celldetective 1.2.0__py3-none-any.whl → 1.2.2__py3-none-any.whl

celldetective/scripts/measure_cells.py

@@ -6,16 +6,14 @@ import argparse
 import os
 import json
 from celldetective.io import auto_load_number_of_frames, load_frames
-from celldetective.utils import extract_experiment_channels, _extract_channel_indices_from_config, _extract_channel_indices, ConfigSectionMap, _extract_nbr_channels_from_config, _get_img_num_per_channel, extract_experiment_channels
+from celldetective.utils import extract_experiment_channels, ConfigSectionMap, _get_img_num_per_channel, extract_experiment_channels
 from celldetective.utils import remove_redundant_features, remove_trajectory_measurements
 from celldetective.measure import drop_tonal_features, measure_features, measure_isotropic_intensity
 from pathlib import Path, PurePath
 from glob import glob
-from shutil import rmtree
 from tqdm import tqdm
 import numpy as np
 import pandas as pd
-import gc
 from natsort import natsorted
 from art import tprint
 from tifffile import imread

celldetective/scripts/measure_relative.py

@@ -1,7 +1,6 @@
 import argparse
 import os
-import json
-from celldetective.relative_measurements import measure_pair_signals_at_position, update_effector_table, extract_neighborhoods_from_pickles
+from celldetective.relative_measurements import measure_pair_signals_at_position, extract_neighborhoods_from_pickles
 from celldetective.utils import ConfigSectionMap, extract_experiment_channels
 
 from pathlib import Path, PurePath

celldetective/scripts/segment_cells.py

@@ -9,7 +9,7 @@ import json
 from stardist.models import StarDist2D
 from cellpose.models import CellposeModel
 from celldetective.io import locate_segmentation_model, auto_load_number_of_frames, load_frames
-from celldetective.utils import interpolate_nan, _estimate_scale_factor, _extract_channel_indices_from_config, _extract_channel_indices, ConfigSectionMap, _extract_nbr_channels_from_config, _get_img_num_per_channel, normalize_per_channel
+from celldetective.utils import interpolate_nan, _estimate_scale_factor, _extract_channel_indices_from_config, ConfigSectionMap, _extract_nbr_channels_from_config, _get_img_num_per_channel
 from pathlib import Path, PurePath
 from glob import glob
 from shutil import rmtree
@@ -20,10 +20,7 @@ from csbdeep.io import save_tiff_imagej_compatible
 import gc
 from art import tprint
 from scipy.ndimage import zoom
-import threading
 
-import matplotlib.pyplot as plt
-import time
 
 tprint("Segment")
 
@@ -210,17 +207,24 @@ def segment_index(indices):
 		del Y_pred;
 		gc.collect()
 
+
+import concurrent.futures
+
 # Multithreading
 indices = list(range(img_num_channels.shape[1]))
 chunks = np.array_split(indices, n_threads)
-threads = []
-for i in range(n_threads):
-	thread_i = threading.Thread(target=segment_index, args=[chunks[i]])
-	threads.append(thread_i)
-for th in threads:
-	th.start()
-for th in threads:
-	th.join()
+
+with concurrent.futures.ThreadPoolExecutor() as executor:
+	executor.map(segment_index, chunks)
+
+# threads = []
+# for i in range(n_threads):
+# 	thread_i = threading.Thread(target=segment_index, args=[chunks[i]])
+# 	threads.append(thread_i)
+# for th in threads:
+# 	th.start()
+# for th in threads:
+# 	th.join()
 
 print('Done.')
 

celldetective/scripts/segment_cells_thresholds.py

@@ -7,7 +7,7 @@ import os
 import json
 from celldetective.io import auto_load_number_of_frames, load_frames
 from celldetective.segmentation import segment_frame_from_thresholds
-from celldetective.utils import _estimate_scale_factor, _extract_channel_indices_from_config, _extract_channel_indices, ConfigSectionMap, _extract_nbr_channels_from_config, _get_img_num_per_channel, extract_experiment_channels
+from celldetective.utils import _extract_channel_indices_from_config, ConfigSectionMap, _extract_nbr_channels_from_config, _get_img_num_per_channel, extract_experiment_channels
 from pathlib import Path, PurePath
 from glob import glob
 from shutil import rmtree
@@ -16,7 +16,6 @@ import numpy as np
 from csbdeep.io import save_tiff_imagej_compatible
 import gc
 from art import tprint
-import threading
 
 tprint("Segment")
 
@@ -120,17 +119,25 @@ def segment_index(indices):
 		del mask;
 		gc.collect()
 
+import concurrent.futures
+
 # Multithreading
 indices = list(range(img_num_channels.shape[1]))
 chunks = np.array_split(indices, n_threads)
-threads = []
-for i in range(n_threads):
-	thread_i = threading.Thread(target=segment_index, args=[chunks[i]])
-	threads.append(thread_i)
-for th in threads:
-	th.start()
-for th in threads:
-	th.join()
+
+with concurrent.futures.ThreadPoolExecutor() as executor:
+	executor.map(segment_index, chunks)
+
+# indices = list(range(img_num_channels.shape[1]))
+# chunks = np.array_split(indices, n_threads)
+# threads = []
+# for i in range(n_threads):
+# 	thread_i = threading.Thread(target=segment_index, args=[chunks[i]])
+# 	threads.append(thread_i)
+# for th in threads:
+# 	th.start()
+# for th in threads:
+# 	th.join()
 
 print('Done.')
 gc.collect()

celldetective/scripts/track_cells.py

@@ -7,12 +7,11 @@ import datetime
 import os
 import json
 from celldetective.io import auto_load_number_of_frames, load_frames, interpret_tracking_configuration
-from celldetective.utils import extract_experiment_channels, _extract_channel_indices_from_config, _extract_channel_indices, ConfigSectionMap, _extract_nbr_channels_from_config, _get_img_num_per_channel, extract_experiment_channels
+from celldetective.utils import extract_experiment_channels, ConfigSectionMap, _get_img_num_per_channel, extract_experiment_channels
 from celldetective.measure import drop_tonal_features, measure_features
 from celldetective.tracking import track
 from pathlib import Path, PurePath
 from glob import glob
-from shutil import rmtree
 from tqdm import tqdm
 import numpy as np
 import pandas as pd
@@ -21,7 +20,6 @@ import os
 from natsort import natsorted
 from art import tprint
 from tifffile import imread
-import threading
 
 tprint("Track")
 
@@ -60,7 +58,6 @@ parent1 = Path(pos).parent
 expfolder = parent1.parent
 config = PurePath(expfolder,Path("config.ini"))
 assert os.path.exists(config),'The configuration file for the experiment could not be located. Abort.'
-print("Configuration file: ",config)
 
 # from exp config fetch spatial calib, channel names
 movie_prefix = ConfigSectionMap(config,"MovieSettings")["movie_prefix"]
@@ -76,10 +73,9 @@ nbr_channels = len(channel_names)
 # from tracking instructions, fetch btrack config, features, haralick, clean_traj, idea: fetch custom timeline?
 instr_path = PurePath(expfolder,Path(f"{instruction_file}"))
 if os.path.exists(instr_path):
-	print(f"Tracking instructions for the {mode} population has been successfully located.")
+	print(f"Tracking instructions for the {mode} population have been successfully loaded...")
 	with open(instr_path, 'r') as f:
 		instructions = json.load(f)
-		print("Reading the following instructions: ",instructions)
 	btrack_config = interpret_tracking_configuration(instructions['btrack_config_path'])
 
 	if 'features' in instructions:
@@ -102,7 +98,7 @@ if os.path.exists(instr_path):
 	else:
 		post_processing_options = None
 else:
-	print('No tracking instructions found. Use standard bTrack motion model.')
+	print('Tracking instructions could not be located... Using a standard bTrack motion model instead...')
 	btrack_config = interpret_tracking_configuration(None)
 	features = None
 	mask_channels = None
@@ -117,7 +113,7 @@ label_path = natsorted(glob(pos+f"{label_folder}"+os.sep+"*.tif"))
 if len(label_path)>0:
 	print(f"Found {len(label_path)} segmented frames...")
 else:
-	print(f"No segmented frames have been found. Please run segmentation first, skipping...")
+	print(f"No segmented frames have been found. Please run segmentation first. Abort...")
 	os.abort()
 
 # Do this if features or Haralick is not None, else don't need stack
@@ -168,14 +164,20 @@ def measure_index(indices):
 # Multithreading
 indices = list(range(img_num_channels.shape[1]))
 chunks = np.array_split(indices, n_threads)
-threads = []
-for i in range(n_threads):
-	thread_i = threading.Thread(target=measure_index, args=[chunks[i]])
-	threads.append(thread_i)
-for th in threads:
-	th.start()
-for th in threads:
-	th.join()
+
+import concurrent.futures
+
+with concurrent.futures.ThreadPoolExecutor() as executor:
+	executor.map(measure_index, chunks)
+
+# threads = []
+# for i in range(n_threads):
+# 	thread_i = threading.Thread(target=measure_index, args=[chunks[i]])
+# 	threads.append(thread_i)
+# for th in threads:
+# 	th.start()
+# for th in threads:
+# 	th.join()
 
 df = pd.concat(timestep_dataframes)	
 df.reset_index(inplace=True, drop=True)
@@ -202,8 +204,6 @@ trajectories, napari_data = track(None,
 		  			clean_trajectories_kwargs=post_processing_options, 
 		  			volume=(shape_x, shape_y),
 		  			)
-print(trajectories)
-print(trajectories.columns)
 
 # out trajectory table, create POSITION_X_um, POSITION_Y_um, TIME_min (new ones)
 # Save napari data

celldetective/scripts/train_segmentation_model.py

@@ -11,11 +11,10 @@ from tqdm import tqdm
 import numpy as np
 import random
 
-from celldetective.utils import load_image_dataset, normalize_per_channel, augmenter, interpolate_nan
+from celldetective.utils import load_image_dataset, augmenter, interpolate_nan
 from celldetective.io import normalize_multichannel
 from stardist import fill_label_holes
 from art import tprint
-import matplotlib.pyplot as plt
 from distutils.dir_util import copy_tree
 from csbdeep.utils import save_json
 

celldetective/scripts/train_signal_model.py

@@ -5,11 +5,8 @@ Copright © 2023 Laboratoire Adhesion et Inflammation, Authored by Remy Torro.
 import argparse
 import os
 import json
-from pathlib import Path, PurePath
 from glob import glob
-from tqdm import tqdm
 import numpy as np
-import gc
 from art import tprint
 from celldetective.signals import SignalDetectionModel
 from celldetective.io import locate_signal_model

celldetective/segmentation.py

@@ -3,7 +3,7 @@ Segmentation module
 """
 import json
 import os
-from .io import locate_segmentation_model, get_stack_normalization_values, normalize_multichannel
+from .io import locate_segmentation_model, normalize_multichannel
 from .utils import _estimate_scale_factor, _extract_channel_indices
 from pathlib import Path
 from tqdm import tqdm

celldetective/signals.py

@@ -9,7 +9,7 @@ from tensorflow.keras.losses import CategoricalCrossentropy, MeanSquaredError, M
 from tensorflow.keras.metrics import Precision, Recall, MeanIoU
 from tensorflow.keras.models import load_model,clone_model
 from tensorflow.config.experimental import list_physical_devices, set_memory_growth
-from tensorflow.keras.utils import to_categorical, plot_model
+from tensorflow.keras.utils import to_categorical
 from tensorflow.keras import Input, Model
 from tensorflow.keras.layers import Conv1D, BatchNormalization, Dense, Activation, Add, MaxPooling1D, Dropout, GlobalAveragePooling1D, Concatenate, ZeroPadding1D, Flatten
 from tensorflow.keras.callbacks import Callback
@@ -18,13 +18,12 @@ from sklearn.metrics import jaccard_score, balanced_accuracy_score, precision_sc
 from scipy.interpolate import interp1d
 from scipy.ndimage import shift
 
-from celldetective.io import get_signal_models_list, locate_signal_model, get_position_pickle, get_position_table
+from celldetective.io import locate_signal_model, get_position_pickle, get_position_table
 from celldetective.tracking import clean_trajectories, interpolate_nan_properties
 from celldetective.utils import regression_plot, train_test_split, compute_weights
 import matplotlib.pyplot as plt
 from natsort import natsorted
 from glob import glob
-import shutil
 import random
 from celldetective.utils import color_from_status, color_from_class
 from math import floor, ceil
@@ -155,6 +154,7 @@ def analyze_signals(trajectories, model, interpolate_na=True,
 	f = open(model_config_path)
 	config = json.load(f)
 	required_signals = config["channels"]
+	model_signal_length = config['model_signal_length']
 
 	try:
 		label = config['label']
@@ -190,6 +190,8 @@ def analyze_signals(trajectories, model, interpolate_na=True,
 	trajectories_clean = clean_trajectories(trajectories, interpolate_na=interpolate_na, interpolate_position_gaps=interpolate_na, column_labels=column_labels)
 
 	max_signal_size = int(trajectories_clean[column_labels['time']].max()) + 2
+	assert max_signal_size <= model_signal_length,f'The current signals are longer ({max_signal_size}) than the maximum expected input ({model_signal_length}) for this signal analysis model. Abort...'
+
 	tracks = trajectories_clean[column_labels['track']].unique()
 	signals = np.zeros((len(tracks),max_signal_size, len(selected_signals)))
 
@@ -3071,7 +3073,7 @@ def mean_signal(df, signal_name, class_col, time_col=None, class_value=[0], retu
 	3. Tracks with missing or NaN values in the specified signal are ignored during calculation.
 	4. Tracks are aligned based on their 'FRAME' values and the specified `time_col` (if provided).
 	"""
-	
+
 	assert signal_name in list(df.columns),"The signal you want to plot is not one of the measured features."
 	if isinstance(class_value,int):
 		class_value = [class_value]
@@ -3080,6 +3082,11 @@ def mean_signal(df, signal_name, class_col, time_col=None, class_value=[0], retu
 		max_duration = ceil(np.amax(df.groupby(['position','TRACK_ID']).size().values))
 	else:
 		max_duration = forced_max_duration
+	
+	abs_time = False
+	if isinstance(time_col, (int,float)):
+		abs_time = True
+
 	n_tracks = len(df.groupby(['position','TRACK_ID']))
 	signal_matrix = np.zeros((n_tracks,int(max_duration)*2 + 1))
 	signal_matrix[:,:] = np.nan
@@ -3091,11 +3098,16 @@ def mean_signal(df, signal_name, class_col, time_col=None, class_value=[0], retu
 		cclass = track_group[class_col].to_numpy()[0]
 		if cclass != 0:
 			ref_time = 0
+			if abs_time:
+				ref_time = time_col
 		else:
-			try:
-				ref_time = floor(track_group[time_col].to_numpy()[0])
-			except:
-				continue
+			if not abs_time:
+				try:
+					ref_time = floor(track_group[time_col].to_numpy()[0])
+				except:
+					continue
+			else:
+				ref_time = time_col
 		if conflict_mode=='mean':
 			signal = track_group.groupby('FRAME')[signal_name].mean().to_numpy()
 		elif conflict_mode=='first':

celldetective/tracking.py

@@ -10,7 +10,6 @@ from celldetective.measure import measure_features
 from celldetective.utils import rename_intensity_column, velocity_per_track
 from celldetective.io import view_on_napari_btrack, interpret_tracking_configuration
 
-from btrack.datasets import cell_config
 import os
 import subprocess
 
@@ -153,6 +152,8 @@ def track(labels, configuration=None, stack=None, spatial_calibration=1, feature
 		df_temp = pd.DataFrame(x_scaled, columns=columns, index = df.index)
 		df[columns] = df_temp
 
+	# set dummy features to NaN
+	df.loc[df['dummy'],['class_id']+columns] = np.nan 
 	df = df.sort_values(by=[column_labels['track'],column_labels['time']])
 	df = velocity_per_track(df, window_size=3, mode='bi')
 

celldetective/utils.py

@@ -17,7 +17,6 @@ import json
 from csbdeep.utils import normalize_mi_ma
 from glob import glob
 from urllib.request import urlopen
-from urllib.parse import urlparse
 import zipfile
 from tqdm import tqdm
 import shutil
@@ -1289,16 +1288,27 @@ def _extract_channel_indices_from_config(config, channels_to_extract):
 	# V2
 	channels = []
 	for c in channels_to_extract:
-		if c!='None' and c is not None:
-			try:
-				c1 = int(ConfigSectionMap(config,"Channels")[c])
-				channels.append(c1)
-			except Exception as e:
-				print(f"Error {e}. The channel required by the model is not available in your data... Check the configuration file.")
-				channels = None
-				break
-		else:
+		try:
+			c1 = int(ConfigSectionMap(config,"Channels")[c])
+			channels.append(c1)
+		except Exception as e:
+			print(f"Warning... The channel {c} required by the model is not available in your data...")
 			channels.append(None)
+	if np.all([c is None for c in channels]):
+		channels = None
+
+	# channels = []
+	# for c in channels_to_extract:
+	# 	if c!='None' and c is not None:
+	# 		try:
+	# 			c1 = int(ConfigSectionMap(config,"Channels")[c])
+	# 			channels.append(c1)
+	# 		except Exception as e:
+	# 			print(f"Error {e}. The channel required by the model is not available in your data... Check the configuration file.")
+	# 			channels = None
+	# 			break
+	# 	else:
+	# 		channels.append(None)
 
 	# LEGACY
 	if channels is None:
@@ -2164,6 +2174,8 @@ def load_image_dataset(datasets, channels, train_spatial_calibration=None, mask_
 	- Spatial calibration adjustment involves rescaling the images and masks to match the `train_spatial_calibration`.
 	- Only images with a corresponding mask and a valid configuration file specifying channel indices and
 	  spatial calibration are loaded.
+	- The image samples must have at least one channel in common with the required channels to be accepted. The missing
+	  channels are passed as black frames.
 
 	Examples
 	--------
@@ -2202,24 +2214,29 @@ def load_image_dataset(datasets, channels, train_spatial_calibration=None, mask_
 					# Load config
 					with open(config_path, 'r') as f:
 						config = json.load(f)
-					try:
+
+					existing_channels = config['channels']
+					intersection = list(set(list(channels)) & set(list(existing_channels)))
+					print(f'{existing_channels=} {intersection=}')
+					if len(intersection)==0:
+						print(e,' channels could not be found in the config... Skipping image.')
+						continue
+					else:
 						ch_idx = []
 						for c in channels:
-							if c!='None':
-								idx = config['channels'].index(c)
+							if c in existing_channels:
+								idx = existing_channels.index(c)
 								ch_idx.append(idx)
 							else:
+								# For None or missing channel pass black frame
 								ch_idx.append(np.nan)
 						im_calib = config['spatial_calibration']
-					except Exception as e:
-						print(e,' channels and/or spatial calibration could not be found in the config... Skipping image.')
-						continue
 				
 				ch_idx = np.array(ch_idx)
 				ch_idx_safe = np.copy(ch_idx)
 				ch_idx_safe[ch_idx_safe!=ch_idx_safe] = 0
 				ch_idx_safe = ch_idx_safe.astype(int)
-				print(ch_idx_safe)
+				
 				image = image[ch_idx_safe]
 				image[np.where(ch_idx!=ch_idx)[0],:,:] = 0
 
@@ -2233,6 +2250,14 @@ def load_image_dataset(datasets, channels, train_spatial_calibration=None, mask_
 					
 			X.append(image)
 			Y.append(mask)
+
+			# fig,ax = plt.subplots(1,image.shape[-1]+1)
+			# for k in range(image.shape[-1]):
+			# 	ax[k].imshow(image[:,:,k],cmap='gray')
+			# ax[image.shape[-1]].imshow(mask)
+			# plt.pause(1)
+			# plt.close()
+
 			files.append(im)
 
 	assert len(X)==len(Y),'The number of images does not match with the number of masks... Abort.'
@@ -2367,4 +2392,87 @@ def interpolate_nan(img, method='nearest'):
 		interp_grid = griddata(points, values, (x_grid, y_grid), method=method)
 		return interp_grid
 	else:
-		return img
+		return img
+
+def collapse_trajectories_by_status(df, status=None, projection='mean', population='effectors', groupby_columns=['position','TRACK_ID']):
+	
+	static_columns = ['well_index', 'well_name', 'pos_name', 'position', 'well', 'status', 't0', 'class','cell_type','concentration', 'antibody', 'pharmaceutical_agent','TRACK_ID','position', 'neighbor_population', 'reference_population', 'NEIGHBOR_ID', 'REFERENCE_ID', 'FRAME']
+
+	if status is None or status not in list(df.columns):
+		print('invalid status selection...')
+		return None
+
+	df = df.dropna(subset=status,ignore_index=True)
+	unique_statuses = np.unique(df[status].to_numpy())
+
+	df_sections = []
+	for s in unique_statuses:
+		subtab = df.loc[df[status]==s,:]
+		op = getattr(subtab.groupby(groupby_columns), projection)
+		subtab_projected = op(subtab.groupby(groupby_columns))
+		frame_duration = subtab.groupby(groupby_columns).size().to_numpy()
+		for c in static_columns:
+			try:
+				subtab_projected[c] = subtab.groupby(groupby_columns)[c].apply(lambda x: x.unique()[0])
+			except Exception as e:
+				print(e)
+				pass
+		subtab_projected['duration_in_state'] = frame_duration
+		df_sections.append(subtab_projected)
+
+	group_table = pd.concat(df_sections,axis=0,ignore_index=True)
+	if population=='pairs':
+		for col in ['duration_in_state',status, 'neighbor_population', 'reference_population', 'NEIGHBOR_ID', 'REFERENCE_ID']:
+			first_column = group_table.pop(col) 
+			group_table.insert(0, col, first_column)				
+	else:
+		for col in ['duration_in_state',status,'TRACK_ID']:
+			first_column = group_table.pop(col) 
+			group_table.insert(0, col, first_column)
+
+	group_table.pop('FRAME')
+	group_table = group_table.sort_values(by=groupby_columns + [status],ignore_index=True)
+	group_table = group_table.reset_index(drop=True)
+
+	return group_table
+
+def step_function(t, t_shift, dt):
+
+	"""
+	Computes a step function using the logistic sigmoid function.
+
+	This function calculates the value of a sigmoid function, which is often used to model
+	a step change or transition. The sigmoid function is defined as:
+	
+	.. math::
+		f(t) = \\frac{1}{1 + \\exp{\\left( -\\frac{t - t_{shift}}{dt} \\right)}}
+	
+	where `t` is the input variable, `t_shift` is the point of the transition, and `dt` controls
+	the steepness of the transition.
+
+	Parameters
+	----------
+	t : array_like
+		The input values for which the step function will be computed.
+	t_shift : float
+		The point in the `t` domain where the transition occurs.
+	dt : float
+		The parameter that controls the steepness of the transition. Smaller values make the
+		transition steeper, while larger values make it smoother.
+
+	Returns
+	-------
+	array_like
+		The computed values of the step function for each value in `t`.
+
+	Examples
+	--------
+	>>> import numpy as np
+	>>> t = np.array([0, 1, 2, 3, 4, 5])
+	>>> t_shift = 2
+	>>> dt = 1
+	>>> step_function(t, t_shift, dt)
+	array([0.26894142, 0.37754067, 0.5       , 0.62245933, 0.73105858, 0.81757448])
+	"""
+
+	return 1/(1+np.exp(-(t-t_shift)/dt))

{celldetective-1.2.0.dist-info → celldetective-1.2.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: celldetective
-Version: 1.2.0
+Version: 1.2.2
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro
@@ -12,14 +12,14 @@ Requires-Dist: wheel
 Requires-Dist: nbsphinx
 Requires-Dist: nbsphinx-link
 Requires-Dist: sphinx-rtd-theme
-Requires-Dist: sphinx==5.0.2
-Requires-Dist: jinja2<3.1
+Requires-Dist: sphinx
+Requires-Dist: jinja2
 Requires-Dist: ipykernel
 Requires-Dist: stardist
 Requires-Dist: cellpose<3
 Requires-Dist: scikit-learn
 Requires-Dist: btrack
-Requires-Dist: tensorflow<=2.12.1
+Requires-Dist: tensorflow~=2.15.0
 Requires-Dist: napari
 Requires-Dist: tqdm
 Requires-Dist: mahotas
@@ -32,9 +32,10 @@ Requires-Dist: seaborn
 Requires-Dist: opencv-python-headless==4.7.0.72
 Requires-Dist: liblapack
 Requires-Dist: gputools
-Requires-Dist: lmfit~=1.2.2
-Requires-Dist: superqt[cmap]>=0.6.1
+Requires-Dist: lmfit
+Requires-Dist: superqt[cmap]
 Requires-Dist: matplotlib-scalebar
+Requires-Dist: numpy==1.26.4
 
 # Celldetective
 
@@ -165,23 +166,25 @@ steps.
 
 To use the software, you must install python, *e.g.* through
 [Anaconda](https://www.anaconda.com/download). We developed and tested
-the software in Python 3.9.18.
+the software in Python 3.9 and more recently 3.11.
 
 # Installation
 
 ## Stable release
 
-Celldetective can be installed with `pip`:
+Celldetective requires a version of Python between 3.9 and 3.11 (included). If your Python version is older or more recent, consider using `conda` to create an environment as described below.
+
+With the proper Python version, Celldetective can be directly installed with `pip`:
 
 ``` bash
 pip install celldetective
 ```
 
-We recommend that you create an environment to use Celldetective, *e.g.*
+We recommend that you create an environment to use Celldetective, to protect your package versions and fix the Python version *e.g.*
 with `conda`:
 
 ``` bash
-conda create -n celldetective python=3.9.18 pyqt
+conda create -n celldetective python=3.11 pyqt
 conda activate celldetective
 pip install celldetective
 ```
@@ -207,6 +210,10 @@ will be immediately available in the python environment:
 git clone git://github.com/remyeltorro/celldetective.git
 cd celldetective
 
+# optional: create an environment
+conda create -n celldetective python=3.11 pyqt
+conda activate celldetective
+
 # install the celldetective package in editable/development mode
 pip install -r requirements.txt
 pip install -e .
@@ -229,10 +236,10 @@ with package requirements for other projects. Run the following lines to
 create an environment named \"celldetective\":
 
 ``` bash
-conda create -n celldetective python=3.9.18 pyqt
+conda create -n celldetective python=3.11 pyqt
 conda activate celldetective
 pip install -r requirements.txt
-pip install .
+pip install -e .
 ```
 
 The installation of the dependencies will take a few minutes (up to half