celldetective 1.3.2__py3-none-any.whl → 1.3.4__py3-none-any.whl

celldetective/signals.py

@@ -27,7 +27,7 @@ from natsort import natsorted
 from glob import glob
 import random
 from celldetective.utils import color_from_status, color_from_class
-from math import floor, ceil
+from math import floor
 from scipy.optimize import curve_fit
 import time
 import math
@@ -193,73 +193,74 @@ def analyze_signals(trajectories, model, interpolate_na=True,
 			signals[i,max(frames):,j] = signal[-1]
 
 	model = SignalDetectionModel(pretrained=complete_path)
+	if not model.pretrained is None:
 
-	classes = model.predict_class(signals)
-	times_recast = model.predict_time_of_interest(signals)
+		classes = model.predict_class(signals)
+		times_recast = model.predict_time_of_interest(signals)
 
-	if label is None:
-		class_col = 'class'
-		time_col = 't0'
-		status_col = 'status'
-	else:
-		class_col = 'class_'+label
-		time_col = 't_'+label
-		status_col = 'status_'+label
+		if label is None:
+			class_col = 'class'
+			time_col = 't0'
+			status_col = 'status'
+		else:
+			class_col = 'class_'+label
+			time_col = 't_'+label
+			status_col = 'status_'+label
 
-	for i,(tid,group) in enumerate(trajectories.groupby(column_labels['track'])):
-		indices = group.index
-		trajectories.loc[indices,class_col] = classes[i]
-		trajectories.loc[indices,time_col] = times_recast[i]
-	print('Done.')
+		for i,(tid,group) in enumerate(trajectories.groupby(column_labels['track'])):
+			indices = group.index
+			trajectories.loc[indices,class_col] = classes[i]
+			trajectories.loc[indices,time_col] = times_recast[i]
+		print('Done.')
 
-	for tid, group in trajectories.groupby(column_labels['track']):
-		
-		indices = group.index
-		t0 = group[time_col].to_numpy()[0]
-		cclass = group[class_col].to_numpy()[0]
-		timeline = group[column_labels['time']].to_numpy()
-		status = np.zeros_like(timeline)
-		if t0 > 0:
-			status[timeline>=t0] = 1.
-		if cclass==2:
-			status[:] = 2
-		if cclass>2:
-			status[:] = 42
-		status_color = [color_from_status(s) for s in status]
-		class_color = [color_from_class(cclass) for i in range(len(status))]
-
-		trajectories.loc[indices, status_col] = status
-		trajectories.loc[indices, 'status_color'] = status_color
-		trajectories.loc[indices, 'class_color'] = class_color
-
-	if plot_outcome:
-		fig,ax = plt.subplots(1,len(selected_signals), figsize=(10,5))
-		for i,s in enumerate(selected_signals):
-			for k,(tid,group) in enumerate(trajectories.groupby(column_labels['track'])):
-				cclass = group[class_col].to_numpy()[0]
-				t0 = group[time_col].to_numpy()[0]
-				timeline = group[column_labels['time']].to_numpy()
-				if cclass==0:
-					if len(selected_signals)>1:
-						ax[i].plot(timeline - t0, group[s].to_numpy(),c='tab:blue',alpha=0.1)
-					else:
-						ax.plot(timeline - t0, group[s].to_numpy(),c='tab:blue',alpha=0.1)
-		if len(selected_signals)>1:				
-			for a,s in zip(ax,selected_signals):
-				a.set_title(s)
-				a.set_xlabel(r'time - t$_0$ [frame]')
-				a.spines['top'].set_visible(False)
-				a.spines['right'].set_visible(False)
-		else:
-			ax.set_title(s)
-			ax.set_xlabel(r'time - t$_0$ [frame]')
-			ax.spines['top'].set_visible(False)
-			ax.spines['right'].set_visible(False)			
-		plt.tight_layout()
-		if output_dir is not None:
-			plt.savefig(output_dir+'signal_collapse.png',bbox_inches='tight',dpi=300)
-		plt.pause(3)
-		plt.close()
+		for tid, group in trajectories.groupby(column_labels['track']):
+			
+			indices = group.index
+			t0 = group[time_col].to_numpy()[0]
+			cclass = group[class_col].to_numpy()[0]
+			timeline = group[column_labels['time']].to_numpy()
+			status = np.zeros_like(timeline)
+			if t0 > 0:
+				status[timeline>=t0] = 1.
+			if cclass==2:
+				status[:] = 2
+			if cclass>2:
+				status[:] = 42
+			status_color = [color_from_status(s) for s in status]
+			class_color = [color_from_class(cclass) for i in range(len(status))]
+
+			trajectories.loc[indices, status_col] = status
+			trajectories.loc[indices, 'status_color'] = status_color
+			trajectories.loc[indices, 'class_color'] = class_color
+
+		if plot_outcome:
+			fig,ax = plt.subplots(1,len(selected_signals), figsize=(10,5))
+			for i,s in enumerate(selected_signals):
+				for k,(tid,group) in enumerate(trajectories.groupby(column_labels['track'])):
+					cclass = group[class_col].to_numpy()[0]
+					t0 = group[time_col].to_numpy()[0]
+					timeline = group[column_labels['time']].to_numpy()
+					if cclass==0:
+						if len(selected_signals)>1:
+							ax[i].plot(timeline - t0, group[s].to_numpy(),c='tab:blue',alpha=0.1)
+						else:
+							ax.plot(timeline - t0, group[s].to_numpy(),c='tab:blue',alpha=0.1)
+			if len(selected_signals)>1:				
+				for a,s in zip(ax,selected_signals):
+					a.set_title(s)
+					a.set_xlabel(r'time - t$_0$ [frame]')
+					a.spines['top'].set_visible(False)
+					a.spines['right'].set_visible(False)
+			else:
+				ax.set_title(s)
+				ax.set_xlabel(r'time - t$_0$ [frame]')
+				ax.spines['top'].set_visible(False)
+				ax.spines['right'].set_visible(False)			
+			plt.tight_layout()
+			if output_dir is not None:
+				plt.savefig(output_dir+'signal_collapse.png',bbox_inches='tight',dpi=300)
+			plt.pause(3)
+			plt.close()
 
 	return trajectories
 
@@ -800,8 +801,12 @@ class SignalDetectionModel(object):
 
 
 		if self.pretrained is not None:
-			print(f"Load pretrained models from {path}...")
-			self.load_pretrained_model()
+			print(f"Load pretrained models from {pretrained}...")
+			test = self.load_pretrained_model()
+			if test is None:
+				self.pretrained = None
+				print('Pretrained model could not be loaded. Check the log for error. Abort...')
+				return None
 		else:
 			print("Create models from scratch...")
 			self.create_models_from_scratch()
@@ -828,6 +833,9 @@ class SignalDetectionModel(object):
 		- The configuration file is expected to be named "config_input.json" and located in the same directory as the models.
 		"""
 
+		if self.pretrained.endswith(os.sep):
+			self.pretrained = os.sep.join(self.pretrained.split(os.sep)[:-1])
+
 		try:
 			self.model_class = load_model(os.sep.join([self.pretrained,"classifier.h5"]),compile=False)
 			self.model_class.load_weights(os.sep.join([self.pretrained,"classifier.h5"]))
@@ -843,6 +851,9 @@ class SignalDetectionModel(object):
 			print(f"Error {e}...")
 			self.model_reg = None
 
+		if self.model_class is None and self.model_reg is None:
+			return None
+
 		# load config
 		with open(os.sep.join([self.pretrained,"config_input.json"])) as config_file:
 			model_config = json.load(config_file)

celldetective/tracking.py

@@ -959,22 +959,28 @@ def write_first_detection_class(tab, column_labels={'track': "TRACK_ID", 'time':
 		indices = track_group.index
 		detection = track_group[column_labels['x']].values
 		timeline = track_group[column_labels['time']].values
-		if len(timeline)>2:
-			dt = timeline[1] - timeline[0]
-			if np.any(detection==detection):
-				t_first = timeline[detection==detection][0]
-				cclass = 0
-				if t_first<=0:
-					t_first = -1
-					cclass = 2
-				else:
-					t_first =  float(t_first) - float(dt)
-			else:
+		dt = 1
+		
+		# Initialize
+		cclass = 2; t_first = np.nan;
+
+		if np.any(detection==detection):
+			t_first = timeline[detection==detection][0]
+			cclass = 0
+			if t_first<=0:
 				t_first = -1
 				cclass = 2
+			else:
+				t_first =  float(t_first) - float(dt)
+				if t_first==0:
+					t_first += 0.01
+		else:
+			t_first = -1
+			cclass = 2
+
+		tab.loc[indices, 'class_firstdetection'] = cclass
+		tab.loc[indices, 't_firstdetection'] = t_first
 
-			tab.loc[indices, 'class_firstdetection'] = cclass
-			tab.loc[indices, 't_firstdetection'] = t_first
 	return tab
 
 

{celldetective-1.3.2.dist-info → celldetective-1.3.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: celldetective
-Version: 1.3.2
+Version: 1.3.4
 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 +34,14 @@ 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
+Requires-Dist: requests
 
 # Celldetective
 
@@ -171,20 +173,20 @@ 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-1.3.4.dist-info}/RECORD

@@ -1,48 +1,48 @@
 celldetective/__init__.py,sha256=bi3SGTMo6s2qQBsJAaKy-a4xaGcTQVW8zsqaiX5XKeY,139
-celldetective/__main__.py,sha256=_H9B620ntENFx9RBvlV6ybxpvtHzCbv5NnIPmDBr9Z0,1127
-celldetective/_version.py,sha256=HgKA3RqZvC7slo8MgLyffCGwJbQ3cY6I7oUMFvGLWps,22
+celldetective/__main__.py,sha256=bxTlSvbKhqn3LW_azd2baDCnDsgb37PAP9DfuAJ1_5M,1844
+celldetective/_version.py,sha256=U6E-HRsrit7kgSGgIeTI2eMUeyUCny5DH8LDV4I1o0g,22
 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/neighborhood.py,sha256=66fsOPDtjbrUTww97wVFmPk-UZakJgglua8O1Jl-RC4,56745
+celldetective/extra_properties.py,sha256=y556D6EMjLGhtjDqRoOTRGa85XxTIe0K1Asb26VZXmo,5643
+celldetective/filters.py,sha256=9w4JyPH2cISRu7gtUDVsm9whiMMWxuc1vwhfaq3zWkY,3683
+celldetective/io.py,sha256=_SO32G5Sc60vHQhQj7gXvDNTXjVd1uZ8x1HnFxCYU0g,90833
+celldetective/measure.py,sha256=PXi13O6wjXbgj53o-C8DEWLVkmy9qb4vocmq1irPVV0,57450
+celldetective/neighborhood.py,sha256=s-zVsfGnPlqs6HlDJCXRh21lLiPKbA_S1JC6uZvfG_0,56712
 celldetective/preprocessing.py,sha256=WmetQCgmHK6fo8AuwESPLab05WgeIy8ElBs-9KM-Cco,44081
 celldetective/relative_measurements.py,sha256=av5DiGlGsbILPav8aVcFlhbmbPLPZPxCB5qQejzhiRY,30400
 celldetective/segmentation.py,sha256=NjAVaVpZufpJ-LIvBx5UFH6j5kjRKE6EVLjttDrqaqs,30826
-celldetective/signals.py,sha256=XGBTyAPVp7hhXDK1qRFrC4H2U65jj2nBR4FQJ4LvUvA,121028
-celldetective/tracking.py,sha256=zZ9J1plUCTjKuK4HAPiuj3BysoR6hLehqYVsBEqhCnk,37995
+celldetective/signals.py,sha256=ngBcl6xYlLX4KE7UFgLDzugmoJvrKG7URSPzlhUFNVE,121461
+celldetective/tracking.py,sha256=e6XMunjVRhBnv1cRF66hkK-Hbti5KyPrs2mnR6qKpvU,38027
 celldetective/utils.py,sha256=oP_GHPdJJHK9s8sIlzKEXfTjCvzxAifdYYynkSMfu7A,89145
 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=OyEyWF6KJ4YzGK-8ZeMwYmPEG1maHcHlxmdsCJyUiEs,14963
+celldetective/gui/InitWindow.py,sha256=sQSwfZ6SIQeZDQ_3KZoMO2MH9Fs9rhWeqxzEf9PFjEM,14534
 celldetective/gui/__init__.py,sha256=2_r2xfOj4_2xj0yBkCTIfzlF94AHKm-j6Pvpd7DddQc,989
 celldetective/gui/about.py,sha256=FJZrj6C-p6uqp_3UaprKosuW-Sw9_HPNQAvFbis9Gdk,1749
-celldetective/gui/analyze_block.py,sha256=sat8RECEeZxlaconZZIxI0IrIjwJo121PcBXqJmA1-o,24756
+celldetective/gui/analyze_block.py,sha256=h0sp7Tk3hZFM8w0yTidwIjZX4WRI-lQF3JCFObrLCPo,2761
 celldetective/gui/btrack_options.py,sha256=OrvbG5coZhLRk5jtXiLFJu34z1hWHN9kHkBiZ7XMZoI,39269
-celldetective/gui/classifier_widget.py,sha256=4239jKQb1uZMQU6iBBicavE05QAgmBQBM0YnmDesoPs,18430
+celldetective/gui/classifier_widget.py,sha256=mo7Gel3DKhFTUt184WvF0AOsw4HQ7kC8qrkSf8jr3hY,18412
 celldetective/gui/configure_new_exp.py,sha256=Eyr-M4FH-4xrUJbIGNdKXAtXb_ULr8lCol26JSzXEww,20125
-celldetective/gui/control_panel.py,sha256=5twtX3-gKAJZVNXkuAkX4PLcOgmRhAyFHZSG3bk7xpk,19144
-celldetective/gui/generic_signal_plot.py,sha256=KPJU5uP7uHxWQ6txmZx6gFalGPGxC165LSsx7AvB7zA,35605
-celldetective/gui/gui_utils.py,sha256=og9iz2DkkJc_4UZmnvhN2oCMMPbJVnx-FAF10JfR8Eo,30441
+celldetective/gui/control_panel.py,sha256=Xr8W37KkRoR2R4ILsZbclnU6-g3WP1WjjTz6k39PN_8,21645
+celldetective/gui/generic_signal_plot.py,sha256=cfPvNcLtsVp3xvKyOg1ekMKXcomN6fEnlowUnXrYK2c,36293
+celldetective/gui/gui_utils.py,sha256=b6L4mThjN8upgXx4YeNRrfSSCF2l1epb_uEU8cc31F8,34171
 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/layouts.py,sha256=XsqiHR58DXsG5SSD5S8KOtUv4yw-y-s2_wZx_XsHeJs,52013
+celldetective/gui/measurement_options.py,sha256=MnJ9dToJb-_UppqHEyFoIvqY8M2cneTGmqxMToeTJ48,39579
 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/plot_measurements.py,sha256=n0pDUcYcsKlSMaUaBSVplGziuWp_7jKaeXdREs-MqyI,50848
+celldetective/gui/plot_signals_ui.py,sha256=dLClQYdQcs98Dq6RWixWXM7_iS67CicOe695bA9LM-w,16447
+celldetective/gui/process_block.py,sha256=tk3zhhXhutszmFP3T7zbXnoCOZRbFUHPBR4cNNaHQOk,68683
+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
-celldetective/gui/signal_annotator2.py,sha256=Phft2_mjwtadd_BFNnZwofOGtrzXL9AEBG46hHvlZow,108888
+celldetective/gui/signal_annotator.py,sha256=gZtuWoVWjaIzxy5SL1Cg2rBrsH9-s-oYSxJe7CQeEiY,88656
+celldetective/gui/signal_annotator2.py,sha256=fAgkNexxvcnY4KvIxtgHKF3B9K-wsgfA8KbkALq4UPY,108945
 celldetective/gui/signal_annotator_options.py,sha256=ztFFgA70SJ0QkntxYGsgDNCvSuSR5GjF7_J6pYVYc1g,11020
-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/styles.py,sha256=awg5NfGWUoM4V_LpVlmPP7JorpofiLVNqLBv4zRy89E,5058
+celldetective/gui/survival_ui.py,sha256=7qUenqEIaWEwdf-nKE1gN0LAdybgQbRLb3OJMTI9bfk,10193
+celldetective/gui/tableUI.py,sha256=2tBZN3X1nrBD_t58yaCY4NENWeHtgvaN0IcKzZn18SM,50500
+celldetective/gui/thresholds_gui.py,sha256=6Lgr_CK2LBn_gMsWf0gIQvQIQSMg3oIhFfknFeg8Fh4,50721
+celldetective/gui/viewers.py,sha256=0KmtAKZUNY5xpKFcFajgc1Jbnf_86rw_ooX6UrMmEHc,46328
 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
@@ -75,7 +80,7 @@ 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/scripts/analyze_signals.py,sha256=YE05wZujl2hQFWkvqATBcCx-cAd_V3RxnvKoh0SB7To,2194
-celldetective/scripts/measure_cells.py,sha256=hKBLX6qT1K5asq0e53kLs2_Xr9oPYwliiEaPQgpnNrU,11734
+celldetective/scripts/measure_cells.py,sha256=jUwPSjIzR4sCvjer_K5vSlRQX3e8AhJE3xhUbevES7c,12143
 celldetective/scripts/measure_relative.py,sha256=L_NjIUfHSGupkAKLZkubBHJdZh0ugPhCTJem80b0zMM,4261
 celldetective/scripts/segment_cells.py,sha256=bnNacgp_6qpb1fvwPizxVctsUNiFBegKalo-PSpXPEU,8262
 celldetective/scripts/segment_cells_thresholds.py,sha256=6ERg-hxdHMSgXPQSBPtYt2lccTlkz9ZLktYgb57Avmw,5168
@@ -89,14 +94,14 @@ 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_preprocessing.py,sha256=FI-Wk-kc4wWmOQg_NLCUIZC1oti396wr5cC-BauBai0,1436
-tests/test_qt.py,sha256=eYqOoff-vfvZAZM6H_IY19IqK7qzyETcyj54f9T0bQA,3906
+tests/test_qt.py,sha256=Mx8qxUofHyMo2NnPOKQq108sJ-7skVFGWAA_VMyehMw,4042
 tests/test_segmentation.py,sha256=k1b_zIZdlytEdJcHjAUQEO3gTBAHtv5WvrwQN2xD4kc,3470
 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-1.3.4.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+celldetective-1.3.4.dist-info/METADATA,sha256=h45Xti2RUbcEQk5Om87dsNhfDQnRCHPOl_Pw3kFfH48,10528
+celldetective-1.3.4.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+celldetective-1.3.4.dist-info/entry_points.txt,sha256=2NU6_EOByvPxqBbCvjwxlVlvnQreqZ3BKRCVIKEv3dg,62
+celldetective-1.3.4.dist-info/top_level.txt,sha256=6rsIKKfGMKgud7HPuATcpq6EhdXwcg_yknBVWn9x4C4,20
+celldetective-1.3.4.dist-info/RECORD,,

{celldetective-1.3.2.dist-info → celldetective-1.3.4.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
 

tests/test_qt.py

@@ -1,6 +1,7 @@
 import pytest
 from PyQt5 import QtCore
 from celldetective.gui.InitWindow import AppInitWindow
+from celldetective.utils import get_software_location
 import time
 import os
 
@@ -9,7 +10,8 @@ print(abs_path)
 
 @pytest.fixture
 def app(qtbot):
-	test_app = AppInitWindow()
+	software_location = get_software_location()
+	test_app = AppInitWindow(software_location=software_location)
 	qtbot.addWidget(test_app)
 	return test_app
 
@@ -33,8 +35,8 @@ def test_app(app, qtbot):
 	qtbot.mouseClick(app.validate_button, QtCore.Qt.LeftButton)
 
 	# Set a position
-	app.control_panel.position_list.setCurrentIndex(1)
-	app.control_panel.update_position_options()
+	#app.control_panel.position_list.setCurrentIndex(0)
+	#app.control_panel.update_position_options()
 
 	# View stacl
 	qtbot.mouseClick(app.control_panel.view_stack_btn, QtCore.Qt.LeftButton)