a given position, based on distance criteria and additional parameters.
+
+    This function assesses the neighborhood interactions between two specified cell populations (or within a single population) at a given position.
+    It computes various neighborhood metrics based on specified distances, considering the entire image or excluding edge regions.
+    The results are optionally cleared of previous neighborhood calculations and can be returned as updated tables.
+
+    Parameters
+    ----------
+    pos : str
+            The path to the position directory where the analysis is to be performed.
+    distance : float or list of float
+            The distance(s) in pixels to define neighborhoods.
+    population : list of str, optional
+            Names of the cell populations to analyze. If a single population is provided, it is used for both populations in the analysis (default is ['targets', 'effectors']).
+    theta_dist : float or list of float, optional
+            Edge threshold(s) in pixels to exclude cells close to the image boundaries from the analysis. If not provided, defaults to 90% of each specified distance.
+    img_shape : tuple of int, optional
+            The dimensions (height, width) of the images in pixels (default is (2048, 2048)).
+    return_tables : bool, optional
+            If True, returns the updated data tables for both populations (default is False).
+    clear_neigh : bool, optional
+            If True, clears existing neighborhood columns from the data tables before computing new metrics (default is False).
+    event_time_col : str, optional
+            The column name indicating the event time for each cell, required if mean neighborhood metrics are to be computed before events.
+    neighborhood_kwargs : dict, optional
+            Additional keyword arguments for neighborhood computation, including mode, status options, and metrics (default includes mode 'two-pop', and symmetrization).
+
+    Returns
+    -------
+    pandas.DataFrame or (pandas.DataFrame, pandas.DataFrame)
+            If `return_tables` is True, returns the updated data tables for the specified populations. If only one population is analyzed, both returned data frames will be identical.
+
+    Raises
+    ------
+    AssertionError
+            If the specified position path does not exist or if the number of distances and edge thresholds do not match.
+
+    """
+
+    pos = pos.replace("\\", "/")
+    pos = rf"{pos}"
+    assert os.path.exists(pos), f"Position {pos} is not a valid path."
+
+    if isinstance(population, str):
+        population = [population, population]
+
+    if not isinstance(distance, list):
+        distance = [distance]
+    if not theta_dist is None and not isinstance(theta_dist, list):
+        theta_dist = [theta_dist]
+
+    if theta_dist is None:
+        theta_dist = [0.9 * d for d in distance]
+    assert len(theta_dist) == len(
+        distance
+    ), "Incompatible number of distances and number of edge thresholds."
+
+    if population[0] == population[1]:
+        neighborhood_kwargs.update({"mode": "self"})
+    if population[1] != population[0]:
+        neighborhood_kwargs.update({"mode": "two-pop"})
+
+    df_A, path_A = get_position_table(pos, population=population[0], return_path=True)
+    df_B, path_B = get_position_table(pos, population=population[1], return_path=True)
+    if df_A is None or df_B is None:
+        return None
+
+    if clear_neigh:
+        if os.path.exists(path_A.replace(".csv", ".pkl")):
+            os.remove(path_A.replace(".csv", ".pkl"))
+        if os.path.exists(path_B.replace(".csv", ".pkl")):
+            os.remove(path_B.replace(".csv", ".pkl"))
+        df_pair, pair_path = get_position_table(
+            pos, population="pairs", return_path=True
+        )
+        if df_pair is not None:
+            os.remove(pair_path)
+
+    df_A_pkl = get_position_pickle(pos, population=population[0], return_path=False)
+    df_B_pkl = get_position_pickle(pos, population=population[1], return_path=False)
+
+    if df_A_pkl is not None:
+        pkl_columns = np.array(df_A_pkl.columns)
+        neigh_columns = np.array([c.startswith("neighborhood") for c in pkl_columns])
+        cols = list(pkl_columns[neigh_columns]) + ["FRAME"]
+
+        id_col = extract_identity_col(df_A_pkl)
+        cols.append(id_col)
+        on_cols = [id_col, "FRAME"]
+
+        print(f"Recover {cols} from the pickle file...")
+        try:
+            df_A = pd.merge(df_A, df_A_pkl.loc[:, cols], how="outer", on=on_cols)
+            print(df_A.columns)
+        except Exception as e:
+            print(f"Failure to merge pickle and csv files: {e}")
+
+    if df_B_pkl is not None and df_B is not None:
+        pkl_columns = np.array(df_B_pkl.columns)
+        neigh_columns = np.array([c.startswith("neighborhood") for c in pkl_columns])
+        cols = list(pkl_columns[neigh_columns]) + ["FRAME"]
+
+        id_col = extract_identity_col(df_B_pkl)
+        cols.append(id_col)
+        on_cols = [id_col, "FRAME"]
+
+        print(f"Recover {cols} from the pickle file...")
+        try:
+            df_B = pd.merge(df_B, df_B_pkl.loc[:, cols], how="outer", on=on_cols)
+        except Exception as e:
+            print(f"Failure to merge pickle and csv files: {e}")
+
+    if clear_neigh:
+        unwanted = df_A.columns[df_A.columns.str.contains("neighborhood")]
+        df_A = df_A.drop(columns=unwanted)
+        unwanted = df_B.columns[df_B.columns.str.contains("neighborhood")]
+        df_B = df_B.drop(columns=unwanted)
+
+    df_A, df_B = distance_cut_neighborhood(df_A, df_B, distance, **neighborhood_kwargs)
+
+    if df_A is None or df_B is None or len(df_A) == 0:
+        return None
+
+    for td, d in zip(theta_dist, distance):
+
+        if neighborhood_kwargs["mode"] == "two-pop":
+            neigh_col = f"neighborhood_2_circle_{d}_px"
+
+        elif neighborhood_kwargs["mode"] == "self":
+            neigh_col = f"neighborhood_self_circle_{d}_px"
+
+        # edge_filter_A = (df_A['POSITION_X'] > td)&(df_A['POSITION_Y'] > td)&(df_A['POSITION_Y'] < (img_shape[0] - td))&(df_A['POSITION_X'] < (img_shape[1] - td))
+        # edge_filter_B = (df_B['POSITION_X'] > td)&(df_B['POSITION_Y'] > td)&(df_B['POSITION_Y'] < (img_shape[0] - td))&(df_B['POSITION_X'] < (img_shape[1] - td))
+        # df_A.loc[~edge_filter_A, neigh_col] = np.nan
+        # df_B.loc[~edge_filter_B, neigh_col] = np.nan
+
+        print("Count neighborhood...")
+        df_A = compute_neighborhood_metrics(
+            df_A,
+            neigh_col,
+            metrics=["inclusive", "exclusive", "intermediate"],
+            decompose_by_status=True,
+        )
+        # if neighborhood_kwargs['symmetrize']:
+        # 	df_B = compute_neighborhood_metrics(df_B, neigh_col, metrics=['inclusive','exclusive','intermediate'], decompose_by_status=True)
+        print("Done...")
+
+        if "TRACK_ID" in list(df_A.columns):
+            if not np.all(df_A["TRACK_ID"].isnull()):
+                print("Estimate average neighborhood before/after event...")
+                df_A = mean_neighborhood_before_event(df_A, neigh_col, event_time_col)
+                if event_time_col is not None:
+                    df_A = mean_neighborhood_after_event(
+                        df_A, neigh_col, event_time_col
+                    )
+                print("Done...")
+
+    if not population[0] == population[1]:
+        # Remove neighborhood column from neighbor table, rename with actual population name
+        for td, d in zip(theta_dist, distance):
+            if neighborhood_kwargs["mode"] == "two-pop":
+                neigh_col = f"neighborhood_2_circle_{d}_px"
+                new_neigh_col = neigh_col.replace(
+                    "_2_", f"_({population[0]}-{population[1]})_"
+                )
+                df_A = df_A.rename(columns={neigh_col: new_neigh_col})
+            elif neighborhood_kwargs["mode"] == "self":
+                neigh_col = f"neighborhood_self_circle_{d}_px"
+            df_B = df_B.drop(columns=[neigh_col])
+        df_B.to_pickle(path_B.replace(".csv", ".pkl"))
+
+    cols_to_rename = [
+        c
+        for c in list(df_A.columns)
+        if c.startswith("intermediate_count_")
+        or c.startswith("inclusive_count_")
+        or c.startswith("exclusive_count_")
+        or c.startswith("mean_count_")
+    ]
+    new_col_names = [
+        c.replace("_2_", f"_({population[0]}-{population[1]})_") for c in cols_to_rename
+    ]
+    new_name_map = {}
+    for k, c in enumerate(cols_to_rename):
+        new_name_map.update({c: new_col_names[k]})
+    df_A = df_A.rename(columns=new_name_map)
+
+    df_A.to_pickle(path_A.replace(".csv", ".pkl"))
+
+    unwanted = df_A.columns[df_A.columns.str.startswith("neighborhood_")]
+    df_A2 = df_A.drop(columns=unwanted)
+    df_A2.to_csv(path_A, index=False)
+
+    if not population[0] == population[1]:
+        unwanted = df_B.columns[df_B.columns.str.startswith("neighborhood_")]
+        df_B_csv = df_B.drop(unwanted, axis=1, inplace=False)
+        df_B_csv.to_csv(path_B, index=False)
+
+    if return_tables:
+        return df_A, df_B
+
+
+def compute_neighborhood_metrics(
+    neigh_table,
+    neigh_col,
+    metrics=["inclusive", "exclusive", "intermediate"],
+    decompose_by_status=False,
+):
+    """
+    Computes and appends neighborhood metrics to a dataframe based on specified neighborhood characteristics.
+
+    This function iterates through a dataframe grouped by either 'TRACK_ID' or ['position', 'TRACK_ID'] (if 'position' column exists)
+    and computes various neighborhood metrics (inclusive, exclusive, intermediate counts) for each cell. It can also decompose these
+    metrics by cell status (e.g., live or dead) if specified.
+
+    Parameters
+    ----------
+    neigh_table : pandas.DataFrame
+            A dataframe containing neighborhood information for each cell, including position, track ID, frame, and a specified neighborhood column.
+    neigh_col : str
+            The column name in `neigh_table` that contains neighborhood information (e.g., a list of neighbors with their attributes).
+    metrics : list of str, optional
+            The metrics to be computed from the neighborhood information. Possible values include 'inclusive', 'exclusive', and 'intermediate'.
+            Default is ['inclusive', 'exclusive', 'intermediate'].
+    decompose_by_status : bool, optional
+            If True, the metrics are computed separately for different statuses (e.g., live or dead) of the neighboring cells. Default is False.
+
+    Returns
+    -------
+    pandas.DataFrame
+            The input dataframe with additional columns for each of the specified metrics, and, if `decompose_by_status` is True, separate
+            metrics for each status.
+
+    Notes
+    -----
+    - 'inclusive' count refers to the total number of neighbors.
+    - 'exclusive' count refers to the number of neighbors that are closest.
+    - 'intermediate' count refers to the sum of weights attributed to neighbors, representing a weighted count.
+    - If `decompose_by_status` is True, metrics are appended with '_s0' or '_s1' to indicate the status they correspond to.
+
+    Examples
+    --------
+    >>> neigh_table = pd.DataFrame({
+    ...     'TRACK_ID': [1, 1, 2, 2],
+    ...     'FRAME': [1, 2, 1, 2],
+    ...     'neighborhood_info': [{'weight': 1, 'status': 1, 'closest': 1}, ...]  # example neighborhood info
+    ... })
+    >>> neigh_col = 'neighborhood_info'
+    >>> updated_neigh_table = compute_neighborhood_metrics(neigh_table, neigh_col, metrics=['inclusive'], decompose_by_status=True)
+    # Computes the inclusive count of neighbors for each cell, decomposed by cell status.
+
+    """
+
+    neigh_table = neigh_table.reset_index(drop=True)
+    if "position" in list(neigh_table.columns):
+        groupbycols = ["position"]
+    else:
+        groupbycols = []
+
+    id_col = extract_identity_col(neigh_table)
+    groupbycols.append(id_col)
+
+    neigh_table.sort_values(by=groupbycols + ["FRAME"], inplace=True)
+
+    for tid, group in neigh_table.groupby(groupbycols):
+        group = group.dropna(subset=neigh_col)
+        indices = list(group.index)
+        neighbors = group[neigh_col].to_numpy()
+
+        if "inclusive" in metrics:
+            n_inclusive = [len(n) for n in neighbors]
+
+        if "intermediate" in metrics:
+            n_intermediate = np.zeros(len(neighbors))
+            n_intermediate[:] = np.nan
+
+        if "exclusive" in metrics:
+            n_exclusive = np.zeros(len(neighbors))
+            n_exclusive[:] = np.nan
+
+        if decompose_by_status:
+
+            if "inclusive" in metrics:
+                n_inclusive_status_0 = np.zeros(len(neighbors))
+                n_inclusive_status_0[:] = np.nan
+                n_inclusive_status_1 = np.zeros(len(neighbors))
+                n_inclusive_status_1[:] = np.nan
+
+            if "intermediate" in metrics:
+                n_intermediate_status_0 = np.zeros(len(neighbors))
+                n_intermediate_status_0[:] = np.nan
+                n_intermediate_status_1 = np.zeros(len(neighbors))
+                n_intermediate_status_1[:] = np.nan
+
+            if "exclusive" in metrics:
+                n_exclusive_status_0 = np.zeros(len(neighbors))
+                n_exclusive_status_0[:] = np.nan
+                n_exclusive_status_1 = np.zeros(len(neighbors))
+                n_exclusive_status_1[:] = np.nan
+
+        for t in range(len(neighbors)):
+
+            neighs_at_t = neighbors[t]
+            weights_at_t = [n["weight"] for n in neighs_at_t]
+            status_at_t = [n["status"] for n in neighs_at_t]
+            closest_at_t = [n["closest"] for n in neighs_at_t]
+
+            if "intermediate" in metrics:
+                n_intermediate[t] = np.sum(weights_at_t)
+            if "exclusive" in metrics:
+                n_exclusive[t] = sum([c == 1.0 for c in closest_at_t])
+
+            if decompose_by_status:
+
+                if "inclusive" in metrics:
+                    n_inclusive_status_0[t] = sum([s == 0.0 for s in status_at_t])
+                    n_inclusive_status_1[t] = sum([s == 1.0 for s in status_at_t])
+
+                if "intermediate" in metrics:
+                    weights_at_t = np.array(weights_at_t)
+
+                    # intermediate
+                    weights_status_1 = weights_at_t[
+                        np.array([s == 1.0 for s in status_at_t], dtype=bool)
+                    ]
+                    weights_status_0 = weights_at_t[
+                        np.array([s == 0.0 for s in status_at_t], dtype=bool)
+                    ]
+                    n_intermediate_status_1[t] = np.sum(weights_status_1)
+                    n_intermediate_status_0[t] = np.sum(weights_status_0)
+
+                if "exclusive" in metrics:
+                    n_exclusive_status_0[t] = sum(
+                        [
+                            c == 1.0 if s == 0.0 else False
+                            for c, s in zip(closest_at_t, status_at_t)
+                        ]
+                    )
+                    n_exclusive_status_1[t] = sum(
+                        [
+                            c == 1.0 if s == 1.0 else False
+                            for c, s in zip(closest_at_t, status_at_t)
+                        ]
+                    )
+
+        if "inclusive" in metrics:
+            neigh_table.loc[indices, "inclusive_count_" + neigh_col] = n_inclusive
+        if "intermediate" in metrics:
+            neigh_table.loc[indices, "intermediate_count_" + neigh_col] = n_intermediate
+        if "exclusive" in metrics:
+            neigh_table.loc[indices, "exclusive_count_" + neigh_col] = n_exclusive
+
+        if decompose_by_status:
+            if "inclusive" in metrics:
+                neigh_table.loc[indices, "inclusive_count_s0_" + neigh_col] = (
+                    n_inclusive_status_0
+                )
+                neigh_table.loc[indices, "inclusive_count_s1_" + neigh_col] = (
+                    n_inclusive_status_1
+                )
+            if "intermediate" in metrics:
+                neigh_table.loc[indices, "intermediate_count_s0_" + neigh_col] = (
+                    n_intermediate_status_0
+                )
+                neigh_table.loc[indices, "intermediate_count_s1_" + neigh_col] = (
+                    n_intermediate_status_1
+                )
+            if "exclusive" in metrics:
+                neigh_table.loc[indices, "exclusive_count_s0_" + neigh_col] = (
+                    n_exclusive_status_0
+                )
+                neigh_table.loc[indices, "exclusive_count_s1_" + neigh_col] = (
+                    n_exclusive_status_1
+                )
+
+    return neigh_table
+
+
+def mean_neighborhood_before_event(
+    neigh_table,
+    neigh_col,
+    event_time_col,
+    metrics=["inclusive", "exclusive", "intermediate"],
+):
+    """
+    Computes the mean neighborhood metrics for each cell track before a specified event time.
+
+    This function calculates the mean values of specified neighborhood metrics (inclusive, exclusive, intermediate)
+    for each cell track up to and including the frame of an event. The function requires the neighborhood metrics to
+    have been previously computed and appended to the input dataframe. It operates on grouped data based on position
+    and track ID, handling cases with or without position information.
+
+    Parameters
+    ----------
+    neigh_table : pandas.DataFrame
+            A dataframe containing cell track data with precomputed neighborhood metrics and event time information.
+    neigh_col : str
+            The base name of the neighborhood metric columns in `neigh_table`.
+    event_time_col : str or None
+            The column name indicating the event time for each cell track. If None, the maximum frame number in the
+            dataframe is used as the event time for all tracks.
+
+    Returns
+    -------
+    pandas.DataFrame
+            The input dataframe with added columns for the mean neighborhood metrics before the event for each cell track.
+            The new columns are named as 'mean_count_{metric}_{neigh_col}_before_event', where {metric} is one of
+            'inclusive', 'exclusive', 'intermediate'.
+
+    """
+
+    neigh_table = neigh_table.reset_index(drop=True)
+    if "position" in list(neigh_table.columns):
+        groupbycols = ["position"]
+    else:
+        groupbycols = []
+
+    id_col = extract_identity_col(neigh_table)
+    groupbycols.append(id_col)
+
+    neigh_table.sort_values(by=groupbycols + ["FRAME"], inplace=True)
+    suffix = "_before_event"
+
+    if event_time_col is None:
+        print(
+            "No event time was provided... Estimating the mean neighborhood over the whole observation time..."
+        )
+        neigh_table.loc[:, "event_time_temp"] = neigh_table["FRAME"].max()
+        event_time_col = "event_time_temp"
+        suffix = ""
+
+    for tid, group in neigh_table.groupby(groupbycols):
+
+        group = group.dropna(subset=neigh_col)
+        indices = list(group.index)
+
+        event_time_values = group[event_time_col].to_numpy()
+        if len(event_time_values) > 0:
+            event_time = event_time_values[0]
+        else:
+            continue
+
+        if event_time < 0.0:
+            event_time = group["FRAME"].max()
+
+        if "intermediate" in metrics:
+            valid_counts_intermediate = group.loc[
+                group["FRAME"] <= event_time, "intermediate_count_s1_" + neigh_col
+            ].to_numpy()
+            if (
+                len(
+                    valid_counts_intermediate[
+                        valid_counts_intermediate == valid_counts_intermediate
+                    ]
+                )
+                > 0
+            ):
+                neigh_table.loc[
+                    indices, f"mean_count_intermediate_{neigh_col}{suffix}"
+                ] = np.nanmean(valid_counts_intermediate)
+        if "inclusive" in metrics:
+            valid_counts_inclusive = group.loc[
+                group["FRAME"] <= event_time, "inclusive_count_s1_" + neigh_col
+            ].to_numpy()
+            if (
+                len(
+                    valid_counts_inclusive[
+                        valid_counts_inclusive == valid_counts_inclusive
+                    ]
+                )
+                > 0
+            ):
+                neigh_table.loc[
+                    indices, f"mean_count_inclusive_{neigh_col}{suffix}"
+                ] = np.nanmean(valid_counts_inclusive)
+        if "exclusive" in metrics:
+            valid_counts_exclusive = group.loc[
+                group["FRAME"] <= event_time, "exclusive_count_s1_" + neigh_col
+            ].to_numpy()
+            if (
+                len(
+                    valid_counts_exclusive[
+                        valid_counts_exclusive == valid_counts_exclusive
+                    ]
+                )
+                > 0
+            ):
+                neigh_table.loc[
+                    indices, f"mean_count_exclusive_{neigh_col}{suffix}"
+                ] = np.nanmean(valid_counts_exclusive)
+
+    if event_time_col == "event_time_temp":
+        neigh_table = neigh_table.drop(columns="event_time_temp")
+    return neigh_table
+
+
+def mean_neighborhood_after_event(
+    neigh_table,
+    neigh_col,
+    event_time_col,
+    metrics=["inclusive", "exclusive", "intermediate"],
+):
+    """
+    Computes the mean neighborhood metrics for each cell track after a specified event time.
+
+    This function calculates the mean values of specified neighborhood metrics (inclusive, exclusive, intermediate)
+    for each cell track after the event time. The function requires the neighborhood metrics to
+    have been previously computed and appended to the input dataframe. It operates on grouped data based on position
+    and track ID, handling cases with or without position information.
+
+    Parameters
+    ----------
+    neigh_table : pandas.DataFrame
+            A dataframe containing cell track data with precomputed neighborhood metrics and event time information.
+    neigh_col : str
+            The base name of the neighborhood metric columns in `neigh_table`.
+    event_time_col : str or None
+            The column name indicating the event time for each cell track. If None, the maximum frame number in the
+            dataframe is used as the event time for all tracks.
+
+    Returns
+    -------
+    pandas.DataFrame
+            The input dataframe with added columns for the mean neighborhood metrics before the event for each cell track.
+            The new columns are named as 'mean_count_{metric}_{neigh_col}_before_event', where {metric} is one of
+            'inclusive', 'exclusive', 'intermediate'.
+
+    """
+
+    neigh_table = neigh_table.reset_index(drop=True)
+    if "position" in list(neigh_table.columns):
+        groupbycols = ["position"]
+    else:
+        groupbycols = []
+
+    id_col = extract_identity_col(neigh_table)
+    groupbycols.append(id_col)
+
+    neigh_table.sort_values(by=groupbycols + ["FRAME"], inplace=True)
+    suffix = "_after_event"
+
+    if event_time_col is None:
+        neigh_table.loc[:, "event_time_temp"] = None  # neigh_table['FRAME'].max()
+        event_time_col = "event_time_temp"
+        suffix = ""
+
+    for tid, group in neigh_table.groupby(groupbycols):
+
+        group = group.dropna(subset=neigh_col)
+        indices = list(group.index)
+
+        event_time_values = group[event_time_col].to_numpy()
+        if len(event_time_values) > 0:
+            event_time = event_time_values[0]
+        else:
+            continue
+
+        if event_time is not None and (event_time >= 0.0):
+
+            if "intermediate" in metrics:
+                valid_counts_intermediate = group.loc[
+                    group["FRAME"] > event_time, "intermediate_count_s1_" + neigh_col
+                ].to_numpy()
+                if (
+                    len(
+                        valid_counts_intermediate[
+                            valid_counts_intermediate == valid_counts_intermediate
+                        ]
+                    )
+                    > 0
+                ):
+                    neigh_table.loc[
+                        indices, f"mean_count_intermediate_{neigh_col}{suffix}"
+                    ] = np.nanmean(valid_counts_intermediate)
+            if "inclusive" in metrics:
+                valid_counts_inclusive = group.loc[
+                    group["FRAME"] > event_time, "inclusive_count_s1_" + neigh_col
+                ].to_numpy()
+                if (
+                    len(
+                        valid_counts_inclusive[
+                            valid_counts_inclusive == valid_counts_inclusive
+                        ]
+                    )
+                    > 0
+                ):
+                    neigh_table.loc[
+                        indices, f"mean_count_inclusive_{neigh_col}{suffix}"
+                    ] = np.nanmean(valid_counts_inclusive)
+            if "exclusive" in metrics:
+                valid_counts_exclusive = group.loc[
+                    group["FRAME"] > event_time, "exclusive_count_s1_" + neigh_col
+                ].to_numpy()
+                if (
+                    len(
+                        valid_counts_exclusive[
+                            valid_counts_exclusive == valid_counts_exclusive
+                        ]
+                    )
+                    > 0
+                ):
+                    neigh_table.loc[
+                        indices, f"mean_count_exclusive_{neigh_col}{suffix}"
+                    ] = np.nanmean(valid_counts_exclusive)
+
+    if event_time_col == "event_time_temp":
+        neigh_table = neigh_table.drop(columns="event_time_temp")
+
+    return neigh_table
 
 
 # New functions for direct cell-cell contact neighborhood
 
+
 def sign(num):
-	return -1 if num < 0 else 1
+    return -1 if num < 0 else 1
 
 
 def contact_neighborhood(labelsA, labelsB=None, border=3, connectivity=2):
 
-	labelsA = labelsA.astype(float)
-	if labelsB is not None:
-		labelsB = labelsB.astype(float)
-
-	if border > 0:
-		labelsA_edge = contour_of_instance_segmentation(label=labelsA, distance=border * (-1)).astype(float)
-		labelsA[np.where(labelsA_edge > 0)] = labelsA_edge[np.where(labelsA_edge > 0)]
-		if labelsB is not None:
-			labelsB_edge = contour_of_instance_segmentation(label=labelsB, distance=border * (-1)).astype(float)
-			labelsB[np.where(labelsB_edge > 0)] = labelsB_edge[np.where(labelsB_edge > 0)]
-
-	if labelsB is not None:
-		labelsA[labelsA != 0] = -labelsA[labelsA != 0]
-		labelsAB = merge_labels(labelsA, labelsB)
-		labelsBA = merge_labels(labelsB, labelsA)
-		label_cases = [labelsAB, labelsBA]
-	else:
-		label_cases = [labelsA]
-
-	coocurrences = []
-	for lbl in label_cases:
-		coocurrences.extend(find_contact_neighbors(lbl, connectivity=connectivity))
-
-	unique_pairs = np.unique(coocurrences, axis=0)
+    labelsA = labelsA.astype(float)
+    if labelsB is not None:
+        labelsB = labelsB.astype(float)
+
+    if border > 0:
+        labelsA_edge = contour_of_instance_segmentation(
+            label=labelsA, distance=border * (-1)
+        ).astype(float)
+        labelsA[np.where(labelsA_edge > 0)] = labelsA_edge[np.where(labelsA_edge > 0)]
+        if labelsB is not None:
+            labelsB_edge = contour_of_instance_segmentation(
+                label=labelsB, distance=border * (-1)
+            ).astype(float)
+            labelsB[np.where(labelsB_edge > 0)] = labelsB_edge[
+                np.where(labelsB_edge > 0)
+            ]
+
+    if labelsB is not None:
+        labelsA[labelsA != 0] = -labelsA[labelsA != 0]
+        labelsAB = merge_labels(labelsA, labelsB)
+        labelsBA = merge_labels(labelsB, labelsA)
+        label_cases = [labelsAB, labelsBA]
+    else:
+        label_cases = [labelsA]
+
+    coocurrences = []
+    for lbl in label_cases:
+        coocurrences.extend(find_contact_neighbors(lbl, connectivity=connectivity))
+
+    unique_pairs = np.unique(coocurrences, axis=0)
+
+    if labelsB is not None:
+        neighs = np.unique(
+            [
+                tuple(sorted(p))
+                for p in unique_pairs
+                if p[0] != p[1] and sign(p[0]) != sign(p[1])
+            ],
+            axis=0,
+        )
+    else:
+        neighs = np.unique(
+            [tuple(sorted(p)) for p in unique_pairs if p[0] != p[1]], axis=0
+        )
+
+    return neighs
 
-	if labelsB is not None:
-		neighs = np.unique([tuple(sorted(p)) for p in unique_pairs if p[0] != p[1] and sign(p[0]) != sign(p[1])],
-						   axis=0)
-	else:
-		neighs = np.unique([tuple(sorted(p)) for p in unique_pairs if p[0] != p[1]], axis=0)
-
-	return neighs
 
 def merge_labels(labelsA, labelsB):
 
-	labelsA = labelsA.astype(float)
-	labelsB = labelsB.astype(float)
+    labelsA = labelsA.astype(float)
+    labelsB = labelsB.astype(float)
 
-	labelsAB = labelsA.copy()
-	labelsAB[np.where(labelsB != 0)] = labelsB[np.where(labelsB != 0)]
+    labelsAB = labelsA.copy()
+    labelsAB[np.where(labelsB != 0)] = labelsB[np.where(labelsB != 0)]
 
-	return labelsAB
+    return labelsAB
 
 
 def find_contact_neighbors(labels, connectivity=2):
-	
-	assert labels.ndim == 2, "Wrong dimension for labels..."
-	g, nodes = pixel_graph(labels, mask=labels.astype(bool), connectivity=connectivity)
-	g.eliminate_zeros()
-
-	coo = g.tocoo()
-	center_coords = nodes[coo.row]
-	neighbor_coords = nodes[coo.col]
-
-	center_values = labels.ravel()[center_coords]
-	neighbor_values = labels.ravel()[neighbor_coords]
-	touching_masks = np.column_stack((center_values, neighbor_values))
-
-	return touching_masks
-
-
-def mask_contact_neighborhood(setA, setB, labelsA, labelsB, distance, mode='two-pop', status=None,
-							  not_status_option=None, compute_cum_sum=True,
-							  attention_weight=True, symmetrize=True, include_dead_weight=True,
-							  column_labels={'track': "TRACK_ID", 'time': 'FRAME', 'x': 'POSITION_X', 'y': 'POSITION_Y',
-											 'mask_id': 'class_id'}):
-	"""
-
-	Match neighbors in set A and B within a circle of radius d.
-
-	Parameters
-	----------
-	setA,setB : pandas DataFrame
-		Trajectory or position sets A and B.
-	distance : float
-		Cut-distance in pixels to match neighboring pairs.
-	mode: str
-		neighboring mode, between 'two-pop' (e.g. target-effector) and 'self' (target-target or effector-effector).
-	status: None or status
-		name to look for cells to ignore (because they are dead). By default all cells are kept.
-	compute_cum_sum: bool,
-		compute cumulated time of presence of neighbours (only if trajectories available for both sets)
-	attention_weight: bool,
-		compute the attention weight (how much a cell of set B is shared across cells of set A)
-	symmetrize: bool,
-		write in set B the neighborhood of set A
-	include_dead_weight: bool
-		do not count dead cells when establishing attention weight
-	"""
-
-	if setA is not None and setB is not None:
-		setA, setB, status = set_live_status(setA, setB, status, not_status_option)
-	else:
-		return None, None
-
-	# Check distance option
-	if not isinstance(distance, list):
-		distance = [distance]
-
-	cl = []
-	for s in [setA, setB]:
-
-		# Check whether data can be tracked
-		temp_column_labels = column_labels.copy()
-
-		id_col = extract_identity_col(s)
-		temp_column_labels.update({'track': id_col})
-		if id_col=='ID':
-			compute_cum_sum = False
-		
-		cl.append(temp_column_labels)
-	
-	setA = setA.loc[~setA[cl[0]['track']].isnull(),:].copy()
-	setB = setB.loc[~setB[cl[1]['track']].isnull(),:].copy()
-
-	if labelsB is None:
-		labelsB = [None] * len(labelsA)
-
-	for d in distance:
-		# loop over each provided distance
-
-		if mode == 'two-pop':
-			neigh_col = f'neighborhood_2_contact_{d}_px'
-		elif mode == 'self':
-			neigh_col = f'neighborhood_self_contact_{d}_px'
-		else:
-			print("Please provide a valid mode between `two-pop` and `self`...")
-			return None
-
-		setA[neigh_col] = np.nan
-		setA[neigh_col] = setA[neigh_col].astype(object)
-
-		setB[neigh_col] = np.nan
-		setB[neigh_col] = setB[neigh_col].astype(object)
-
-		# Loop over each available timestep
-		timeline = np.unique(np.concatenate([setA[cl[0]['time']].to_numpy(), setB[cl[1]['time']].to_numpy()])).astype(
-			int)
-		for t in tqdm(timeline):
-
-			setA_t = setA.loc[setA[cl[0]['time']] == t, :]
-			setB_t = setB.loc[setB[cl[1]['time']] == t, :]
-
-			if len(setA_t) > 0 and len(setB_t) > 0:
-				dist_map, intersection_map = _compute_mask_contact_dist_map(setA_t, setB_t, labelsA[t], labelsB[t],
-																			distance=d, mode=mode, column_labelsA=cl[0],
-																			column_labelsB=cl[1])
-
-				d_filter = 1.0E05
-				if attention_weight:
-					status_A = setA_t[status[0]].to_numpy()
-					ids_A = setA_t[cl[0]["track"]].to_numpy()
-					weights, closest_A = compute_attention_weight(dist_map, d_filter, status_A, ids_A, axis=1,
-																  include_dead_weight=include_dead_weight)
-				else:
-					weights = None
-					closest_A = None
-
-				_fill_contact_neighborhood_at_t(t, setA, setB, dist_map, intersection_map=intersection_map,
-												attention_weight=attention_weight,
-												include_dead_weight=include_dead_weight, symmetrize=symmetrize,
-												compute_cum_sum=compute_cum_sum, weights=weights, closest_A=closest_A,
-												neigh_col=neigh_col, column_labelsA=cl[0], column_labelsB=cl[1],
-												statusA=status[0], statusB=status[1], d_filter=d_filter)
-
-	return setA, setB
-
-
-def compute_contact_neighborhood_at_position(pos, distance, population=['targets', 'effectors'], theta_dist=None,
-											 img_shape=(2048, 2048), return_tables=False, clear_neigh=False,
-											 event_time_col=None,
-											 neighborhood_kwargs={'mode': 'two-pop', 'status': None,
-																  'not_status_option': None,
-																  'include_dead_weight': True, "compute_cum_sum": False,
-																  "attention_weight": True, 'symmetrize': True}):
-	"""
-	Computes neighborhood metrics for specified cell populations within a given position, based on distance criteria and additional parameters.
-
-	This function assesses the neighborhood interactions between two specified cell populations (or within a single population) at a given position.
-	It computes various neighborhood metrics based on specified distances, considering the entire image or excluding edge regions.
-	The results are optionally cleared of previous neighborhood calculations and can be returned as updated tables.
-
-	Parameters
-	----------
-	pos : str
-		The path to the position directory where the analysis is to be performed.
-	distance : float or list of float
-		The distance(s) in pixels to define neighborhoods.
-	population : list of str, optional
-		Names of the cell populations to analyze. If a single population is provided, it is used for both populations in the analysis (default is ['targets', 'effectors']).
-	theta_dist : float or list of float, optional
-		Edge threshold(s) in pixels to exclude cells close to the image boundaries from the analysis. If not provided, defaults to 90% of each specified distance.
-	img_shape : tuple of int, optional
-		The dimensions (height, width) of the images in pixels (default is (2048, 2048)).
-	return_tables : bool, optional
-		If True, returns the updated data tables for both populations (default is False).
-	clear_neigh : bool, optional
-		If True, clears existing neighborhood columns from the data tables before computing new metrics (default is False).
-	event_time_col : str, optional
-		The column name indicating the event time for each cell, required if mean neighborhood metrics are to be computed before events.
-	neighborhood_kwargs : dict, optional
-		Additional keyword arguments for neighborhood computation, including mode, status options, and metrics (default includes mode 'two-pop', and symmetrization).
-
-	Returns
-	-------
-	pandas.DataFrame or (pandas.DataFrame, pandas.DataFrame)
-		If `return_tables` is True, returns the updated data tables for the specified populations. If only one population is analyzed, both returned data frames will be identical.
-
-	Raises
-	------
-	AssertionError
-		If the specified position path does not exist or if the number of distances and edge thresholds do not match.
-
-	"""
-
-	pos = pos.replace('\\', '/')
-	pos = rf"{pos}"
-	assert os.path.exists(pos), f'Position {pos} is not a valid path.'
-
-	if isinstance(population, str):
-		population = [population, population]
-
-	if not isinstance(distance, list):
-		distance = [distance]
-	if not theta_dist is None and not isinstance(theta_dist, list):
-		theta_dist = [theta_dist]
-
-	if theta_dist is None:
-		theta_dist = [0 for d in distance]  # 0.9*d
-	assert len(theta_dist) == len(distance), 'Incompatible number of distances and number of edge thresholds.'
-
-	if population[0] == population[1]:
-		neighborhood_kwargs.update({'mode': 'self'})
-	if population[1] != population[0]:
-		neighborhood_kwargs.update({'mode': 'two-pop'})
-
-	df_A, path_A = get_position_table(pos, population=population[0], return_path=True)
-	df_B, path_B = get_position_table(pos, population=population[1], return_path=True)
-	if df_A is None or df_B is None:
-		return None
-
-	if clear_neigh:
-		if os.path.exists(path_A.replace('.csv','.pkl')):
-			os.remove(path_A.replace('.csv','.pkl'))
-		if os.path.exists(path_B.replace('.csv','.pkl')):
-			os.remove(path_B.replace('.csv','.pkl'))
-		df_pair, pair_path = get_position_table(pos, population='pairs', return_path=True)
-		if df_pair is not None:
-			os.remove(pair_path)
-
-	df_A_pkl = get_position_pickle(pos, population=population[0], return_path=False)
-	df_B_pkl = get_position_pickle(pos, population=population[1], return_path=False)
-
-	if df_A_pkl is not None:
-		pkl_columns = np.array(df_A_pkl.columns)
-		neigh_columns = np.array([c.startswith('neighborhood') for c in pkl_columns])
-		cols = list(pkl_columns[neigh_columns]) + ['FRAME']
-		
-		id_col = extract_identity_col(df_A_pkl)
-		cols.append(id_col)
-		on_cols = [id_col, 'FRAME']
-
-		print(f'Recover {cols} from the pickle file...')
-		try:
-			df_A = pd.merge(df_A, df_A_pkl.loc[:,cols], how="outer", on=on_cols)
-			print(df_A.columns)
-		except Exception as e:
-			print(f'Failure to merge pickle and csv files: {e}')
-
-	if df_B_pkl is not None and df_B is not None:
-		pkl_columns = np.array(df_B_pkl.columns)
-		neigh_columns = np.array([c.startswith('neighborhood') for c in pkl_columns])
-		cols = list(pkl_columns[neigh_columns]) + ['FRAME']
-
-		id_col = extract_identity_col(df_B_pkl)
-		cols.append(id_col)
-		on_cols = [id_col, 'FRAME']
-
-		print(f'Recover {cols} from the pickle file...')
-		try:
-			df_B = pd.merge(df_B, df_B_pkl.loc[:,cols], how="outer", on=on_cols)
-		except Exception as e:
-			print(f'Failure to merge pickle and csv files: {e}')
-
-	labelsA = locate_labels(pos, population=population[0])
-	if population[1] == population[0]:
-		labelsB = None
-	else:
-		labelsB = locate_labels(pos, population=population[1])
-
-	if clear_neigh:
-		unwanted = df_A.columns[df_A.columns.str.contains('neighborhood')]
-		df_A = df_A.drop(columns=unwanted)
-		unwanted = df_B.columns[df_B.columns.str.contains('neighborhood')]
-		df_B = df_B.drop(columns=unwanted)
-
-	print(f"Distance: {distance} for mask contact")
-	df_A, df_B = mask_contact_neighborhood(df_A, df_B, labelsA, labelsB, distance, **neighborhood_kwargs)
-	if df_A is None or df_B is None or len(df_A)==0:
-		return None
-
-	for td, d in zip(theta_dist, distance):
-
-		if neighborhood_kwargs['mode'] == 'two-pop':
-			neigh_col = f'neighborhood_2_contact_{d}_px'
-		elif neighborhood_kwargs['mode'] == 'self':
-			neigh_col = f'neighborhood_self_contact_{d}_px'
-
-		df_A.loc[df_A['class_id'].isnull(),neigh_col] = np.nan
-
-		# edge_filter_A = (df_A['POSITION_X'] > td)&(df_A['POSITION_Y'] > td)&(df_A['POSITION_Y'] < (img_shape[0] - td))&(df_A['POSITION_X'] < (img_shape[1] - td))
-		# edge_filter_B = (df_B['POSITION_X'] > td)&(df_B['POSITION_Y'] > td)&(df_B['POSITION_Y'] < (img_shape[0] - td))&(df_B['POSITION_X'] < (img_shape[1] - td))
-		# df_A.loc[~edge_filter_A, neigh_col] = np.nan
-		# df_B.loc[~edge_filter_B, neigh_col] = np.nan
-
-		df_A = compute_neighborhood_metrics(df_A, neigh_col, metrics=['inclusive', 'intermediate'],
-											decompose_by_status=True)
-		if 'TRACK_ID' in list(df_A.columns):
-			if not np.all(df_A['TRACK_ID'].isnull()):
-				df_A = mean_neighborhood_before_event(df_A, neigh_col, event_time_col, metrics=['inclusive','intermediate'])
-				if event_time_col is not None:
-					df_A = mean_neighborhood_after_event(df_A, neigh_col, event_time_col, metrics=['inclusive', 'intermediate'])
-				print('Done...')
-				
-	if not population[0] == population[1]:
-		# Remove neighborhood column from neighbor table, rename with actual population name
-		for td, d in zip(theta_dist, distance):
-			if neighborhood_kwargs['mode'] == 'two-pop':
-				neigh_col = f'neighborhood_2_contact_{d}_px'
-				new_neigh_col = neigh_col.replace('_2_',f'_({population[0]}-{population[1]})_')
-				df_A = df_A.rename(columns={neigh_col: new_neigh_col})
-			elif neighborhood_kwargs['mode'] == 'self':
-				neigh_col = f'neighborhood_self_contact_{d}_px'
-			df_B = df_B.drop(columns=[neigh_col])
-		df_B.to_pickle(path_B.replace('.csv', '.pkl'))
-
-	cols_to_rename = [c for c in list(df_A.columns) if c.startswith('intermediate_count_') or c.startswith('inclusive_count_') or c.startswith('exclusive_count_') or c.startswith('mean_count_')]
-	new_col_names = [c.replace('_2_',f'_({population[0]}-{population[1]})_') for c in cols_to_rename]
-	new_name_map = {}
-	for k,c in enumerate(cols_to_rename):
-		new_name_map.update({c: new_col_names[k]})
-	df_A = df_A.rename(columns=new_name_map)
-
-	print(f'{df_A.columns=}')
-	df_A.to_pickle(path_A.replace('.csv', '.pkl'))
-
-	unwanted = df_A.columns[df_A.columns.str.startswith('neighborhood_')]
-	df_A2 = df_A.drop(columns=unwanted)
-	df_A2.to_csv(path_A, index=False)
-
-	if not population[0] == population[1]:
-		unwanted = df_B.columns[df_B.columns.str.startswith('neighborhood_')]
-		df_B_csv = df_B.drop(unwanted, axis=1, inplace=False)
-		df_B_csv.to_csv(path_B, index=False)
-
-	if return_tables:
-		return df_A, df_B
-
-
-def extract_neighborhood_in_pair_table(df, distance=None, reference_population="targets", neighbor_population="effectors",  mode="circle", neighborhood_key=None, contact_only=True,):
-
-	"""
-	Extracts data from a pair table that matches specific neighborhood criteria based on reference and neighbor 
-	populations, distance, and mode of neighborhood computation (e.g., circular or contact-based).
-
-	Parameters
-	----------
-	df : pandas.DataFrame
-		DataFrame containing the pair table, which includes columns for 'reference_population', 'neighbor_population', 
-		and a column for neighborhood status.
-	distance : int, optional
-		Radius in pixels for neighborhood calculation, used only if `neighborhood_key` is not provided.
-	reference_population : str, default="targets"
-		The reference population to consider. Must be either "targets" or "effectors".
-	neighbor_population : str, default="effectors"
-		The neighbor population to consider. Must be either "targets" or "effectors", used only if `neighborhood_key` is not provided.
-	mode : str, default="circle"
-		Neighborhood computation mode. Options are "circle" for radius-based or "contact" for contact-based neighborhood, used only if `neighborhood_key` is not provided.
-	neighborhood_key : str, optional
-		A precomputed neighborhood key to identify specific neighborhoods. If provided, this key overrides `distance`, 
-		`mode`, and `neighbor_population`.
-	contact_only : bool, default=True
-		If True, only rows indicating contact with the neighbor population (status=1) are kept; if False, both 
-		contact (status=1) and no-contact (status=0) rows are included.
-
-	Returns
-	-------
-	pandas.DataFrame
-		Filtered DataFrame containing rows that meet the specified neighborhood criteria.
-
-	Notes
-	-----
-	- When `neighborhood_key` is None, the neighborhood column is generated based on the provided `reference_population`, 
-	  `neighbor_population`, `distance`, and `mode`.
-	- The function uses `status_<neigh_col>` to filter rows based on `contact_only` criteria.
-	- Ensures that `reference_population` and `neighbor_population` are valid inputs and consistent with the neighborhood 
-	  mode and key.
-
-	Example
-	-------
-	>>> neighborhood_data = extract_neighborhood_in_pair_table(df, distance=50, reference_population="targets", 
-															   neighbor_population="effectors", mode="circle")
-	>>> neighborhood_data.head()
-
-	Raises
-	------
-	AssertionError
-		If `reference_population` or `neighbor_population` is not valid, or if the required neighborhood status 
-		column does not exist in `df`.
-	"""
-
-
-	#assert reference_population in ["targets", "effectors"], "Please set a valid reference population ('targets' or 'effectors')"
-	if neighborhood_key is None:
-		#assert neighbor_population in ["targets", "effectors"], "Please set a valid neighbor population ('targets' or 'effectors')"
-		assert mode in ["circle", "contact"], "Please set a valid neighborhood computation mode ('circle' or 'contact')"
-		type = '('+'-'.join([reference_population, neighbor_population])+')'
-		neigh_col = f"neighborhood_{type}_{mode}_{distance}_px"
-	else:
-		neigh_col = neighborhood_key.replace('status_','')
-		if '_(' in neigh_col and ')_' in neigh_col:
-			neighbor_population = neigh_col.split('_(')[-1].split(')_')[0].split('-')[-1]
-		else:
-			if 'self' in neigh_col:
-				neighbor_population = reference_population
-			else:
-				if reference_population=="effectors":
-					neighbor_population='targets'
-				else:
-					neighbor_population='effectors'
-
-	assert "status_"+neigh_col in list(df.columns),"The selected neighborhood does not appear in the data..."
-
-	print(df[['reference_population','neighbor_population', "status_"+neigh_col]])
-
-	if contact_only:
-		s_keep = [1]
-	else:
-		s_keep = [0,1]
-
-	data = df.loc[(df['reference_population']==reference_population)&(df['neighbor_population']==neighbor_population)&(df["status_"+neigh_col].isin(s_keep))]
-
-	return data
+
+    assert labels.ndim == 2, "Wrong dimension for labels..."
+    g, nodes = pixel_graph(labels, mask=labels.astype(bool), connectivity=connectivity)
+    g.eliminate_zeros()
+
+    coo = g.tocoo()
+    center_coords = nodes[coo.row]
+    neighbor_coords = nodes[coo.col]
+
+    center_values = labels.ravel()[center_coords]
+    neighbor_values = labels.ravel()[neighbor_coords]
+    touching_masks = np.column_stack((center_values, neighbor_values))
+
+    return touching_masks
+
+
+def mask_contact_neighborhood(
+    setA,
+    setB,
+    labelsA,
+    labelsB,
+    distance,
+    mode="two-pop",
+    status=None,
+    not_status_option=None,
+    compute_cum_sum=True,
+    attention_weight=True,
+    symmetrize=True,
+    include_dead_weight=True,
+    column_labels={
+        "track": "TRACK_ID",
+        "time": "FRAME",
+        "x": "POSITION_X",
+        "y": "POSITION_Y",
+        "mask_id": "class_id",
+    },
+):
+    """
+
+    Match neighbors in set A and B within a circle of radius d.
+
+    Parameters
+    ----------
+    setA,setB : pandas DataFrame
+            Trajectory or position sets A and B.
+    distance : float
+            Cut-distance in pixels to match neighboring pairs.
+    mode: str
+            neighboring mode, between 'two-pop' (e.g. target-effector) and 'self' (target-target or effector-effector).
+    status: None or status
+            name to look for cells to ignore (because they are dead). By default all cells are kept.
+    compute_cum_sum: bool,
+            compute cumulated time of presence of neighbours (only if trajectories available for both sets)
+    attention_weight: bool,
+            compute the attention weight (how much a cell of set B is shared across cells of set A)
+    symmetrize: bool,
+            write in set B the neighborhood of set A
+    include_dead_weight: bool
+            do not count dead cells when establishing attention weight
+    """
+
+    if setA is not None and setB is not None:
+        setA, setB, status = set_live_status(setA, setB, status, not_status_option)
+    else:
+        return None, None
+
+    # Check distance option
+    if not isinstance(distance, list):
+        distance = [distance]
+
+    cl = []
+    for s in [setA, setB]:
+
+        # Check whether data can be tracked
+        temp_column_labels = column_labels.copy()
+
+        id_col = extract_identity_col(s)
+        temp_column_labels.update({"track": id_col})
+        if id_col == "ID":
+            compute_cum_sum = False
+
+        cl.append(temp_column_labels)
+
+    setA = setA.loc[~setA[cl[0]["track"]].isnull(), :].copy()
+    setB = setB.loc[~setB[cl[1]["track"]].isnull(), :].copy()
+
+    if labelsB is None:
+        labelsB = [None] * len(labelsA)
+
+    for d in distance:
+        # loop over each provided distance
+
+        if mode == "two-pop":
+            neigh_col = f"neighborhood_2_contact_{d}_px"
+        elif mode == "self":
+            neigh_col = f"neighborhood_self_contact_{d}_px"
+        else:
+            print("Please provide a valid mode between `two-pop` and `self`...")
+            return None
+
+        setA[neigh_col] = np.nan
+        setA[neigh_col] = setA[neigh_col].astype(object)
+
+        setB[neigh_col] = np.nan
+        setB[neigh_col] = setB[neigh_col].astype(object)
+
+        # Loop over each available timestep
+        timeline = np.unique(
+            np.concatenate(
+                [setA[cl[0]["time"]].to_numpy(), setB[cl[1]["time"]].to_numpy()]
+            )
+        ).astype(int)
+        for t in tqdm(timeline):
+
+            setA_t = setA.loc[setA[cl[0]["time"]] == t, :]
+            setB_t = setB.loc[setB[cl[1]["time"]] == t, :]
+
+            if len(setA_t) > 0 and len(setB_t) > 0:
+                dist_map, intersection_map = _compute_mask_contact_dist_map(
+                    setA_t,
+                    setB_t,
+                    labelsA[t],
+                    labelsB[t],
+                    distance=d,
+                    mode=mode,
+                    column_labelsA=cl[0],
+                    column_labelsB=cl[1],
+                )
+
+                d_filter = 1.0e05
+                if attention_weight:
+                    status_A = setA_t[status[0]].to_numpy()
+                    ids_A = setA_t[cl[0]["track"]].to_numpy()
+                    weights, closest_A = compute_attention_weight(
+                        dist_map,
+                        d_filter,
+                        status_A,
+                        ids_A,
+                        axis=1,
+                        include_dead_weight=include_dead_weight,
+                    )
+                else:
+                    weights = None
+                    closest_A = None
+
+                _fill_contact_neighborhood_at_t(
+                    t,
+                    setA,
+                    setB,
+                    dist_map,
+                    intersection_map=intersection_map,
+                    attention_weight=attention_weight,
+                    include_dead_weight=include_dead_weight,
+                    symmetrize=symmetrize,
+                    compute_cum_sum=compute_cum_sum,
+                    weights=weights,
+                    closest_A=closest_A,
+                    neigh_col=neigh_col,
+                    column_labelsA=cl[0],
+                    column_labelsB=cl[1],
+                    statusA=status[0],
+                    statusB=status[1],
+                    d_filter=d_filter,
+                )
+
+    return setA, setB
+
+
+def compute_contact_neighborhood_at_position(
+    pos,
+    distance,
+    population=["targets", "effectors"],
+    theta_dist=None,
+    img_shape=(2048, 2048),
+    return_tables=False,
+    clear_neigh=False,
+    event_time_col=None,
+    neighborhood_kwargs={
+        "mode": "two-pop",
+        "status": None,
+        "not_status_option": None,
+        "include_dead_weight": True,
+        "compute_cum_sum": False,
+        "attention_weight": True,
+        "symmetrize": True,
+    },
+):
+    """
+    Computes neighborhood metrics for specified cell populations within a given position, based on distance criteria and additional parameters.
+
+    This function assesses the neighborhood interactions between two specified cell populations (or within a single population) at a given position.
+    It computes various neighborhood metrics based on specified distances, considering the entire image or excluding edge regions.
+    The results are optionally cleared of previous neighborhood calculations and can be returned as updated tables.
+
+    Parameters
+    ----------
+    pos : str
+            The path to the position directory where the analysis is to be performed.
+    distance : float or list of float
+            The distance(s) in pixels to define neighborhoods.
+    population : list of str, optional
+            Names of the cell populations to analyze. If a single population is provided, it is used for both populations in the analysis (default is ['targets', 'effectors']).
+    theta_dist : float or list of float, optional
+            Edge threshold(s) in pixels to exclude cells close to the image boundaries from the analysis. If not provided, defaults to 90% of each specified distance.
+    img_shape : tuple of int, optional
+            The dimensions (height, width) of the images in pixels (default is (2048, 2048)).
+    return_tables : bool, optional
+            If True, returns the updated data tables for both populations (default is False).
+    clear_neigh : bool, optional
+            If True, clears existing neighborhood columns from the data tables before computing new metrics (default is False).
+    event_time_col : str, optional
+            The column name indicating the event time for each cell, required if mean neighborhood metrics are to be computed before events.
+    neighborhood_kwargs : dict, optional
+            Additional keyword arguments for neighborhood computation, including mode, status options, and metrics (default includes mode 'two-pop', and symmetrization).
+
+    Returns
+    -------
+    pandas.DataFrame or (pandas.DataFrame, pandas.DataFrame)
+            If `return_tables` is True, returns the updated data tables for the specified populations. If only one population is analyzed, both returned data frames will be identical.
+
+    Raises
+    ------
+    AssertionError
+            If the specified position path does not exist or if the number of distances and edge thresholds do not match.
+
+    """
+
+    pos = pos.replace("\\", "/")
+    pos = rf"{pos}"
+    assert os.path.exists(pos), f"Position {pos} is not a valid path."
+
+    if isinstance(population, str):
+        population = [population, population]
+
+    if not isinstance(distance, list):
+        distance = [distance]
+    if not theta_dist is None and not isinstance(theta_dist, list):
+        theta_dist = [theta_dist]
+
+    if theta_dist is None:
+        theta_dist = [0 for d in distance]  # 0.9*d
+    assert len(theta_dist) == len(
+        distance
+    ), "Incompatible number of distances and number of edge thresholds."
+
+    if population[0] == population[1]:
+        neighborhood_kwargs.update({"mode": "self"})
+    if population[1] != population[0]:
+        neighborhood_kwargs.update({"mode": "two-pop"})
+
+    df_A, path_A = get_position_table(pos, population=population[0], return_path=True)
+    df_B, path_B = get_position_table(pos, population=population[1], return_path=True)
+    if df_A is None or df_B is None:
+        return None
+
+    if clear_neigh:
+        if os.path.exists(path_A.replace(".csv", ".pkl")):
+            os.remove(path_A.replace(".csv", ".pkl"))
+        if os.path.exists(path_B.replace(".csv", ".pkl")):
+            os.remove(path_B.replace(".csv", ".pkl"))
+        df_pair, pair_path = get_position_table(
+            pos, population="pairs", return_path=True
+        )
+        if df_pair is not None:
+            os.remove(pair_path)
+
+    df_A_pkl = get_position_pickle(pos, population=population[0], return_path=False)
+    df_B_pkl = get_position_pickle(pos, population=population[1], return_path=False)
+
+    if df_A_pkl is not None:
+        pkl_columns = np.array(df_A_pkl.columns)
+        neigh_columns = np.array([c.startswith("neighborhood") for c in pkl_columns])
+        cols = list(pkl_columns[neigh_columns]) + ["FRAME"]
+
+        id_col = extract_identity_col(df_A_pkl)
+        cols.append(id_col)
+        on_cols = [id_col, "FRAME"]
+
+        print(f"Recover {cols} from the pickle file...")
+        try:
+            df_A = pd.merge(df_A, df_A_pkl.loc[:, cols], how="outer", on=on_cols)
+            print(df_A.columns)
+        except Exception as e:
+            print(f"Failure to merge pickle and csv files: {e}")
+
+    if df_B_pkl is not None and df_B is not None:
+        pkl_columns = np.array(df_B_pkl.columns)
+        neigh_columns = np.array([c.startswith("neighborhood") for c in pkl_columns])
+        cols = list(pkl_columns[neigh_columns]) + ["FRAME"]
+
+        id_col = extract_identity_col(df_B_pkl)
+        cols.append(id_col)
+        on_cols = [id_col, "FRAME"]
+
+        print(f"Recover {cols} from the pickle file...")
+        try:
+            df_B = pd.merge(df_B, df_B_pkl.loc[:, cols], how="outer", on=on_cols)
+        except Exception as e:
+            print(f"Failure to merge pickle and csv files: {e}")
+
+    labelsA = locate_labels(pos, population=population[0])
+    if population[1] == population[0]:
+        labelsB = None
+    else:
+        labelsB = locate_labels(pos, population=population[1])
+
+    if clear_neigh:
+        unwanted = df_A.columns[df_A.columns.str.contains("neighborhood")]
+        df_A = df_A.drop(columns=unwanted)
+        unwanted = df_B.columns[df_B.columns.str.contains("neighborhood")]
+        df_B = df_B.drop(columns=unwanted)
+
+    print(f"Distance: {distance} for mask contact")
+    df_A, df_B = mask_contact_neighborhood(
+        df_A, df_B, labelsA, labelsB, distance, **neighborhood_kwargs
+    )
+    if df_A is None or df_B is None or len(df_A) == 0:
+        return None
+
+    for td, d in zip(theta_dist, distance):
+
+        if neighborhood_kwargs["mode"] == "two-pop":
+            neigh_col = f"neighborhood_2_contact_{d}_px"
+        elif neighborhood_kwargs["mode"] == "self":
+            neigh_col = f"neighborhood_self_contact_{d}_px"
+
+        df_A.loc[df_A["class_id"].isnull(), neigh_col] = np.nan
+
+        # edge_filter_A = (df_A['POSITION_X'] > td)&(df_A['POSITION_Y'] > td)&(df_A['POSITION_Y'] < (img_shape[0] - td))&(df_A['POSITION_X'] < (img_shape[1] - td))
+        # edge_filter_B = (df_B['POSITION_X'] > td)&(df_B['POSITION_Y'] > td)&(df_B['POSITION_Y'] < (img_shape[0] - td))&(df_B['POSITION_X'] < (img_shape[1] - td))
+        # df_A.loc[~edge_filter_A, neigh_col] = np.nan
+        # df_B.loc[~edge_filter_B, neigh_col] = np.nan
+
+        df_A = compute_neighborhood_metrics(
+            df_A,
+            neigh_col,
+            metrics=["inclusive", "intermediate"],
+            decompose_by_status=True,
+        )
+        if "TRACK_ID" in list(df_A.columns):
+            if not np.all(df_A["TRACK_ID"].isnull()):
+                df_A = mean_neighborhood_before_event(
+                    df_A,
+                    neigh_col,
+                    event_time_col,
+                    metrics=["inclusive", "intermediate"],
+                )
+                if event_time_col is not None:
+                    df_A = mean_neighborhood_after_event(
+                        df_A,
+                        neigh_col,
+                        event_time_col,
+                        metrics=["inclusive", "intermediate"],
+                    )
+                print("Done...")
+
+    if not population[0] == population[1]:
+        # Remove neighborhood column from neighbor table, rename with actual population name
+        for td, d in zip(theta_dist, distance):
+            if neighborhood_kwargs["mode"] == "two-pop":
+                neigh_col = f"neighborhood_2_contact_{d}_px"
+                new_neigh_col = neigh_col.replace(
+                    "_2_", f"_({population[0]}-{population[1]})_"
+                )
+                df_A = df_A.rename(columns={neigh_col: new_neigh_col})
+            elif neighborhood_kwargs["mode"] == "self":
+                neigh_col = f"neighborhood_self_contact_{d}_px"
+            df_B = df_B.drop(columns=[neigh_col])
+        df_B.to_pickle(path_B.replace(".csv", ".pkl"))
+
+    cols_to_rename = [
+        c
+        for c in list(df_A.columns)
+        if c.startswith("intermediate_count_")
+        or c.startswith("inclusive_count_")
+        or c.startswith("exclusive_count_")
+        or c.startswith("mean_count_")
+    ]
+    new_col_names = [
+        c.replace("_2_", f"_({population[0]}-{population[1]})_") for c in cols_to_rename
+    ]
+    new_name_map = {}
+    for k, c in enumerate(cols_to_rename):
+        new_name_map.update({c: new_col_names[k]})
+    df_A = df_A.rename(columns=new_name_map)
+
+    print(f"{df_A.columns=}")
+    df_A.to_pickle(path_A.replace(".csv", ".pkl"))
+
+    unwanted = df_A.columns[df_A.columns.str.startswith("neighborhood_")]
+    df_A2 = df_A.drop(columns=unwanted)
+    df_A2.to_csv(path_A, index=False)
+
+    if not population[0] == population[1]:
+        unwanted = df_B.columns[df_B.columns.str.startswith("neighborhood_")]
+        df_B_csv = df_B.drop(unwanted, axis=1, inplace=False)
+        df_B_csv.to_csv(path_B, index=False)
+
+    if return_tables:
+        return df_A, df_B
+
+
+def extract_neighborhood_in_pair_table(
+    df,
+    distance=None,
+    reference_population="targets",
+    neighbor_population="effectors",
+    mode="circle",
+    neighborhood_key=None,
+    contact_only=True,
+):
+    """
+    Extracts data from a pair table that matches specific neighborhood criteria based on reference and neighbor
+    populations, distance, and mode of neighborhood computation (e.g., circular or contact-based).
+
+    Parameters
+    ----------
+    df : pandas.DataFrame
+            DataFrame containing the pair table, which includes columns for 'reference_population', 'neighbor_population',
+            and a column for neighborhood status.
+    distance : int, optional
+            Radius in pixels for neighborhood calculation, used only if `neighborhood_key` is not provided.
+    reference_population : str, default="targets"
+            The reference population to consider. Must be either "targets" or "effectors".
+    neighbor_population : str, default="effectors"
+            The neighbor population to consider. Must be either "targets" or "effectors", used only if `neighborhood_key` is not provided.
+    mode : str, default="circle"
+            Neighborhood computation mode. Options are "circle" for radius-based or "contact" for contact-based neighborhood, used only if `neighborhood_key` is not provided.
+    neighborhood_key : str, optional
+            A precomputed neighborhood key to identify specific neighborhoods. If provided, this key overrides `distance`,
+            `mode`, and `neighbor_population`.
+    contact_only : bool, default=True
+            If True, only rows indicating contact with the neighbor population (status=1) are kept; if False, both
+            contact (status=1) and no-contact (status=0) rows are included.
+
+    Returns
+    -------
+    pandas.DataFrame
+            Filtered DataFrame containing rows that meet the specified neighborhood criteria.
+
+    Notes
+    -----
+    - When `neighborhood_key` is None, the neighborhood column is generated based on the provided `reference_population`,
+      `neighbor_population`, `distance`, and `mode`.
+    - The function uses `status_<neigh_col>` to filter rows based on `contact_only` criteria.
+    - Ensures that `reference_population` and `neighbor_population` are valid inputs and consistent with the neighborhood
+      mode and key.
+
+    Example
+    -------
+    >>> neighborhood_data = extract_neighborhood_in_pair_table(df, distance=50, reference_population="targets",
+                                                                                                                       neighbor_population="effectors", mode="circle")
+    >>> neighborhood_data.head()
+
+    Raises
+    ------
+    AssertionError
+            If `reference_population` or `neighbor_population` is not valid, or if the required neighborhood status
+            column does not exist in `df`.
+    """
+
+    # assert reference_population in ["targets", "effectors"], "Please set a valid reference population ('targets' or 'effectors')"
+    if neighborhood_key is None:
+        # assert neighbor_population in ["targets", "effectors"], "Please set a valid neighbor population ('targets' or 'effectors')"
+        assert mode in [
+            "circle",
+            "contact",
+        ], "Please set a valid neighborhood computation mode ('circle' or 'contact')"
+        type = "(" + "-".join([reference_population, neighbor_population]) + ")"
+        neigh_col = f"neighborhood_{type}_{mode}_{distance}_px"
+    else:
+        neigh_col = neighborhood_key.replace("status_", "")
+        if "_(" in neigh_col and ")_" in neigh_col:
+            neighbor_population = (
+                neigh_col.split("_(")[-1].split(")_")[0].split("-")[-1]
+            )
+        else:
+            if "self" in neigh_col:
+                neighbor_population = reference_population
+            else:
+                if reference_population == "effectors":
+                    neighbor_population = "targets"
+                else:
+                    neighbor_population = "effectors"
+
+    assert "status_" + neigh_col in list(
+        df.columns
+    ), "The selected neighborhood does not appear in the data..."
+
+    print(df[["reference_population", "neighbor_population", "status_" + neigh_col]])
+
+    if contact_only:
+        s_keep = [1]
+    else:
+        s_keep = [0, 1]
+
+    data = df.loc[
+        (df["reference_population"] == reference_population)
+        & (df["neighbor_population"] == neighbor_population)
+        & (df["status_" + neigh_col].isin(s_keep))
+    ]
+
+    return data
 
 
 # def mask_intersection_neighborhood(setA, labelsA, setB, labelsB, threshold_iou=0.5, viewpoint='B'):
@@ -1467,17 +1922,28 @@ def extract_neighborhood_in_pair_table(df, distance=None, reference_population="
 
 if __name__ == "__main__":
 
-	print('None')
-	pos = "/home/torro/Documents/Experiments/NKratio_Exp/W5/500"
-
-	test, _ = compute_neighborhood_at_position(pos, [62], population=['targets', 'effectors'], theta_dist=None,
-											   img_shape=(2048, 2048), return_tables=True, clear_neigh=True,
-											   neighborhood_kwargs={'mode': 'two-pop', 'status': ['class', None],
-																	'not_status_option': [True, False],
-																	'include_dead_weight': True,
-																	"compute_cum_sum": False, "attention_weight": True,
-																	'symmetrize': False})
-
-	# test = compute_neighborhood_metrics(test, 'neighborhood_self_circle_150_px', metrics=['inclusive','exclusive','intermediate'], decompose_by_status=True)
-	print(test.columns)
-	#print(segment(None,'test'))
+    print("None")
+    pos = "/home/torro/Documents/Experiments/NKratio_Exp/W5/500"
+
+    test, _ = compute_neighborhood_at_position(
+        pos,
+        [62],
+        population=["targets", "effectors"],
+        theta_dist=None,
+        img_shape=(2048, 2048),
+        return_tables=True,
+        clear_neigh=True,
+        neighborhood_kwargs={
+            "mode": "two-pop",
+            "status": ["class", None],
+            "not_status_option": [True, False],
+            "include_dead_weight": True,
+            "compute_cum_sum": False,
+            "attention_weight": True,
+            "symmetrize": False,
+        },
+    )
+
+    # test = compute_neighborhood_metrics(test, 'neighborhood_self_circle_150_px', metrics=['inclusive','exclusive','intermediate'], decompose_by_status=True)
+    print(test.columns)
+    # print(segment(None,'test'))