celldetective 1.3.7.post2__py3-none-any.whl → 1.3.8.post1__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- celldetective/_version.py +1 -1
- celldetective/gui/btrack_options.py +8 -8
- celldetective/gui/classifier_widget.py +8 -0
- celldetective/gui/configure_new_exp.py +1 -1
- celldetective/gui/json_readers.py +2 -4
- celldetective/gui/plot_signals_ui.py +38 -29
- celldetective/gui/process_block.py +1 -0
- celldetective/gui/processes/segment_cells.py +50 -23
- celldetective/gui/seg_model_loader.py +71 -25
- celldetective/gui/signal_annotator2.py +10 -7
- celldetective/gui/signal_annotator_options.py +1 -1
- celldetective/gui/tableUI.py +252 -20
- celldetective/gui/viewers.py +1 -1
- celldetective/io.py +28 -20
- celldetective/links/zenodo.json +233 -93
- celldetective/models/signal_detection/NucCond/classification_loss.png +0 -0
- celldetective/models/signal_detection/NucCond/classifier.h5 +0 -0
- celldetective/models/signal_detection/NucCond/config_input.json +1 -0
- celldetective/models/signal_detection/NucCond/log_classifier.csv +126 -0
- celldetective/models/signal_detection/NucCond/log_regressor.csv +282 -0
- celldetective/models/signal_detection/NucCond/regression_loss.png +0 -0
- celldetective/models/signal_detection/NucCond/regressor.h5 +0 -0
- celldetective/models/signal_detection/NucCond/scores.npy +0 -0
- celldetective/models/signal_detection/NucCond/test_confusion_matrix.png +0 -0
- celldetective/models/signal_detection/NucCond/test_regression.png +0 -0
- celldetective/models/signal_detection/NucCond/validation_confusion_matrix.png +0 -0
- celldetective/models/signal_detection/NucCond/validation_regression.png +0 -0
- celldetective/segmentation.py +48 -1
- celldetective/signals.py +43 -13
- celldetective/tracking.py +7 -2
- celldetective/utils.py +1 -1
- {celldetective-1.3.7.post2.dist-info → celldetective-1.3.8.post1.dist-info}/METADATA +1 -1
- {celldetective-1.3.7.post2.dist-info → celldetective-1.3.8.post1.dist-info}/RECORD +37 -25
- {celldetective-1.3.7.post2.dist-info → celldetective-1.3.8.post1.dist-info}/LICENSE +0 -0
- {celldetective-1.3.7.post2.dist-info → celldetective-1.3.8.post1.dist-info}/WHEEL +0 -0
- {celldetective-1.3.7.post2.dist-info → celldetective-1.3.8.post1.dist-info}/entry_points.txt +0 -0
- {celldetective-1.3.7.post2.dist-info → celldetective-1.3.8.post1.dist-info}/top_level.txt +0 -0
celldetective/signals.py
CHANGED
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@@ -33,6 +33,7 @@ import time
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import math
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import pandas as pd
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from pandas.api.types import is_numeric_dtype
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from scipy.stats import median_abs_deviation
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abs_path = os.sep.join([os.path.split(os.path.dirname(os.path.realpath(__file__)))[0],'celldetective'])
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@@ -680,11 +681,22 @@ class SignalDetectionModel(object):
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if 'label' in model_config:
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self.label = model_config['label']
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try:
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self.n_channels = self.model_class.layers[0].input_shape[0][-1]
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self.model_signal_length = self.model_class.layers[0].input_shape[0][-2]
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self.n_classes = self.model_class.layers[-1].output_shape[-1]
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model_class_input_shape = self.model_class.layers[0].input_shape[0]
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model_reg_input_shape = self.model_reg.layers[0].input_shape[0]
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except AttributeError:
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self.n_channels = self.model_class.input_shape[-1] #self.model_class.layers[0].input.shape[0][-1]
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self.model_signal_length = self.model_class.input_shape[-2] #self.model_class.layers[0].input[0].shape[0][-2]
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self.n_classes = self.model_class.output_shape[-1] #self.model_class.layers[-1].output[0].shape[-1]
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model_class_input_shape = self.model_class.input_shape
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model_reg_input_shape = self.model_reg.input_shape
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except Exception as e:
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print(e)
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assert
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assert model_class_input_shape==model_reg_input_shape, f"mismatch between input shape of classification: {self.model_class.layers[0].input_shape[0]} and regression {self.model_reg.layers[0].input_shape[0]} models... Error."
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return True
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@@ -1015,8 +1027,15 @@ class SignalDetectionModel(object):
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# plt.plot(self.x[i,:,0])
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# plt.show()
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try:
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n_channels = self.model_class.layers[0].input_shape[0][-1]
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model_signal_length = self.model_class.layers[0].input_shape[0][-2]
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except AttributeError:
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n_channels = self.model_class.input_shape[-1]
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model_signal_length = self.model_class.input_shape[-2]
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assert self.x.shape[-1] == n_channels, f"Shape mismatch between the input shape and the model input shape..."
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assert self.x.shape[-2] == model_signal_length, f"Shape mismatch between the input shape and the model input shape..."
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self.class_predictions_one_hot = self.model_class.predict(self.x)
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self.class_predictions = self.class_predictions_one_hot.argmax(axis=1)
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@@ -1072,8 +1091,15 @@ class SignalDetectionModel(object):
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normalization_values=self.normalization_values, normalization_clip=self.normalization_clip,
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)
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try:
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n_channels = self.model_reg.layers[0].input_shape[0][-1]
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model_signal_length = self.model_reg.layers[0].input_shape[0][-2]
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except AttributeError:
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n_channels = self.model_reg.input_shape[-1]
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model_signal_length = self.model_reg.input_shape[-2]
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assert self.x.shape[-1] == n_channels, f"Shape mismatch between the input shape and the model input shape..."
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assert self.x.shape[-2] == model_signal_length, f"Shape mismatch between the input shape and the model input shape..."
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if np.any(self.class_predictions==0):
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self.time_predictions = self.model_reg.predict(self.x[self.class_predictions==0])*self.model_signal_length
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@@ -2749,7 +2775,7 @@ def sliding_msd_drift(x, y, timeline, window, mode='bi', n_points_migration=7,
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return s_diffusion, s_velocity
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def columnwise_mean(matrix, min_nbr_values = 1):
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def columnwise_mean(matrix, min_nbr_values = 1, projection='mean'):
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"""
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Calculate the column-wise mean and standard deviation of non-NaN elements in the input matrix.
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values = matrix[:,k]
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values = values[values==values]
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if len(values[values==values])>min_nbr_values:
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if projection=='mean':
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mean_line[k] = np.nanmean(values)
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mean_line_std[k] = np.nanstd(values)
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elif projection=='median':
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mean_line[k] = np.nanmedian(values)
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mean_line_std[k] = median_abs_deviation(values, center=np.nanmedian, nan_policy='omit')
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return mean_line, mean_line_std
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def mean_signal(df, signal_name, class_col, time_col=None, class_value=[0], return_matrix=False, forced_max_duration=None, min_nbr_values=2,conflict_mode='mean'):
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def mean_signal(df, signal_name, class_col, time_col=None, class_value=[0], return_matrix=False, forced_max_duration=None, min_nbr_values=2,conflict_mode='mean', projection='mean'):
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"""
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Calculate the mean and standard deviation of a specified signal for tracks of a given class in the input DataFrame.
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signal_matrix[trackid,timeline_shifted.astype(int)] = signal
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trackid+=1
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mean_signal, std_signal = columnwise_mean(signal_matrix, min_nbr_values=min_nbr_values)
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mean_signal, std_signal = columnwise_mean(signal_matrix, min_nbr_values=min_nbr_values, projection=projection)
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actual_timeline = np.linspace(-max_duration, max_duration, 2*max_duration+1)
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if return_matrix:
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return mean_signal, std_signal, actual_timeline, signal_matrix
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celldetective/tracking.py
CHANGED
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@@ -441,9 +441,14 @@ def interpolate_per_track(group_df):
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"""
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for c in list(group_df.columns):
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group_df_new_dtype = group_df[c].infer_objects(copy=False)
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if group_df_new_dtype.dtype!='O':
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group_df[c] = group_df_new_dtype.interpolate(method='linear',limit_direction="both")
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#interpolated_group = group_df.interpolate(method='linear',limit_direction="both")
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return
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return group_df
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def interpolate_nan_properties(trajectories, track_label="TRACK_ID"):
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celldetective/utils.py
CHANGED
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celldetective/__init__.py,sha256=bi3SGTMo6s2qQBsJAaKy-a4xaGcTQVW8zsqaiX5XKeY,139
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celldetective/__main__.py,sha256=bxTlSvbKhqn3LW_azd2baDCnDsgb37PAP9DfuAJ1_5M,1844
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celldetective/_version.py,sha256=
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celldetective/_version.py,sha256=Gwdlkn6lk8YInJKr89NJRcSacpWsCYBBBhoLN4FGb2Y,28
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celldetective/events.py,sha256=UkjY_-THo6WviWWCLnDbma7jWOd_O9a60C4IOX2htG8,8254
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celldetective/extra_properties.py,sha256=y556D6EMjLGhtjDqRoOTRGa85XxTIe0K1Asb26VZXmo,5643
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celldetective/filters.py,sha256=DT3MyqNBSj3EMtb74oZUirdonKcwcowjtehTT72mrrk,4181
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celldetective/io.py,sha256=
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celldetective/io.py,sha256=kD8jvaZJHndlYXM-NwVjesKs8tRQNYiZJCH5VHmk2uA,123067
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celldetective/measure.py,sha256=IfmyRaGzYjlTKh6uVBdn4qLEm6LgXQstb5NlB_Blc8I,58291
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celldetective/neighborhood.py,sha256=s-zVsfGnPlqs6HlDJCXRh21lLiPKbA_S1JC6uZvfG_0,56712
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celldetective/preprocessing.py,sha256=Wlt_PJua97CpMuWe_M65znUmz_yjYPqWIcs2ZK_RLgk,44109
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celldetective/relative_measurements.py,sha256=-GWig0lC5UWAcJSPlo9Sp45khGj80fxuQfFk-bdBca0,30117
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celldetective/segmentation.py,sha256=
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celldetective/signals.py,sha256=
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celldetective/tracking.py,sha256=
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celldetective/utils.py,sha256=
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celldetective/segmentation.py,sha256=ul8E-cjjaWxaMZfjAtbrH7joUjxbZSeb77GL3Alp5Os,30779
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celldetective/signals.py,sha256=nMyyGUpla8D2sUYKY1zjbWsAueVPI_gUalY0KXfWteI,111595
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celldetective/tracking.py,sha256=VBJLd-1EeJarOVPBNEomhVBh9UYAMdSnH0tmUiUoTrY,40242
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celldetective/utils.py,sha256=lX9W8H7y4z8B5DajUDqAoXlycJbIIzOmX7O-2b7eb04,108440
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celldetective/datasets/segmentation_annotations/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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celldetective/datasets/signal_annotations/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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celldetective/gui/InitWindow.py,sha256=TPKWYczhPHvPKWg654sXnE9xCEx6U-oWX0_OJgLTWbU,15044
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celldetective/gui/__init__.py,sha256=2_r2xfOj4_2xj0yBkCTIfzlF94AHKm-j6Pvpd7DddQc,989
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celldetective/gui/about.py,sha256=FJZrj6C-p6uqp_3UaprKosuW-Sw9_HPNQAvFbis9Gdk,1749
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celldetective/gui/analyze_block.py,sha256=h0sp7Tk3hZFM8w0yTidwIjZX4WRI-lQF3JCFObrLCPo,2761
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celldetective/gui/btrack_options.py,sha256=
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celldetective/gui/classifier_widget.py,sha256=
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celldetective/gui/configure_new_exp.py,sha256=
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celldetective/gui/btrack_options.py,sha256=ZXaJuCdqB_BK1CFRbgZErlAlXMbzDF2DP7opLSd6III,44682
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celldetective/gui/classifier_widget.py,sha256=nHWmaWXse2CxxRFmR4mA0JRADr5i0MsWldaqJQIQ-i8,19992
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celldetective/gui/configure_new_exp.py,sha256=N4SdL-4Xo0XbTAkCtt1ywr74HmHc5eaPlHGv1XgxAX0,20772
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celldetective/gui/control_panel.py,sha256=1TWUCvEif19ZLy4pDUupPrGzIKnG6Tg6kWGp_R8OSG4,22045
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celldetective/gui/generic_signal_plot.py,sha256=Gv4KhA5vhbgVSj5jteE42T0aNCoQZtmIAUkEsMi6JNA,36309
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celldetective/gui/gui_utils.py,sha256=n9JVXBantJK3RFt8fQ7HJYKdCC4ezBMBwlgT5QT2I9o,39343
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celldetective/gui/json_readers.py,sha256=
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celldetective/gui/json_readers.py,sha256=SkI_bR1MlAKd8NLBmQUVjJfZ7mKiU_FEjgC4dUwBACk,3698
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celldetective/gui/layouts.py,sha256=XsqiHR58DXsG5SSD5S8KOtUv4yw-y-s2_wZx_XsHeJs,52013
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celldetective/gui/measurement_options.py,sha256=cfiC4lq-XqY4Sa4Vkw5mys7JKaa9tE2BgeN8_k-SIDY,40355
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celldetective/gui/neighborhood_options.py,sha256=FBNDvlzMPKp8s0Grxds90pCPHG1s27XrpMN0HV2gf0I,19839
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celldetective/gui/plot_measurements.py,sha256=n0pDUcYcsKlSMaUaBSVplGziuWp_7jKaeXdREs-MqyI,50848
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celldetective/gui/plot_signals_ui.py,sha256
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celldetective/gui/process_block.py,sha256=
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celldetective/gui/plot_signals_ui.py,sha256=u7b36pmjF8sf0Ctb9KCrnRcvAD3vlNaaIVkX3-rHCA0,17332
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celldetective/gui/process_block.py,sha256=3v4q5kAq5uY6w0f3zyImXi_iTp8Qv2EFvzNjTEvqG9E,71210
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celldetective/gui/retrain_segmentation_model_options.py,sha256=7iawDN4kwq56Z-dX9kQe9tLW8B3YMrIW_D85LMAAYwk,23906
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celldetective/gui/retrain_signal_model_options.py,sha256=GCa0WKKsgmH2CFDHAKxPGbHtCE19p1_bbcWNasyZw5o,22482
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celldetective/gui/seg_model_loader.py,sha256=
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celldetective/gui/seg_model_loader.py,sha256=b1BiHuAf_ZqroE4jSEVCo7ASQv-xyWMPWU799alpbNM,19727
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celldetective/gui/signal_annotator.py,sha256=9l_qbIO9V862eGk6mVOCXo0jsG8Z3WP9kx7wCBFGvKU,89014
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celldetective/gui/signal_annotator2.py,sha256=
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celldetective/gui/signal_annotator_options.py,sha256=
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celldetective/gui/signal_annotator2.py,sha256=qBDPk3UHmMoY4_i5KJt3Nr8kxjLOkYay_xNc6xrn_pE,106340
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celldetective/gui/signal_annotator_options.py,sha256=ekxy7Qtw5EGqXa82KdZezaSlmprSAGMW2ZZoE1SObRM,11013
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{celldetective-1.3.7.post2.dist-info → celldetective-1.3.8.post1.dist-info}/entry_points.txt
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