celldetective 1.3.2__py3-none-any.whl → 1.3.3.post1__py3-none-any.whl

celldetective/measure.py

@@ -15,6 +15,7 @@ import subprocess
 from math import ceil
 
 from skimage.draw import disk as dsk
+from skimage.feature import blob_dog, blob_log
 
 from celldetective.utils import rename_intensity_column, create_patch_mask, remove_redundant_features, \
 	remove_trajectory_measurements, contour_of_instance_segmentation, extract_cols_from_query, step_function, interpolate_nan
@@ -24,6 +25,8 @@ from celldetective.extra_properties import *
 from inspect import getmembers, isfunction
 from skimage.morphology import disk
 
+import matplotlib.pyplot as plt
+
 abs_path = os.sep.join([os.path.split(os.path.dirname(os.path.realpath(__file__)))[0], 'celldetective'])
 
 def measure(stack=None, labels=None, trajectories=None, channel_names=None,
@@ -325,12 +328,7 @@ def measure_features(img, label, features=['area', 'intensity_mean'], channels=N
 			for index, channel in enumerate(channels):
 				if channel == spot_detection['channel']:
 					ind = index
-					blobs = blob_detection(img[:, :, ind], label, diameter=spot_detection['diameter'],
-								   threshold=spot_detection['threshold'])
-					df_spots = pd.DataFrame.from_dict(blobs, orient='index',
-													  columns=['count', 'spot_mean_intensity']).reset_index()
-			# Rename columns
-			df_spots.columns = ['label', 'spot_count', 'spot_mean_intensity']
+					df_spots = blob_detection(img, label, diameter=spot_detection['diameter'],threshold=spot_detection['threshold'], channel_name=spot_detection['channel'], target_channel=ind)
 		
 		if normalisation_list:
 			for norm in normalisation_list:
@@ -362,47 +360,27 @@ def measure_features(img, label, features=['area', 'intensity_mean'], channels=N
 	props = regionprops_table(label, intensity_image=img, properties=feats, extra_properties=extra_props_list)
 	df_props = pd.DataFrame(props)
 	if spot_detection is not None:
-		df_props = df_props.merge(df_spots, how='outer', on='label')
-		df_props['spot_count'] = df_props['spot_count'].replace(np.nan, 0).infer_objects(copy=False)
-		df_props['spot_mean_intensity'] = df_props['spot_mean_intensity'].replace(np.nan, 0).infer_objects(copy=False)
-
-
-
-	# if spot_detection is not None:
-	#     for index, channel in enumerate(channels):
-	#         if channel == spot_detection['channel']:
-	#             ind = index
-	#     blobs = blob_detection(img[:, :, ind], label, diameter=spot_detection['diameter'],
-	#                            threshold=spot_detection['threshold'])
-	#     df_spots = pd.DataFrame.from_dict(blobs, orient='index', columns=['count', 'spot_mean_intensity']).reset_index()
-	#     # Rename columns
-	#     df_spots.columns = ['label', 'spot_count', 'spot_mean_intensity']
-	#     df_props = df_props.merge(df_spots, how='outer', on='label')
-	#     df_props['spot_count'] = df_props['spot_count'].replace(np.nan, 0)
-	#     df_props['spot_mean_intensity'] = df_props['spot_mean_intensity'].replace(np.nan, 0)
-
+		if df_spots is not None:
+			df_props = df_props.merge(df_spots, how='outer', on='label',suffixes=('_delme', ''))
+			df_props = df_props[[c for c in df_props.columns if not c.endswith('_delme')]]
 
 	if border_dist is not None:
 		# automatically drop all non intensity features
 		intensity_features_test = [('intensity' in s and 'centroid' not in s and 'peripheral' not in s) for s in
 								   features]
 		intensity_features = list(np.array(features)[np.array(intensity_features_test)])
-		# intensity_extra = [(s in extra_props_list)for s in intensity_features]
-		# print(intensity_extra)
 		intensity_extra = []
 		for s in intensity_features:
 			if s in extra_props:
 				intensity_extra.append(getattr(extra_properties, s))
 				intensity_features.remove(s)
-		# print(intensity_features)
-		# If no intensity feature was passed still measure mean intensity
+
 		if len(intensity_features) == 0:
 			if verbose:
 				print('No intensity feature was passed... Adding mean intensity for edge measurement...')
 			intensity_features = np.append(intensity_features, 'intensity_mean')
 		intensity_features = list(np.append(intensity_features, 'label'))
 
-		# Remove extra intensity properties from border measurements
 		new_intensity_features = intensity_features.copy()
 		for int_feat in intensity_features:
 			if int_feat in extra_props:
@@ -439,8 +417,9 @@ def measure_features(img, label, features=['area', 'intensity_mean'], channels=N
 	if haralick_options is not None:
 		try:
 			df_haralick = compute_haralick_features(img, label, channels=channels, **haralick_options)
-			df_props = df_props.merge(df_haralick, left_on='label',right_on='cell_id')
-			#df_props = df_props.drop(columns=['cell_label'])
+			df_haralick = df_haralick.rename(columns={"cell_id": "label"})
+			df_props = df_props.merge(df_haralick, how='outer', on='label', suffixes=('_delme', ''))
+			df_props = df_props[[c for c in df_props.columns if not c.endswith('_delme')]]
 		except Exception as e:
 			print(e)
 			pass
@@ -916,67 +895,125 @@ def normalise_by_cell(image, labels, distance=5, model='median', operation='subt
 	return normalised_frame
 
 
-def blob_detection(image, label, threshold, diameter):
-	"""
-	Perform blob detection on an image based on labeled regions.
+def extract_blobs_in_image(image, label, diameter, threshold=0., method="log"):
+	
+	if np.percentile(image.flatten(),99.9)==0.0:
+		return None
 
-	Parameters:
-	- image (numpy.ndarray): The input image data.
-	- label (numpy.ndarray): An array specifying labeled regions in the image.
-	- threshold (float): The threshold value for blob detection.
-	- diameter (float): The expected diameter of blobs.
+	dilated_image = ndimage.grey_dilation(label, footprint=disk(10))
 
-	Returns:
-	- dict: A dictionary containing information about detected blobs.
+	masked_image = image.copy()
+	masked_image[np.where((dilated_image == 0)|(image!=image))] = 0
+	min_sigma = (1 / (1 + math.sqrt(2))) * diameter
+	max_sigma = math.sqrt(2) * min_sigma
+	if method=="dog":
+		blobs = blob_dog(masked_image, threshold=threshold, min_sigma=min_sigma, max_sigma=max_sigma, overlap=0.75)
+	elif method=="log":
+		blobs = blob_log(masked_image, threshold=threshold, min_sigma=min_sigma, max_sigma=max_sigma, overlap=0.75)		
+	# Exclude spots outside of cell masks
+	mask = np.array([label[int(y), int(x)] != 0 for y, x, _ in blobs])
+	if np.any(mask):
+		blobs_filtered = blobs[mask]
+	else:
+		blobs_filtered=[]
 
-	This function performs blob detection on an image based on labeled regions. It iterates over each labeled region
-	and detects blobs within the region using the Difference of Gaussians (DoG) method. Detected blobs are filtered
-	based on the specified threshold and expected diameter. The function returns a dictionary containing the number of
-	detected blobs and their mean intensity for each labeled region.
+	return blobs_filtered
 
-	Example:
-	>>> image = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
-	>>> label = np.array([[0, 1, 1], [2, 2, 0], [3, 3, 0]])
-	>>> threshold = 0.1
-	>>> diameter = 5.0
-	>>> result = blob_detection(image, label, threshold, diameter)
-	>>> print(result)
-	{1: [1, 4.0], 2: [0, nan], 3: [0, nan]}
 
-	Note:
-	- Blobs are detected using the Difference of Gaussians (DoG) method.
-	- Detected blobs are filtered based on the specified threshold and expected diameter.
-	- The returned dictionary contains information about the number of detected blobs and their mean intensity
-	  for each labeled region.
-	"""
-	blob_labels = {}
-	dilated_image = ndimage.grey_dilation(label, footprint=disk(10))
-	for mask_index in np.unique(label):
-		if mask_index == 0:
-			continue
-		removed_background = image.copy()
-		one_mask = label.copy()
-		one_mask[np.where(label != mask_index)] = 0
-		dilated_copy = dilated_image.copy()
-		dilated_copy[np.where(dilated_image != mask_index)] = 0
-		removed_background[np.where(dilated_copy == 0)] = 0
-		min_sigma = (1 / (1 + math.sqrt(2))) * diameter
-		max_sigma = math.sqrt(2) * min_sigma
-		blobs = skimage.feature.blob_dog(removed_background, threshold=threshold, min_sigma=min_sigma,
-										 max_sigma=max_sigma)
-
-		mask = np.array([one_mask[int(y), int(x)] != 0 for y, x, r in blobs])
-		if not np.any(mask):
-			continue
-		blobs_filtered = blobs[mask]
-		binary_blobs = np.zeros_like(label)
-		for blob in blobs_filtered:
-			y, x, r = blob
-			rr, cc = dsk((y, x), r, shape=binary_blobs.shape)
-			binary_blobs[rr, cc] = 1
-		spot_intensity = regionprops_table(binary_blobs, removed_background, ['intensity_mean'])
-		blob_labels[mask_index] = [blobs_filtered.shape[0], spot_intensity['intensity_mean'][0]]
-	return blob_labels
+def blob_detection(image, label, diameter, threshold=0., channel_name=None, target_channel=0, method="log"):
+	
+	image = image[:, :, target_channel].copy()
+	if np.percentile(image.flatten(),99.9)==0.0:
+		return None
+
+	detections = []
+	blobs_filtered = extract_blobs_in_image(image, label, diameter, threshold=threshold)
+
+	for lbl in np.unique(label):
+		if lbl>0:
+			
+			blob_selection = np.array([label[int(y), int(x)] == lbl for y, x, _ in blobs_filtered])
+			if np.any(blob_selection):
+				# if any spot
+				blobs_in_cell = blobs_filtered[blob_selection]
+				n_spots = len(blobs_in_cell)
+				binary_blobs = np.zeros_like(label)
+				for blob in blobs_in_cell:
+					y, x, sig = blob
+					r = np.sqrt(2)*sig
+					rr, cc = dsk((y, x), r, shape=binary_blobs.shape)
+					binary_blobs[rr, cc] = 1    
+				intensity_mean = np.nanmean(image[binary_blobs==1].flatten())
+			else:
+				n_spots = 0
+				intensity_mean = np.nan
+			detections.append({'label': lbl, f'{channel_name}_spot_count': n_spots, f'{channel_name}_mean_spot_intensity': intensity_mean})
+	detections = pd.DataFrame(detections)
+
+	return detections
+
+
+# def blob_detectionv0(image, label, threshold, diameter):
+# 	"""
+# 	Perform blob detection on an image based on labeled regions.
+
+# 	Parameters:
+# 	- image (numpy.ndarray): The input image data.
+# 	- label (numpy.ndarray): An array specifying labeled regions in the image.
+# 	- threshold (float): The threshold value for blob detection.
+# 	- diameter (float): The expected diameter of blobs.
+
+# 	Returns:
+# 	- dict: A dictionary containing information about detected blobs.
+
+# 	This function performs blob detection on an image based on labeled regions. It iterates over each labeled region
+# 	and detects blobs within the region using the Difference of Gaussians (DoG) method. Detected blobs are filtered
+# 	based on the specified threshold and expected diameter. The function returns a dictionary containing the number of
+# 	detected blobs and their mean intensity for each labeled region.
+
+# 	Example:
+# 	>>> image = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
+# 	>>> label = np.array([[0, 1, 1], [2, 2, 0], [3, 3, 0]])
+# 	>>> threshold = 0.1
+# 	>>> diameter = 5.0
+# 	>>> result = blob_detection(image, label, threshold, diameter)
+# 	>>> print(result)
+# 	{1: [1, 4.0], 2: [0, nan], 3: [0, nan]}
+
+# 	Note:
+# 	- Blobs are detected using the Difference of Gaussians (DoG) method.
+# 	- Detected blobs are filtered based on the specified threshold and expected diameter.
+# 	- The returned dictionary contains information about the number of detected blobs and their mean intensity
+# 	  for each labeled region.
+# 	"""
+# 	blob_labels = {}
+# 	dilated_image = ndimage.grey_dilation(label, footprint=disk(10))
+# 	for mask_index in np.unique(label):
+# 		if mask_index == 0:
+# 			continue
+# 		removed_background = image.copy()
+# 		one_mask = label.copy()
+# 		one_mask[np.where(label != mask_index)] = 0
+# 		dilated_copy = dilated_image.copy()
+# 		dilated_copy[np.where(dilated_image != mask_index)] = 0
+# 		removed_background[np.where(dilated_copy == 0)] = 0
+# 		min_sigma = (1 / (1 + math.sqrt(2))) * diameter
+# 		max_sigma = math.sqrt(2) * min_sigma
+# 		blobs = blob_dog(removed_background, threshold=threshold, min_sigma=min_sigma,
+# 										 max_sigma=max_sigma)
+
+# 		mask = np.array([one_mask[int(y), int(x)] != 0 for y, x, r in blobs])
+# 		if not np.any(mask):
+# 			continue
+# 		blobs_filtered = blobs[mask]
+# 		binary_blobs = np.zeros_like(label)
+# 		for blob in blobs_filtered:
+# 			y, x, r = blob
+# 			rr, cc = dsk((y, x), r, shape=binary_blobs.shape)
+# 			binary_blobs[rr, cc] = 1
+# 		spot_intensity = regionprops_table(binary_blobs, removed_background, ['intensity_mean'])
+# 		blob_labels[mask_index] = [blobs_filtered.shape[0], spot_intensity['intensity_mean'][0]]
+# 	return blob_labels
 
 ### Classification ####
 

celldetective/models/segmentation_effectors/ricm_bf_all_last/config_input.json

@@ -0,0 +1,79 @@
+{
+    "channels": [
+        "adhesion_channel",
+        "brightfield_channel"
+    ],
+    "diameter": 30.0,
+    "cellprob_threshold": 0.0,
+    "flow_threshold": 0.4,
+    "normalization_percentile": [
+        false,
+        true
+    ],
+    "normalization_clip": [
+        true,
+        true
+    ],
+    "normalization_values": [
+        [
+            0.75,
+            1.25
+        ],
+        [
+            1.0,
+            99.0
+        ]
+    ],
+    "model_type": "cellpose",
+    "spatial_calibration": 0.2,
+    "dataset": {
+        "train": [
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_404_0066_roi_429_935_159_649.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_200_0003_roi_457_991_5_488.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-11-23-analysis-2024_508_0008.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-11-23-analysis-2024_305_0075.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_302_0063_roi_405_865_462_937.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_506_0066_roi_473_944_494_953.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_202_0027_roi_557_998_3_447.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_208_0027_roi_600_997_5_387.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_206_0023_roi_251_707_249_666.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_201_0017_roi_324_961_23_596.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_102_0053_roi_511_996_4_433.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_403_0009_roi_554_996_460_994.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-11-23-analysis-2024_508_0066.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_507_0066_roi_492_998_9_474.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_202_0029_roi_177_746_4_533.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_203_0060_roi_369_906_119_648.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_304_0025.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_207_0030_roi_152_661_531_998.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_105_0018_roi_510_954_13_422.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_507_0016_roi_29_585_462_996.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_504_0066_roi_305_866_382_909.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_605_0060_roi_6_479_351_847.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-11-23-analysis-2024_403_0008.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_203_0029_roi_3_376_622_1000.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_102_0094.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_202_0055_roi_1_514_68_597.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_206_0000.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_302_0023_roi_295_768_6_437.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-11-23-analysis-2024_805_0081.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_605_0010_roi_341_847_162_673.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_205_0002_roi_70_569_6_490.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_200_0055_roi_99_778_341_986.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-11-23-analysis-2024_802_0040.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_206_0028_roi_2_426_487_995.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_706_0042_roi_99_515_11_394.tif"
+        ],
+        "validation": [
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_201_0003_roi_501_957_576_1000.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-11-23-analysis-2024_603_0032.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_706_0030_roi_323_824_488_995.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_202_0014_roi_258_711_504_959.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_207_0007_roi_119_611_5_451.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_206_0030.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_207_0055_roi_519_989_6_429.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_506_0053_roi_190_724_13_490.tif",
+            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_300_0047_roi_416_985_436_972.tif"
+        ]
+    }
+}

celldetective/models/segmentation_effectors/ricm_bf_all_last/training_instructions.json

@@ -0,0 +1,37 @@
+{
+    "model_name": "ricm_bf_all_last",
+    "model_type": "cellpose",
+    "pretrained": null,
+    "spatial_calibration": 0.2,
+    "channel_option": [
+        "adhesion_channel",
+        "brightfield_channel"
+    ],
+    "normalization_percentile": [
+        false,
+        true
+    ],
+    "normalization_clip": [
+        true,
+        true
+    ],
+    "normalization_values": [
+        [
+            0.75,
+            1.25
+        ],
+        [
+            1.0,
+            99.0
+        ]
+    ],
+    "ds": [
+        "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects"
+    ],
+    "augmentation_factor": 3.0,
+    "validation_split": 0.2,
+    "learning_rate": 0.008,
+    "batch_size": 8,
+    "epochs": 3000,
+    "target_directory": "/home/limozin/Documents/GitHub/celldetective/celldetective/models/segmentation_effectors"
+}

celldetective/models/segmentation_effectors/test-transfer/config_input.json

@@ -0,0 +1,39 @@
+{
+    "channels": [
+        "brightfield_channel",
+        "None"
+    ],
+    "diameter": 30.0,
+    "cellprob_threshold": 0.0,
+    "flow_threshold": 0.4,
+    "normalization_percentile": [
+        true,
+        true
+    ],
+    "normalization_clip": [
+        true,
+        true
+    ],
+    "normalization_values": [
+        [
+            1.0,
+            99.0
+        ],
+        [
+            1.0,
+            99.0
+        ]
+    ],
+    "model_type": "cellpose",
+    "spatial_calibration": 0.36666666666666664,
+    "dataset": {
+        "train": [
+            "/home/torro/Documents/Experiments/Marie-03-03-analysis-2024/annotations_effectors/Marie-03-03-analysis-2024_206_0028_roi_2_426_487_995.tif",
+            "/home/torro/Documents/Experiments/Marie-03-03-analysis-2024/annotations_effectors/Marie-03-03-analysis-2024_203_0029_roi_3_376_622_1000.tif",
+            "/home/torro/Documents/Experiments/Marie-03-03-analysis-2024/annotations_effectors/Marie-03-03-analysis-2024_208_0027_roi_600_997_5_387.tif"
+        ],
+        "validation": [
+            "/home/torro/Documents/Experiments/Marie-03-03-analysis-2024/annotations_effectors/Marie-03-03-analysis-2024_206_0023_roi_251_707_249_666.tif"
+        ]
+    }
+}

{celldetective-1.3.2.dist-info → celldetective-1.3.3.post1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: celldetective
-Version: 1.3.2
+Version: 1.3.3.post1
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro
@@ -10,8 +10,8 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: wheel
 Requires-Dist: nbsphinx
-Requires-Dist: nbsphinx-link
-Requires-Dist: sphinx-rtd-theme
+Requires-Dist: nbsphinx_link
+Requires-Dist: sphinx_rtd_theme
 Requires-Dist: sphinx
 Requires-Dist: jinja2
 Requires-Dist: ipykernel
@@ -34,12 +34,13 @@ Requires-Dist: liblapack
 Requires-Dist: gputools
 Requires-Dist: lmfit
 Requires-Dist: superqt[cmap]
-Requires-Dist: matplotlib-scalebar
+Requires-Dist: setuptools
+Requires-Dist: matplotlib_scalebar
 Requires-Dist: numpy==1.26.4
 Requires-Dist: pytest
 Requires-Dist: pytest-qt
 Requires-Dist: h5py
-Requires-Dist: cliffs-delta
+Requires-Dist: cliffs_delta
 
 # Celldetective
 
@@ -171,20 +172,20 @@ For more information about how to get started, please check the [documentation](
 # How to cite?
 
 If you use this software in your research, please cite the
-[Celldetective](https://www.biorxiv.org/content/10.1101/2024.03.15.585250v1)
+[Celldetective](https://www.biorxiv.org/content/10.1101/2024.03.15.585250v3)
 paper (currently preprint):
 
 ``` raw
 @article {Torro2024.03.15.585250,
-    author = {R{\'e}my Torro and Beatriz D{\`\i}az-Bello and Dalia El Arawi and Lorna Ammer and Patrick Chames and Kheya Sengupta and Laurent Limozin},
+    author = {Torro, R{\'e}my and D{\'\i}az-Bello, Beatriz and Arawi, Dalia El and Dervanova, Ksenija and Ammer, Lorna and Dupuy, Florian and Chames, Patrick and Sengupta, Kheya and Limozin, Laurent},
     title = {Celldetective: an AI-enhanced image analysis tool for unraveling dynamic cell interactions},
     elocation-id = {2024.03.15.585250},
     year = {2024},
     doi = {10.1101/2024.03.15.585250},
     publisher = {Cold Spring Harbor Laboratory},
-    abstract = {A current key challenge in bioimaging is the analysis of multimodal and multidimensional data reporting dynamic interactions between diverse cell populations. We developed Celldetective, a software that integrates AI-based segmentation and tracking algorithms and automated signal analysis into a user-friendly graphical interface. It offers complete interactive visualization, annotation, and training capabilities. We demonstrate it by analyzing original experimental data of spreading immune effector cells as well as antibody-dependent cell cytotoxicity events using multimodal fluorescence microscopy.Competing Interest StatementThe authors have declared no competing interest.},
-    URL = {https://www.biorxiv.org/content/early/2024/03/17/2024.03.15.585250},
-    eprint = {https://www.biorxiv.org/content/early/2024/03/17/2024.03.15.585250.full.pdf},
+    abstract = {A current challenge in bioimaging for immunology and immunotherapy research lies in analyzing multimodal and multidimensional data that capture dynamic interactions between diverse cell populations. Here, we introduce Celldetective, an open-source Python-based software designed for high-performance, end-to-end analysis of image-based in vitro immune and immunotherapy assays. Purpose-built for multicondition, 2D multichannel time-lapse microscopy of mixed cell populations, Celldetective is optimized for the needs of immunology assays. The software seamlessly integrates AI-based segmentation, Bayesian tracking, and automated single-cell event detection, all within an intuitive graphical interface that supports interactive visualization, annotation, and training capabilities. We demonstrate its utility with original data on immune effector cell interactions with an activating surface, mediated by bispecific antibodies, and further showcase its potential for analyzing extensive sets of pairwise interactions in antibody-dependent cell cytotoxicity events.Competing Interest StatementThe authors have declared no competing interest.},
+    URL = {https://www.biorxiv.org/content/early/2024/11/13/2024.03.15.585250},
+    eprint = {https://www.biorxiv.org/content/early/2024/11/13/2024.03.15.585250.full.pdf},
     journal = {bioRxiv}
 }
 ```

{celldetective-1.3.2.dist-info → celldetective-1.3.3.post1.dist-info}/RECORD

@@ -1,11 +1,11 @@
 celldetective/__init__.py,sha256=bi3SGTMo6s2qQBsJAaKy-a4xaGcTQVW8zsqaiX5XKeY,139
 celldetective/__main__.py,sha256=_H9B620ntENFx9RBvlV6ybxpvtHzCbv5NnIPmDBr9Z0,1127
-celldetective/_version.py,sha256=HgKA3RqZvC7slo8MgLyffCGwJbQ3cY6I7oUMFvGLWps,22
+celldetective/_version.py,sha256=mDV9xbwx4cdW0zTkJ0d0anqj6e9ntj3IW5BlFM6Gw6A,28
 celldetective/events.py,sha256=R6GDtiH0ZuEbad0R-nrlTHmho0Hly3QyyVYx2dD__P0,8051
 celldetective/extra_properties.py,sha256=88JtyoY883ibon-rqtCX_BCHOpo0MTGfiLciIR7jM24,5176
 celldetective/filters.py,sha256=b0qKwHor1fvNA_dHovP17nQz8EsW5YlyhT2TJnayn08,3615
-celldetective/io.py,sha256=CWwhiJMUwz6-9Ekxo1lWmThhN_0aP8RRg9HUr8BgNZo,88428
-celldetective/measure.py,sha256=ZrhAp2nL0L012aKrlSsJkmIStklj2GQdDu8Yfftp9ZU,56400
+celldetective/io.py,sha256=zSiXczHEa_RwfXu5joHT8zThZ0V7bCkYPutHgZGdBzs,90030
+celldetective/measure.py,sha256=b0ZiTm_lrM1geInh8F1co9ef2w1oXQuLx7ACTo6vFIU,57358
 celldetective/neighborhood.py,sha256=66fsOPDtjbrUTww97wVFmPk-UZakJgglua8O1Jl-RC4,56745
 celldetective/preprocessing.py,sha256=WmetQCgmHK6fo8AuwESPLab05WgeIy8ElBs-9KM-Cco,44081
 celldetective/relative_measurements.py,sha256=av5DiGlGsbILPav8aVcFlhbmbPLPZPxCB5qQejzhiRY,30400
@@ -22,17 +22,17 @@ celldetective/gui/analyze_block.py,sha256=sat8RECEeZxlaconZZIxI0IrIjwJo121PcBXqJ
 celldetective/gui/btrack_options.py,sha256=OrvbG5coZhLRk5jtXiLFJu34z1hWHN9kHkBiZ7XMZoI,39269
 celldetective/gui/classifier_widget.py,sha256=4239jKQb1uZMQU6iBBicavE05QAgmBQBM0YnmDesoPs,18430
 celldetective/gui/configure_new_exp.py,sha256=Eyr-M4FH-4xrUJbIGNdKXAtXb_ULr8lCol26JSzXEww,20125
-celldetective/gui/control_panel.py,sha256=5twtX3-gKAJZVNXkuAkX4PLcOgmRhAyFHZSG3bk7xpk,19144
+celldetective/gui/control_panel.py,sha256=5bU9n1bMiLrtrT9YH8-UfV5dJoOOtZejFcbHFkgX5NY,19185
 celldetective/gui/generic_signal_plot.py,sha256=KPJU5uP7uHxWQ6txmZx6gFalGPGxC165LSsx7AvB7zA,35605
 celldetective/gui/gui_utils.py,sha256=og9iz2DkkJc_4UZmnvhN2oCMMPbJVnx-FAF10JfR8Eo,30441
 celldetective/gui/json_readers.py,sha256=Su3angSobroeGrrumGgQcs3Cr_9l9p52-Hfm3qneVcI,3664
 celldetective/gui/layouts.py,sha256=f_MoRPtl6e1UAsSTVidCSNk4_hoz1me_Z1KFaia29TQ,51783
-celldetective/gui/measurement_options.py,sha256=jc0_RGpbCB3BhDWjqKFBP4j5ncTSIKUz8In7ae306vE,39288
+celldetective/gui/measurement_options.py,sha256=4jnTv3dOeazEzWdsKgAmJaHp_dhalr6pDg8MxE3L_L4,39699
 celldetective/gui/neighborhood_options.py,sha256=BvWwsIX1KWogUgHWRZptqY3ZRmH1aj7r8tiLmbRFhW4,19783
 celldetective/gui/plot_measurements.py,sha256=SBFkY3542hW4H_vllOCMxMOgBz09KUE2FLhhgI8avXk,51024
 celldetective/gui/plot_signals_ui.py,sha256=i3ulnd6_dyFDRRy8RLO-fC6zwkbYjMXLYRc8rTYKTlE,15981
-celldetective/gui/process_block.py,sha256=ekwVETKOAxBv0yIpB2ILkLcPG2dnyK8f0fXsnHNb35s,73618
-celldetective/gui/retrain_segmentation_model_options.py,sha256=jYD9AWzDPacUgaBv9l6ldQxXNZb3BD4EwJc-0t02jXw,23207
+celldetective/gui/process_block.py,sha256=0wD9ffvZwZgnZ79R2BV_It7lbdk8bvOJs658uDfAsBo,69494
+celldetective/gui/retrain_segmentation_model_options.py,sha256=ACeQ_DdSLy1EK0z_S_9v-0HOiLXjUmrz4sdvHWZT6FI,23330
 celldetective/gui/retrain_signal_model_options.py,sha256=XigNdGlNu3KWB_MYBcKQhfXjcWwVZNMmu0qmxNoo14E,21919
 celldetective/gui/seg_model_loader.py,sha256=vWvPMU6nkTiQfI-x2WjQHrdJGFdV4a4Ne-4YIOq_YZ8,18153
 celldetective/gui/signal_annotator.py,sha256=uzX06JYJOCFm4EytQRV2_JR8orbjDh6NjWberQePiGg,88244
@@ -41,8 +41,8 @@ celldetective/gui/signal_annotator_options.py,sha256=ztFFgA70SJ0QkntxYGsgDNCvSuS
 celldetective/gui/styles.py,sha256=fup0_U1Zk0IJAjyruHde_r-X7d7cTMcrpPLPl-HuKAM,4820
 celldetective/gui/survival_ui.py,sha256=SJV-HIcA0hg_ZvyTdxbutvkUwuCSnx2TI3hNHn3AtZE,10362
 celldetective/gui/tableUI.py,sha256=kkgqxopWuC8nnTFPVkf09_h9176OfBmRMZ3E6AsyQIc,50531
-celldetective/gui/thresholds_gui.py,sha256=t1hTDdaJTJWHBt9vtRCE4B1TsVHhobQwCpKfntVgaQI,50510
-celldetective/gui/viewers.py,sha256=rQWJoE45uncNl8-_ktNPnzxvx_Rm8MN3LIawZtWfusU,37723
+celldetective/gui/thresholds_gui.py,sha256=YHtgTDVNM0H-4bKwrRVs5yFAX4wgp5DSfjjfm0RGUKA,50849
+celldetective/gui/viewers.py,sha256=WdNb9J7hNtTvl5wpdmJbWeXWeE0hz06B0wOAOMt1_10,46466
 celldetective/gui/help/DL-segmentation-strategy.json,sha256=59jVtn8pECbCqPQwJifgViVYTF1AxLQDIkNJMS7CJuk,1143
 celldetective/gui/help/Threshold-vs-DL.json,sha256=SELQk3qF8xcwmkX686Bqrr7i5KiXqN7r4jbUydCLRDU,603
 celldetective/gui/help/cell-populations.json,sha256=wP0ekhokb9oHE3XqOQrC5ARewNgOlv0GJrQeVQyMJzg,1075
@@ -66,6 +66,11 @@ celldetective/icons/vignette_signals2.svg,sha256=muGNcQudV1jG-bmFd9FwV-Wb8PcrRV5
 celldetective/links/zenodo.json,sha256=puCKI6vQi_L_7H70Nii_UzIqRcYVWUQGRKpTulyoHPo,30549
 celldetective/models/pair_signal_detection/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 celldetective/models/segmentation_effectors/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+celldetective/models/segmentation_effectors/ricm_bf_all_last/config_input.json,sha256=Sr5AiyJkg_EoAUFSZbUH_FE-jQHTwNR3tiUZdmvPlaA,7068
+celldetective/models/segmentation_effectors/ricm_bf_all_last/ricm_bf_all_last,sha256=HTgeUImhkhjf-HsoziJPL16azPIGt2XiMmgvB_qf7DA,26559970
+celldetective/models/segmentation_effectors/ricm_bf_all_last/training_instructions.json,sha256=4ZcZVti1kA_1zV8_3jj2pZYBST0kX8Z00tlc4AATlxo,847
+celldetective/models/segmentation_effectors/test-transfer/config_input.json,sha256=JytjANaerSQBjMn-cZktHj8ESdMCIvXWdmwmgQGgUYE,1212
+celldetective/models/segmentation_effectors/test-transfer/test-transfer,sha256=eEy7bx3jJcj0MmV893OMbzSF_jagCz4Ov7CGkXGWmqI,26554673
 celldetective/models/segmentation_generic/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 celldetective/models/segmentation_targets/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 celldetective/models/signal_detection/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -94,9 +99,9 @@ tests/test_segmentation.py,sha256=k1b_zIZdlytEdJcHjAUQEO3gTBAHtv5WvrwQN2xD4kc,34
 tests/test_signals.py,sha256=No4cah6KxplhDcKXnU8RrA7eDla4hWw6ccf7xGnBokU,3599
 tests/test_tracking.py,sha256=8hebWSqEIuttD1ABn-6dKCT7EXKRR7-4RwyFWi1WPFo,8800
 tests/test_utils.py,sha256=NKRCAC1d89aBK5cWjTb7-pInYow901RrT-uBlIdz4KI,3692
-celldetective-1.3.2.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-celldetective-1.3.2.dist-info/METADATA,sha256=TDy-Xv2HDKhb-rkNOqiXDYrW9yICk9BJxr4FPmveNEg,9969
-celldetective-1.3.2.dist-info/WHEEL,sha256=R06PA3UVYHThwHvxuRWMqaGcr-PuniXahwjmQRFMEkY,91
-celldetective-1.3.2.dist-info/entry_points.txt,sha256=2NU6_EOByvPxqBbCvjwxlVlvnQreqZ3BKRCVIKEv3dg,62
-celldetective-1.3.2.dist-info/top_level.txt,sha256=6rsIKKfGMKgud7HPuATcpq6EhdXwcg_yknBVWn9x4C4,20
-celldetective-1.3.2.dist-info/RECORD,,
+celldetective-1.3.3.post1.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+celldetective-1.3.3.post1.dist-info/METADATA,sha256=vrBTSR4sY56-qMlzOBKejzf-71YICuEA40HDCBZqx9E,10510
+celldetective-1.3.3.post1.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+celldetective-1.3.3.post1.dist-info/entry_points.txt,sha256=2NU6_EOByvPxqBbCvjwxlVlvnQreqZ3BKRCVIKEv3dg,62
+celldetective-1.3.3.post1.dist-info/top_level.txt,sha256=6rsIKKfGMKgud7HPuATcpq6EhdXwcg_yknBVWn9x4C4,20
+celldetective-1.3.3.post1.dist-info/RECORD,,

{celldetective-1.3.2.dist-info → celldetective-1.3.3.post1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.5.0)
+Generator: setuptools (75.6.0)
 Root-Is-Purelib: true
 Tag: py3-none-any