celldetective 1.5.0b1__py3-none-any.whl → 1.5.0b3__py3-none-any.whl

celldetective/processes/measure_cells.py

@@ -310,6 +310,9 @@ class MeasurementProcess(Process):
 
         for t in tqdm(indices, desc="frame"):
 
+            measurements_at_t = None
+            perform_measurement = True
+
             if self.file is not None:
                 img = load_frames(
                     self.img_num_channels[:, t],
@@ -321,92 +324,115 @@ class MeasurementProcess(Process):
             if self.label_path is not None:
                 lbl = locate_labels(self.pos, population=self.mode, frames=t)
                 if lbl is None:
-                    continue
-
-            if self.trajectories is not None:
-                # Optimized access
-                if self.frame_slices is not None:
-                    # Check if frame t is in our precomputed slices
-                    if t in self.frame_slices:
-                        start, end = self.frame_slices[t]
-                        positions_at_t = self.trajectories.iloc[start:end].copy()
+                    perform_measurement = False
+
+            if perform_measurement:
+
+                if self.trajectories is not None:
+                    # Optimized access
+                    if self.frame_slices is not None:
+                        # Check if frame t is in our precomputed slices
+                        if t in self.frame_slices:
+                            start, end = self.frame_slices[t]
+                            positions_at_t = self.trajectories.iloc[start:end].copy()
+                        else:
+                            # Empty frame for trajectories
+                            positions_at_t = pd.DataFrame(
+                                columns=self.trajectories.columns
+                            )
                     else:
-                        # Empty frame for trajectories
-                        positions_at_t = pd.DataFrame(columns=self.trajectories.columns)
-                else:
-                    # Fallback or original method (should not be reached if optimized)
-                    positions_at_t = self.trajectories.loc[
-                        self.trajectories[self.column_labels["time"]] == t
-                    ].copy()
-
-            if self.do_features:
-                feature_table = measure_features(
-                    img,
-                    lbl,
-                    features=self.features,
-                    border_dist=self.border_distances,
-                    channels=self.channel_names,
-                    haralick_options=self.haralick_options,
-                    verbose=False,
-                    normalisation_list=self.background_correction,
-                    spot_detection=self.spot_detection,
-                )
-                if self.trajectories is None:
-                    positions_at_t = _extract_coordinates_from_features(
-                        feature_table, timepoint=t
+                        # Fallback or original method (should not be reached if optimized)
+                        positions_at_t = self.trajectories.loc[
+                            self.trajectories[self.column_labels["time"]] == t
+                        ].copy()
+
+                if self.do_features:
+                    feature_table = measure_features(
+                        img,
+                        lbl,
+                        features=self.features,
+                        border_dist=self.border_distances,
+                        channels=self.channel_names,
+                        haralick_options=self.haralick_options,
+                        verbose=False,
+                        normalisation_list=self.background_correction,
+                        spot_detection=self.spot_detection,
+                    )
+                    if self.trajectories is None:
+                        positions_at_t = _extract_coordinates_from_features(
+                            feature_table, timepoint=t
+                        )
+                        column_labels = {
+                            "track": "ID",
+                            "time": self.column_labels["time"],
+                            "x": self.column_labels["x"],
+                            "y": self.column_labels["y"],
+                        }
+                    feature_table.rename(
+                        columns={
+                            "centroid-1": "POSITION_X",
+                            "centroid-0": "POSITION_Y",
+                        },
+                        inplace=True,
                     )
-                    column_labels = {
-                        "track": "ID",
-                        "time": self.column_labels["time"],
-                        "x": self.column_labels["x"],
-                        "y": self.column_labels["y"],
-                    }
-                feature_table.rename(
-                    columns={"centroid-1": "POSITION_X", "centroid-0": "POSITION_Y"},
-                    inplace=True,
-                )
 
-            if self.do_iso_intensities and not self.trajectories is None:
-                iso_table = measure_isotropic_intensity(
-                    positions_at_t,
-                    img,
-                    channels=self.channel_names,
-                    intensity_measurement_radii=self.intensity_measurement_radii,
-                    column_labels=self.column_labels,
-                    operations=self.isotropic_operations,
-                    verbose=False,
-                )
+                if self.do_iso_intensities and not self.trajectories is None:
+                    iso_table = measure_isotropic_intensity(
+                        positions_at_t,
+                        img,
+                        channels=self.channel_names,
+                        intensity_measurement_radii=self.intensity_measurement_radii,
+                        column_labels=self.column_labels,
+                        operations=self.isotropic_operations,
+                        verbose=False,
+                    )
 
-            if (
-                self.do_iso_intensities
-                and self.do_features
-                and not self.trajectories is None
-            ):
-                measurements_at_t = iso_table.merge(
-                    feature_table, how="outer", on="class_id", suffixes=("_delme", "")
-                )
-                measurements_at_t = measurements_at_t[
-                    [c for c in measurements_at_t.columns if not c.endswith("_delme")]
-                ]
-            elif (
-                self.do_iso_intensities
-                * (not self.do_features)
-                * (not self.trajectories is None)
-            ):
-                measurements_at_t = iso_table
-            elif self.do_features:
-                measurements_at_t = positions_at_t.merge(
-                    feature_table, how="outer", on="class_id", suffixes=("_delme", "")
+                if (
+                    self.do_iso_intensities
+                    and self.do_features
+                    and not self.trajectories is None
+                ):
+                    measurements_at_t = iso_table.merge(
+                        feature_table,
+                        how="outer",
+                        on="class_id",
+                        suffixes=("_delme", ""),
+                    )
+                    measurements_at_t = measurements_at_t[
+                        [
+                            c
+                            for c in measurements_at_t.columns
+                            if not c.endswith("_delme")
+                        ]
+                    ]
+                elif (
+                    self.do_iso_intensities
+                    * (not self.do_features)
+                    * (not self.trajectories is None)
+                ):
+                    measurements_at_t = iso_table
+                elif self.do_features:
+                    measurements_at_t = positions_at_t.merge(
+                        feature_table,
+                        how="outer",
+                        on="class_id",
+                        suffixes=("_delme", ""),
+                    )
+                    measurements_at_t = measurements_at_t[
+                        [
+                            c
+                            for c in measurements_at_t.columns
+                            if not c.endswith("_delme")
+                        ]
+                    ]
+
+                measurements_at_t = center_of_mass_to_abs_coordinates(measurements_at_t)
+
+                measurements_at_t = measure_radial_distance_to_center(
+                    measurements_at_t,
+                    volume=img.shape,
+                    column_labels=self.column_labels,
                 )
-                measurements_at_t = measurements_at_t[
-                    [c for c in measurements_at_t.columns if not c.endswith("_delme")]
-                ]
-
-            measurements_at_t = center_of_mass_to_abs_coordinates(measurements_at_t)
-
-            measurements_at_t = measure_radial_distance_to_center(
-                measurements_at_t, volume=img.shape, column_labels=self.column_labels
-            )
 
             self.sum_done += 1
             data = {}

celldetective/processes/track_cells.py

@@ -25,6 +25,7 @@ from celldetective.utils.image_loaders import (
     _get_img_num_per_channel,
     auto_load_number_of_frames,
     _load_frames_to_measure,
+    locate_labels,
 )
 from celldetective.utils.io import remove_file_if_exists
 from celldetective.utils.parsing import config_section_to_dict
@@ -210,15 +211,6 @@ class TrackingProcess(Process):
         )
         if len(self.label_path) > 0:
             logger.info(f"Found {len(self.label_path)} segmented frames...")
-            # Optimize: Create a map of frame index to file path
-            self.label_map = {}
-            for path in self.label_path:
-                try:
-                    # Assumes format ####.tif, e.g., 0001.tif
-                    frame_idx = int(os.path.basename(path).split(".")[0])
-                    self.label_map[frame_idx] = path
-                except ValueError:
-                    continue
         else:
             logger.error(
                 f"No segmented frames have been found. Please run segmentation first. Abort..."
@@ -245,37 +237,39 @@ class TrackingProcess(Process):
 
             for t in tqdm(indices, desc="frame"):
 
-                # Load channels at time t
-                img = _load_frames_to_measure(
-                    self.file, indices=self.img_num_channels[:, t]
-                )
-                # Optimize: Direct lookup instead of glob
-                if t in self.label_map:
-                    try:
-                        # Load image from path in map
-                        lbl = np.array(imread(self.label_map[t]))
-                    except Exception as e:
-                        logger.error(f"Failed to load label for frame {t}: {e}")
-                        continue
-                else:
-                    # Fallback or skip if not in map
-                    continue
-
-                df_props = measure_features(
-                    img,
-                    lbl,
-                    features=self.features + ["centroid"],
-                    border_dist=None,
-                    channels=self.channel_names,
-                    haralick_options=self.haralick_options,
-                    verbose=False,
-                )
-                df_props.rename(
-                    columns={"centroid-1": "x", "centroid-0": "y"}, inplace=True
-                )
-                df_props["t"] = int(t)
+                perform_tracking = True
 
-                props.append(df_props)
+                # Load channels at time t
+                try:
+                    img = _load_frames_to_measure(
+                        self.file, indices=self.img_num_channels[:, t]
+                    )
+                except Exception as e:
+                    logger.error(f"Failed to load image for frame {t}: {e}")
+                    perform_tracking = False
+
+                if perform_tracking:
+                    lbl = locate_labels(self.pos, population=self.mode, frames=t)
+                    if lbl is None:
+                        logger.warning(f"Failed to load label for frame {t}")
+                        perform_tracking = False
+
+                if perform_tracking:
+                    df_props = measure_features(
+                        img,
+                        lbl,
+                        features=self.features + ["centroid"],
+                        border_dist=None,
+                        channels=self.channel_names,
+                        haralick_options=self.haralick_options,
+                        verbose=False,
+                    )
+                    df_props.rename(
+                        columns={"centroid-1": "x", "centroid-0": "y"}, inplace=True
+                    )
+                    df_props["t"] = int(t)
+
+                    props.append(df_props)
 
                 # Progress Update
                 self.loop_count += 1
@@ -349,6 +343,7 @@ class TrackingProcess(Process):
             return
 
         df = pd.concat(self.timestep_dataframes)
+        logger.info(f"Aggregated DataFrame shape: {df.shape}")
         if df.empty:
             logger.warning("Dataframe is empty. Skipping position.")
             return
@@ -357,6 +352,7 @@ class TrackingProcess(Process):
 
         df.reset_index(inplace=True, drop=True)
         df = _mask_intensity_measurements(df, self.mask_channels)
+        logger.info(f"DataFrame shape after masking intensity measurements: {df.shape}")
 
         # do tracking
         if self.btrack_option:
@@ -380,6 +376,9 @@ class TrackingProcess(Process):
                 search_range=self.search_range,
                 memory=self.memory,
             )
+            logger.info(
+                f"Tracking output: Trajectories shape: {trajectories.shape} if trajectories is not None else 'None'"
+            )
         except Exception as e:
             logger.error(f"Tracking failed: {e}")
             if "search_range" in str(e) or "SubnetOversizeException" in str(e):
@@ -399,6 +398,7 @@ class TrackingProcess(Process):
             allow_pickle=True,
         )
 
+        logger.info(f"Shape of trajectories before saving: {trajectories.shape}")
         trajectories.to_csv(
             self.pos + os.sep.join(["output", "tables", self.table_name]), index=False
         )

celldetective/segmentation.py

@@ -163,6 +163,7 @@ def segment(
         f"{spatial_calibration=} {required_spatial_calibration=} Scale = {scale}..."
     )
 
+    model = None
     if model_type == "stardist":
         model, scale_model = _prep_stardist_model(
             model_name, Path(model_path).parent, use_gpu=use_gpu, scale=scale
@@ -177,7 +178,6 @@ def segment(
             scale=scale,
         )
 
-
     if model is None:
         logger.error(f"Could not load model {model_name}. Aborting segmentation.")
         return None

celldetective/tracking.py

@@ -176,6 +176,10 @@ def track(
             tracker.optimize(options=optimizer_options)
 
             data, properties, graph = tracker.to_napari()  # ndim=2
+            print(f"DEBUG: tracker.to_napari() returned data shape: {data.shape}")
+            print(
+                f"DEBUG: tracker.to_napari() returned properties keys: {list(properties.keys()) if properties else 'None'}"
+            )
         # do the table post processing and napari options
         if data.shape[1] == 4:
             df = pd.DataFrame(
@@ -258,7 +262,12 @@ def track(
     df = write_first_detection_class(df, img_shape=volume, column_labels=column_labels)
 
     if clean_trajectories_kwargs is not None:
+        print(
+            f"DEBUG: Calling clean_trajectories with kwargs: {clean_trajectories_kwargs}"
+        )
+        print(f"DEBUG: df shape before clean: {df.shape}")
         df = clean_trajectories(df.copy(), **clean_trajectories_kwargs)
+        print(f"DEBUG: df shape after clean: {df.shape}")
 
     df.loc[df["status_firstdetection"].isna(), "status_firstdetection"] = 0
     df["ID"] = np.arange(len(df)).astype(int)

celldetective/utils/data_loaders.py

@@ -148,6 +148,7 @@ def load_experiment_tables(
     position_option="*",
     return_pos_info=False,
     load_pickle=False,
+    progress_callback=None,
 ):
     """
     Load tabular data for an experiment, optionally including position-level information.
@@ -225,7 +226,18 @@ def load_experiment_tables(
     df_pos_info = []
     real_well_index = 0
 
-    for k, well_path in enumerate(tqdm(wells[well_indices])):
+    total_wells = len(well_indices)
+
+    iterator = wells[well_indices]
+    if progress_callback is None:
+        iterator = tqdm(wells[well_indices])
+
+    for k, well_path in enumerate(iterator):
+
+        if progress_callback is not None:
+            well_progress = round(k / total_wells * 100)
+            # Signal keep_going logic if needed, but for now just send progress
+            # If callback returns False, we could abort, but simpler to just update for now.
 
         any_table = False  # assume no table
 
@@ -242,8 +254,16 @@ def load_experiment_tables(
                 continue
 
         real_pos_index = 0
+        total_positions = len(positions)
+
         for pidx, pos_path in enumerate(positions):
 
+            if progress_callback is not None:
+                pos_progress = round(pidx / total_positions * 100)
+                should_continue = progress_callback(well_progress, pos_progress)
+                if should_continue is False:
+                    return None, None if return_pos_info else None
+
             pos_name = extract_position_name(pos_path)
 
             stack_path = get_position_movie_path(pos_path, prefix=movie_prefix)

celldetective/utils/image_loaders.py

@@ -623,6 +623,9 @@ def fix_missing_labels(position, population="target", prefix="Aligned"):
         )
         path = position + os.sep + f"labels_{population}"
 
+    if not os.path.exists(path):
+        os.makedirs(path, exist_ok=True)
+
     if label_path != []:
         # path = os.path.split(label_path[0])[0]
         int_valid = [int(lbl.split(os.sep)[-1].split(".")[0]) for lbl in label_path]

celldetective/utils/masks.py

@@ -2,7 +2,7 @@ from typing import Union, List, Tuple
 
 import numpy as np
 from scipy import ndimage
-from scipy.ndimage.morphology import distance_transform_edt
+from scipy.ndimage import distance_transform_edt
 from skimage.morphology import disk
 from celldetective.log_manager import get_logger
 

celldetective/utils/maths.py

@@ -2,6 +2,11 @@ from typing import Union, List
 import numpy as np
 
 
+from celldetective import get_logger
+
+logger = get_logger()
+
+
 def step_function(t: Union[np.ndarray, List], t_shift: float, dt: float) -> np.ndarray:
     """
     Computes a step function using the logistic sigmoid function.
@@ -40,7 +45,15 @@ def step_function(t: Union[np.ndarray, List], t_shift: float, dt: float) -> np.n
     array([0.26894142, 0.37754067, 0.5       , 0.62245933, 0.73105858, 0.81757448])
     """
 
-    return 1 / (1 + np.exp(-(t - t_shift) / dt))
+    with np.errstate(over="raise", divide="raise"):
+        try:
+            return 1 / (1 + np.exp(-(t - t_shift) / dt))
+        except FloatingPointError as e:
+            logger.warning(
+                f"Math warning in step_function: {e}. t_shift={t_shift}, dt={dt}. Range of t: [{np.min(t)}, {np.max(t)}]"
+            )
+            with np.errstate(over="ignore", divide="ignore"):
+                return 1 / (1 + np.exp(-(t - t_shift) / dt))
 
 
 def derivative(x, timeline, window, mode="bi"):

{celldetective-1.5.0b1.dist-info → celldetective-1.5.0b3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: celldetective
-Version: 1.5.0b1
+Version: 1.5.0b3
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro

{celldetective-1.5.0b1.dist-info → celldetective-1.5.0b3.dist-info}/RECORD

@@ -1,48 +1,49 @@
 celldetective/__init__.py,sha256=LfnOyfUnYPGDc8xcsF_PfYEL7-CqAb7BMBPBIWGv84o,666
 celldetective/__main__.py,sha256=Rzzu9ArxZSgfBVjV-lyn-3oanQB2MumQR6itK5ZaRpA,2597
-celldetective/_version.py,sha256=6QH0Vgfkt-TPgdS6Nql1G9jeZAByFTkMEeYsa6NspPk,24
+celldetective/_version.py,sha256=xyBMhGEXnWbOInuedgW565vK5NILuhG2r2EYCw9E9eU,24
 celldetective/events.py,sha256=n15R53c7QZ2wT8gjb0oeNikQbuRBrVVbyNsRCqXjzXA,8166
 celldetective/exceptions.py,sha256=f3VmIYOthWTiqMEV5xQCox2rw5c5e7yog88h-CcV4oI,356
 celldetective/extra_properties.py,sha256=s_2R4_El2p-gQNZ_EpgDxgrN3UnRitN7KDKHhyLuoHc,21681
 celldetective/filters.py,sha256=QSRSpqvwUfa0YrU5EKoobJWCQFy07fFHwZ2bXxTL3hE,6933
 celldetective/log_manager.py,sha256=Tv7_mVn0TVOyTs_2VnyEKl9_NMeDUtEkLC5njUq-r-Y,2968
-celldetective/measure.py,sha256=Nlbh-YT7D2uafRRGFTl2a63UDkBkbBXnnMqs9zWXP_I,71854
+celldetective/measure.py,sha256=V-1J9l5CIkxJWnEWQp0xMQVv1PPCPZJMS0tkIKCLGXM,72048
 celldetective/neighborhood.py,sha256=Z5wu2nSMvabrQz91oy6DRf2o90LUY0RMXTEwgW7ORAg,74844
 celldetective/preprocessing.py,sha256=tjAMLG4ZMfopMSFulGGjMQox7czEcReV2MzEkWlL2eQ,59948
 celldetective/relative_measurements.py,sha256=j7xIj1FiY3kn5nA_wMqHV3wvjqikjnk99kZ7v9G6I5Q,42928
-celldetective/segmentation.py,sha256=Itg8xbfEziQKApA7YCo9FTk8c44OrlsJbvtkik6tkgE,33567
+celldetective/segmentation.py,sha256=yIFZn0XDaudj9XkSjWW9k6LqZEM-OQdp98ylwQQtlTg,33583
 celldetective/signals.py,sha256=2UURVmeonNgUHpiMQVSps0E9VuskKSbsfsmeCtEmfp8,137484
-celldetective/tracking.py,sha256=pjejp65IltUMjW_tlbxjYW0SoBR1-gaEeSJa0y2cWpw,49286
+celldetective/tracking.py,sha256=iwN6rQ9Bmz20JPrFoewywPBrhD864NUiMaZbIINJVZc,49758
 celldetective/datasets/segmentation_annotations/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 celldetective/datasets/signal_annotations/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-celldetective/gui/InitWindow.py,sha256=fNuY7d8EtNNOB2_ZrijyNdoQ7x5GOlq1IFqPBUv1ElM,20953
+celldetective/gui/InitWindow.py,sha256=uta0lqFsiwcPz3bh8hz44LrTGhzKWa_SQWbylSBZU_w,22366
 celldetective/gui/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 celldetective/gui/about.py,sha256=l9SA7WnQs3ISPvZYAGMmf1A0GRXcinkyGwWJpG8akFQ,1977
 celldetective/gui/analyze_block.py,sha256=R82PVFHXfKn8BvUCpbjDOkLBNF4xRVCzYKFHitjw0kk,4114
-celldetective/gui/base_annotator.py,sha256=zMvfbuijCiEdPFOGTc_LPxGpdBX-BRtq6VuDXGvXk08,32364
+celldetective/gui/base_annotator.py,sha256=xLCg5n4kl_EOajk1KNAdMzB05blaiGdb0kjylx88D_A,32690
 celldetective/gui/classifier_widget.py,sha256=uQ9KQmUFp6qWy0Aic-AKB9DkGNpOLxaERtYBSIX9RHw,25424
 celldetective/gui/configure_new_exp.py,sha256=vgT6ozRIGDvT3R0qENlqvDn17BpKnwyJRhRhDS6ax8A,29954
-celldetective/gui/control_panel.py,sha256=vT8Ny9JHGnx25CygjkjqLHBqwj7tL7q-tE4R_iildiQ,24115
+celldetective/gui/control_panel.py,sha256=dMNzgivt6GdYROPlYpEY5TTNcANenm9ifUI3W3OcpOo,24337
 celldetective/gui/dynamic_progress.py,sha256=wjTmDPy62qssY0zdteP3T9umIGGQk0UvebFIdn54CIc,16676
-celldetective/gui/event_annotator.py,sha256=kCrehnLQagLXqViWHcOF-kHj9i1pbdJ97CLUU-HOM7w,73019
+celldetective/gui/event_annotator.py,sha256=bW6IcZsYOmGJPv-3wZHPYGmg2k43PXo0tvHa1ZAFFF8,36338
 celldetective/gui/generic_signal_plot.py,sha256=D3b6pG1yrSi8C2PPyYzK2yA6711CBBPRp5_OIrjayqs,49348
-celldetective/gui/gui_utils.py,sha256=KbxgwOXGKup_w2FntJxFDSl-eUmc2aqq6h3O5nW8nO0,33258
-celldetective/gui/interactions_block.py,sha256=6HiCvRnVpfxgPJLYOy9gFyPKTApsXjGgojTqri9gW6Y,27401
-celldetective/gui/interactive_timeseries_viewer.py,sha256=BLVOXf2Rx-6DFDW-dKqa8Fw0Q1OeC72J0qwUytuZUaU,15943
+celldetective/gui/gui_utils.py,sha256=t6SjEfjcaRH9a0TlbTGEiVRpCgocaCh4lgkIvRgRRwE,33497
+celldetective/gui/interactions_block.py,sha256=34VaHFrdKsq1hYuXrosmpP15JU26dSfbyx4lyt1jxNg,28440
+celldetective/gui/interactive_timeseries_viewer.py,sha256=u_amAhLdEHRpYSRwPDtVm5v-JZIz0ANTcG4YGksX1Vo,16079
 celldetective/gui/json_readers.py,sha256=t5rhtIxACj0pdwLrnPs-QjyhQo3P25UGWGgOCIBhQxs,4572
+celldetective/gui/measure_annotator.py,sha256=HdhrU3N207evB9s-pqZNfzJC2Jswx3yHdPPLR8CRILc,38354
 celldetective/gui/pair_event_annotator.py,sha256=QJHaM-z0K2I36sLf6XCMFMymfw-nFhzfGJ8oxrMfZco,124091
-celldetective/gui/plot_measurements.py,sha256=pTBA8_XtAZRsxNtWqd8obOHbDqKyz-c1R085xy7y4Ns,56675
-celldetective/gui/plot_signals_ui.py,sha256=oReZwCZw89pFtwuezGQNI6kAz8Q_daKHvNoAKEgzn2w,28195
+celldetective/gui/plot_measurements.py,sha256=a_Mks-5XUTn2QEYih0PlXGp2lX3C34zuhK9ozzE1guM,56593
+celldetective/gui/plot_signals_ui.py,sha256=9VmA1yaTcNf1jY7drtK41R1q87dhEk7bXBCq_cQ94fs,28133
 celldetective/gui/preprocessing_block.py,sha256=cgUBv-eQBwfidK48-cTWJi0PS62wlXhsNLnsKhy6MQY,14967
-celldetective/gui/process_block.py,sha256=byOZ-dz65mUJ66shzu3RNsuVQ4zGhiolAzI5LlKsxAc,67444
+celldetective/gui/process_block.py,sha256=NBSwg32Juz3dyXMe0uRyYE-qttfsTqSDPyoBgVc5T1c,76891
 celldetective/gui/seg_model_loader.py,sha256=6DzpX630JJgtcsaDEuWA8PEkeb8FC3p__3xeSiFqdGo,23549
 celldetective/gui/survival_ui.py,sha256=IwdRm1gRvhkWdMtrQk04OIKKksW3NZSGYtZO_2GptrA,16034
 celldetective/gui/tableUI.py,sha256=kZP2lp9NwHtbWEqIyaDwohX42tRkhI0Hlf_8O5w5BD0,61267
 celldetective/gui/thresholds_gui.py,sha256=w6ke2TyIEi71LxbuFGz0UrwH8h21N_ESU-o6xq_NNKo,33346
-celldetective/gui/workers.py,sha256=6uk4skcwNd3qowBrpSSgv0hvbL-4naH-g-TmF3u7NB4,14363
+celldetective/gui/workers.py,sha256=WAtVxFEvHApBSAZMVyYsya_DHL_bYo8b57dbgUJQHc4,14890
 celldetective/gui/base/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 celldetective/gui/base/channel_norm_generator.py,sha256=JqNAo87zA3nMKzkGjvoeV-SHI89eIATwQj4jHv3-LpI,13973
-celldetective/gui/base/components.py,sha256=DF1sT2AZIpTec7mYYihIMTDYKRrT5k2DoaceZjvAEEw,7452
+celldetective/gui/base/components.py,sha256=jNUsCU_QE7QUFR0_xEvEPFEBYolMJt7YXGUKMjF7uOE,8155
 celldetective/gui/base/feature_choice.py,sha256=n1T2fPoNLiTDS_6fa_GuGReDhBW11HdUrKy2RywotF8,2800
 celldetective/gui/base/figure_canvas.py,sha256=dQlmLfB3PUttFmyHZIvSc_9GQ5JRy7jH9w7lyKAGElk,1523
 celldetective/gui/base/list_widget.py,sha256=_WU3ZRU7UcJZIxm8qx_5HF7IK7dUu8IU1FY2AaW_qgo,4694
@@ -86,9 +87,9 @@ celldetective/gui/table_ops/_merge_one_hot.py,sha256=gKRgem-u_-JENkVkbjRobsH4TkS
 celldetective/gui/table_ops/_query_table.py,sha256=K-XHSZ1I4v2wwqWjyQAgyFRZJbem3CmTfHmO0vijh9g,1345
 celldetective/gui/table_ops/_rename_col.py,sha256=UAgDSpXJo_h4pLJpHaNc2w2VhbaW4D2JZTgJ3cYC4-g,1457
 celldetective/gui/viewers/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-celldetective/gui/viewers/base_viewer.py,sha256=etX9c9Fw-LXXzD_zUrcOHFEaHKF-XZt7VlZ2YmMvFhc,25303
+celldetective/gui/viewers/base_viewer.py,sha256=1U936rVnRqevXtyqlZnu_1o_VbWx3BJVofKh_oKG1jM,29857
 celldetective/gui/viewers/channel_offset_viewer.py,sha256=aQpxrJX9qM_xX848XnFrxrhTqE22DIshtD-uKL8e4gU,12423
-celldetective/gui/viewers/contour_viewer.py,sha256=zN0MKYZRM4mSFIoaeDPf36RcH7D8j1VUsgD_r8HPtDc,14696
+celldetective/gui/viewers/contour_viewer.py,sha256=riHj03LKXLoa-Ys2o2EhCE5nULfcHMohx9LFoXbI6zU,14720
 celldetective/gui/viewers/size_viewer.py,sha256=uXITjaxg5dhQ09Q6TNUxwLxi-ZglyGFcxEH1RtGIZWw,6020
 celldetective/gui/viewers/spot_detection_viewer.py,sha256=JO7kcqATHXR91lLvo8aQ5xVYdtxkMxV-xx36s01VlNQ,12545
 celldetective/gui/viewers/threshold_viewer.py,sha256=CBc6Y7cGK5U3ptAMMkmRLBvm5yl7pjGEUJjB4PKWjfM,11627
@@ -113,15 +114,16 @@ celldetective/models/tracking_configs/no_z_motion.json,sha256=b4RWOJ0w6Y2e0vJYwK
 celldetective/models/tracking_configs/ricm.json,sha256=L-vmwCR1f89U-qnH2Ms0cBfPFR_dxIWoe2ccH8V-QBA,2727
 celldetective/models/tracking_configs/ricm2.json,sha256=DDjJ6ScYcDWvlsy7ujPID8v8H28vcNcMuZmNR8XmGxo,2718
 celldetective/napari/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-celldetective/napari/utils.py,sha256=mjFeG1TDqHJs7cRcpfGWwAoFpWzJYZOEmUue7ZMYmzI,35106
+celldetective/napari/utils.py,sha256=NHaQhaVkgFZ9EuxD3b5N4dNSzQGSJ4dfB9WJ-Ga5N88,35436
 celldetective/processes/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 celldetective/processes/background_correction.py,sha256=fyv2_7ztUex7RDwIRaURweYZsRe-YD_ZPUHeiFmVq6Q,10715
 celldetective/processes/compute_neighborhood.py,sha256=DGi4U3el0OisRNaOQSzUaXpEgHBO440-Q4cUphB6FAA,34393
 celldetective/processes/detect_events.py,sha256=4psWjnYxbMB3p0BrRoQgkXgIdsnUIErrqUkE9CU4hRM,9733
 celldetective/processes/downloader.py,sha256=3SA5T1AoLch90d-VZzIY4wVAlSjDY_kgVLPN3ztRyVk,4589
-celldetective/processes/measure_cells.py,sha256=ccf2j7_6dcRevEhseVXioIjiATx8IvIsi5ZG3IcdhJY,20876
+celldetective/processes/load_table.py,sha256=GxB5ZWmtNbF5Iv6XPaeisNGl3KeNDgfosFm6w64xXrM,1730
+celldetective/processes/measure_cells.py,sha256=yKFEomJ0y2leWn-bp3z4Rs_lAmwDLiQ-Ies3KkFHSxs,21877
 celldetective/processes/segment_cells.py,sha256=klGl5y3tHbLbQFNAQz0PV1FspmiPC-GHVGWYLgyLqwc,26500
-celldetective/processes/track_cells.py,sha256=cgQNn7fsqPCHODhe27sqvMUlubsi7qM_0qjAXbj68oY,15084
+celldetective/processes/track_cells.py,sha256=ndKZpVXonnooOVnHK5AVED5i_i2bZ4FefTt1_dEZS48,15188
 celldetective/processes/train_segmentation_model.py,sha256=j1aPgR4CzF2OR-9njriNmUStVViiWaiicQA9YWRWOTo,25411
 celldetective/processes/train_signal_model.py,sha256=HInUHCXNePhfQs8-DQOreJ19LtLkQopvYSyX8tj0mOo,9498
 celldetective/processes/unified_process.py,sha256=vHAS_LbtwmlOjKho_FpwDy7WHVgyY38s3X2BtHxep7A,11671
@@ -139,19 +141,19 @@ celldetective/scripts/train_signal_model.py,sha256=zPSdlr4WnnL6yTSL9ZreFNVw1is4E
 celldetective/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 celldetective/utils/color_mappings.py,sha256=yarqOTSrTsnOPPiPrrN_vLoPCbgWqF3wjqFwpbp-KsU,1007
 celldetective/utils/data_cleaning.py,sha256=K-2gScxLreX7QkrM0h3dZdP0IsmvCzcxNh2-M9PALZY,22025
-celldetective/utils/data_loaders.py,sha256=tExtC_7gX16VYmYFz8BU7jRKLDug2egVghU1YIcGRh0,16292
+celldetective/utils/data_loaders.py,sha256=6Jg99U93qYjjs2xZErc2cz37tcH5e4vEqDH8PJgoEJs,17077
 celldetective/utils/dataset_helpers.py,sha256=3ezpHO6nytw2Mx0D3maP_4535V2ohOTQn6Qpfk8gnms,6898
 celldetective/utils/downloaders.py,sha256=BIl_8XCeaKvtMVC36WITT2g5-O-n0csoMEQXVoa1B4o,7887
 celldetective/utils/experiment.py,sha256=bgADS70QuW4KGbzDJbVpVM-tw4qmZKMWtDT1cSxugrY,58342
 celldetective/utils/image_augmenters.py,sha256=USYd8z6dVn5z1x96IYJ4mG0smN9I_S21QMGU0wyHmjc,11654
 celldetective/utils/image_cleaning.py,sha256=KliQ3K5hdwPx4eFxJnmg3yi-ZIoimEveunPJkbbA6wA,2388
-celldetective/utils/image_loaders.py,sha256=nsyneHM67R9r-mmWKI7Z6xpe5MQCLOFsaYKFhxw2R-c,34032
+celldetective/utils/image_loaders.py,sha256=9O0kpG2ZQWC2-7VNS5kf7ihmusHTqeBk9po4uiUvsFY,34107
 celldetective/utils/image_transforms.py,sha256=cgaHuEUArWWHgxlBlcQLf--zQa-4VphPJ2s2EyPN29o,11213
 celldetective/utils/io.py,sha256=WQH6B27iS722eVV8HHRaSvxMRZ217LoiEIPOqNGtqJk,1632
 celldetective/utils/mask_cleaning.py,sha256=n1Q2RfyhX0W3AcLO0U6ucSyDGRCofj6bPLSO_xeVZPI,12545
 celldetective/utils/mask_transforms.py,sha256=fX-ajhUhzZwOe7rAnMcQc6w4e2B8SZeRp9jrQLF6DFs,144
-celldetective/utils/masks.py,sha256=wz47NrCsLD_9WX2Goswl_ThgnxyLJokIN6cj8KH7ZjI,7075
-celldetective/utils/maths.py,sha256=cYdIqSgpaDO1JZOpmgGFPPikEvu66absC64op_6kw0o,12003
+celldetective/utils/masks.py,sha256=g3QHtqyVg6RN0BfmDoPXVjwL3O4xa_dKPC_ZeGmzkeE,7064
+celldetective/utils/maths.py,sha256=pbbWWYNIHTnIBiaR2kJHPDaTPO0rpmQSPjHB7liUSG0,12465
 celldetective/utils/model_getters.py,sha256=jVq9FhAF-xUmFOETWP6hByhoWgapmJGlNmSK11fQ69g,11370
 celldetective/utils/model_loaders.py,sha256=CjScJBGtnenb8qRMZkEozdj1-ULYHvsDFS4AVgYbB5s,10576
 celldetective/utils/normalization.py,sha256=SN-nrycZtmtqv8v1S9bAKvDTGiN6cQKfryitwNtH1bA,15635
@@ -164,24 +166,25 @@ celldetective/utils/event_detection/__init__.py,sha256=KX20PwPTevdbZ-25otDy_QTme
 celldetective/utils/plots/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 celldetective/utils/plots/regression.py,sha256=oUCn29-hp7PxMqC-R0yoL60KMw5ZWpZAIoCDh2ErlcY,1764
 celldetective/utils/stardist_utils/__init__.py,sha256=e9s3DEaTKCUOGZb5k_DgShBTl4B0U-Jmg3Ioo8D5PyE,3978
-celldetective-1.5.0b1.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+celldetective-1.5.0b3.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
 tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tests/test_events.py,sha256=eLFwwEEJfQAdwhews3-fn1HSvzozcNNFN_Qn0gOvQkE,685
 tests/test_filters.py,sha256=uj4NVyUnKXa18EpTSiWCetGKI1VFopDyNSJSUxX44wA,1689
 tests/test_io.py,sha256=gk5FmoI7ANEczUtNXYRxc48KzkfYzemwS_eYaLq4_NI,2093
 tests/test_measure.py,sha256=FEUAs1rVHylvIvubCb0bJDNGZLVmkgXNgI3NaGQ1dA8,4542
 tests/test_neighborhood.py,sha256=gk5FmoI7ANEczUtNXYRxc48KzkfYzemwS_eYaLq4_NI,2093
-tests/test_notebooks.py,sha256=WP5TJM1HV1oN8Hp38MLyE2YuLXjUoMvMJBa343vp1Dg,299
+tests/test_notebooks.py,sha256=7HVmYiytsz0QIJ11iRkGGs4_hzNjofXAUs_OZou3Gm0,301
 tests/test_preprocessing.py,sha256=c0rKS9d5h37uDcV7fVOTnn5GMVbEB84b8ZTCTdRmvFs,1422
 tests/test_segmentation.py,sha256=k1b_zIZdlytEdJcHjAUQEO3gTBAHtv5WvrwQN2xD4kc,3470
 tests/test_signals.py,sha256=No4cah6KxplhDcKXnU8RrA7eDla4hWw6ccf7xGnBokU,3599
 tests/test_tracking.py,sha256=_YLjwQ3EChQssoHDfEnUJ7fI1yC5KEcJsFnAVR64L70,18909
 tests/test_utils.py,sha256=aSB_eMw9fzTsnxxdYoNmdQQRrXkWqBXB7Uv4TGU6kYE,4778
 tests/gui/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+tests/gui/test_enhancements.py,sha256=3x9au_rkQtMZ94DRj3OaEHKPr511RrWqBAUAcNQn1ys,13453
 tests/gui/test_new_project.py,sha256=wRjW2vEaZb0LWT-f8G8-Ptk8CW9z8-FDPLpV5uqj6ck,8778
 tests/gui/test_project.py,sha256=KzAnodIc0Ovta0ARL5Kr5PkOR5euA6qczT_GhEZpyE4,4710
-celldetective-1.5.0b1.dist-info/METADATA,sha256=_caTP5XkidOp8X2DIaINXht-jIS1cznMI0IPzzU3K68,10947
-celldetective-1.5.0b1.dist-info/WHEEL,sha256=qELbo2s1Yzl39ZmrAibXA2jjPLUYfnVhUNTlyF1rq0Y,92
-celldetective-1.5.0b1.dist-info/entry_points.txt,sha256=2NU6_EOByvPxqBbCvjwxlVlvnQreqZ3BKRCVIKEv3dg,62
-celldetective-1.5.0b1.dist-info/top_level.txt,sha256=6rsIKKfGMKgud7HPuATcpq6EhdXwcg_yknBVWn9x4C4,20
-celldetective-1.5.0b1.dist-info/RECORD,,
+celldetective-1.5.0b3.dist-info/METADATA,sha256=D4LkOtPQrdeuX4zW5_OKXlN1dxkxaZx_zqdILC36-Hk,10947
+celldetective-1.5.0b3.dist-info/WHEEL,sha256=qELbo2s1Yzl39ZmrAibXA2jjPLUYfnVhUNTlyF1rq0Y,92
+celldetective-1.5.0b3.dist-info/entry_points.txt,sha256=2NU6_EOByvPxqBbCvjwxlVlvnQreqZ3BKRCVIKEv3dg,62
+celldetective-1.5.0b3.dist-info/top_level.txt,sha256=6rsIKKfGMKgud7HPuATcpq6EhdXwcg_yknBVWn9x4C4,20
+celldetective-1.5.0b3.dist-info/RECORD,,