celldetective 1.3.9.post3__tar.gz → 1.5.0b3__tar.gz

{celldetective-1.3.9.post3 → celldetective-1.5.0b3}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: celldetective
-Version: 1.3.9.post3
+Version: 1.5.0b3
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro
@@ -44,12 +44,17 @@ Requires-Dist: h5py
 Requires-Dist: cliffs_delta
 Requires-Dist: requests
 Requires-Dist: trackpy
+Requires-Dist: prettyprint
+Requires-Dist: pandas
+Requires-Dist: matplotlib
+Requires-Dist: prettytable
 Dynamic: author
 Dynamic: author-email
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page
 Dynamic: license
+Dynamic: license-file
 Dynamic: requires-dist
 Dynamic: summary
 
@@ -183,26 +188,29 @@ 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/10.1101/2024.03.15.585250v3)
-paper (currently preprint):
+[Celldetective](https://elifesciences.org/reviewed-preprints/105302)
+paper (currently a reviewed preprint at eLife):
 
 ``` raw
-@article {Torro2024.03.15.585250,
-    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 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}
+@article{torroCelldetectiveAIenhancedImage2025,
+  title = {Celldetective: An {{AI-enhanced}} Image Analysis Tool for Unraveling Dynamic Cell Interactions},
+  shorttitle = {Celldetective},
+  author = {Torro, Rémy and Díaz-Bello, Beatriz and Arawi, Dalia El and Dervanova, Ksenija and Ammer, Lorna and Dupuy, Florian and Chames, Patrick and Sengupta, Kheya and Limozin, Laurent},
+  date = {2025-03-10},
+  journaltitle = {eLife},
+  volume = {14},
+  publisher = {eLife Sciences Publications Limited},
+  doi = {10.7554/eLife.105302.1},
+  url = {https://elifesciences.org/reviewed-preprints/105302},
+  urldate = {2025-03-20},
+  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.},
+  langid = {english},
+  file = {/home/torro/Zotero/storage/VFYBBMQF/Torro et al. - 2025 - Celldetective an AI-enhanced image analysis tool .pdf;/home/torro/Zotero/storage/UGMCKKST/105302.html}
 }
 ```
 
 Make sure you to cite the papers of any segmentation model (StarDist,
-Cellpose) or tracker (bTrack) you used through Celldetective.
+Cellpose) or tracker (bTrack, TrackPy) you used through Celldetective.
 
 # Bibliography
 

{celldetective-1.3.9.post3 → celldetective-1.5.0b3}/README.md

@@ -128,26 +128,29 @@ 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/10.1101/2024.03.15.585250v3)
-paper (currently preprint):
+[Celldetective](https://elifesciences.org/reviewed-preprints/105302)
+paper (currently a reviewed preprint at eLife):
 
 ``` raw
-@article {Torro2024.03.15.585250,
-    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 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}
+@article{torroCelldetectiveAIenhancedImage2025,
+  title = {Celldetective: An {{AI-enhanced}} Image Analysis Tool for Unraveling Dynamic Cell Interactions},
+  shorttitle = {Celldetective},
+  author = {Torro, Rémy and Díaz-Bello, Beatriz and Arawi, Dalia El and Dervanova, Ksenija and Ammer, Lorna and Dupuy, Florian and Chames, Patrick and Sengupta, Kheya and Limozin, Laurent},
+  date = {2025-03-10},
+  journaltitle = {eLife},
+  volume = {14},
+  publisher = {eLife Sciences Publications Limited},
+  doi = {10.7554/eLife.105302.1},
+  url = {https://elifesciences.org/reviewed-preprints/105302},
+  urldate = {2025-03-20},
+  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.},
+  langid = {english},
+  file = {/home/torro/Zotero/storage/VFYBBMQF/Torro et al. - 2025 - Celldetective an AI-enhanced image analysis tool .pdf;/home/torro/Zotero/storage/UGMCKKST/105302.html}
 }
 ```
 
 Make sure you to cite the papers of any segmentation model (StarDist,
-Cellpose) or tracker (bTrack) you used through Celldetective.
+Cellpose) or tracker (bTrack, TrackPy) you used through Celldetective.
 
 # Bibliography
 

celldetective-1.5.0b3/celldetective/__init__.py

@@ -0,0 +1,26 @@
+from ._version import __version__
+import os
+from .log_manager import setup_global_logging, get_logger
+
+# Define default log path in user home
+USER_LOG_DIR = os.path.join(os.path.expanduser("~"), ".celldetective", "logs")
+GLOBAL_LOG_FILE = os.path.join(USER_LOG_DIR, "celldetective.log")
+
+# Setup logging
+setup_global_logging(log_file=GLOBAL_LOG_FILE)
+
+# Expose logger
+logger = get_logger()
+
+
+def get_software_location() -> str:
+    """
+    Get the installation folder of celldetective.
+
+    Returns
+    -------
+    str
+            Path to the celldetective installation folder.
+    """
+
+    return rf"{os.path.split(os.path.dirname(os.path.realpath(__file__)))[0]}"

celldetective-1.5.0b3/celldetective/__main__.py

@@ -0,0 +1,85 @@
+#!/usr/bin/env python3
+import sys
+import os
+
+os.environ["KMP_DUPLICATE_LIB_OK"] = "TRUE"
+
+from PyQt5.QtWidgets import QApplication, QSplashScreen
+from PyQt5.QtGui import QPixmap
+from os import sep
+
+# os.environ['QT_DEBUG_PLUGINS'] = '1'
+
+if __name__ == "__main__":
+
+    splash = True
+    from celldetective import logger
+    from celldetective import get_software_location
+
+    logger.info("Loading the libraries...")
+
+    App = QApplication(sys.argv)
+    App.setStyle("Fusion")
+
+    software_location = get_software_location()
+
+    if splash:
+        splash_pix = QPixmap(
+            sep.join([software_location, "celldetective", "icons", "splash.png"])
+        )
+        splash = QSplashScreen(splash_pix)
+        splash.setMask(splash_pix.mask())
+        splash.show()
+        App.processEvents()
+
+    # Update check in background
+    def check_update():
+        try:
+            import requests
+            import re
+            from celldetective import __version__
+
+            package = "celldetective"
+            response = requests.get(f"https://pypi.org/pypi/{package}/json", timeout=5)
+            latest_version = response.json()["info"]["version"]
+
+            latest_version_num = re.sub("[^0-9]", "", latest_version)
+            current_version_num = re.sub("[^0-9]", "", __version__)
+
+            if len(latest_version_num) != len(current_version_num):
+                max_length = max([len(latest_version_num), len(current_version_num)])
+                latest_version_num = int(
+                    latest_version_num.zfill(max_length - len(latest_version_num))
+                )
+                current_version_num = int(
+                    current_version_num.zfill(max_length - len(current_version_num))
+                )
+
+            if latest_version_num > current_version_num:
+                logger.warning(
+                    "Update is available...\nPlease update using `pip install --upgrade celldetective`..."
+                )
+        except Exception as e:
+            logger.error(
+                f"Update check failed... Please check your internet connection: {e}"
+            )
+
+    import threading
+
+    update_thread = threading.Thread(target=check_update)
+    update_thread.daemon = True
+    update_thread.start()
+
+    from celldetective.gui.InitWindow import AppInitWindow
+
+    logger.info("Libraries successfully loaded...")
+
+    from celldetective.gui.base.utils import center_window
+
+    window = AppInitWindow(App, software_location=software_location)
+    center_window(window)
+
+    if splash:
+        splash.finish(window)
+
+    sys.exit(App.exec())

celldetective-1.5.0b3/celldetective/_version.py

@@ -0,0 +1 @@
+__version__ = "1.5.0b3"

{celldetective-1.3.9.post3 → celldetective-1.5.0b3}/celldetective/events.py

@@ -52,7 +52,7 @@ def switch_to_events(classes, event_times, max_times, origin_times=None, left_ce
 	>>> event_times = [5, 10, 15]
 	>>> max_times = [20, 20, 20]
 	>>> origin_times = [0, 0, 5]
-	>>> events, survival_times = switch_to_events_v2(classes, event_times, max_times, origin_times, FrameToMin=0.5)
+	>>> events, survival_times = switch_to_events(classes, event_times, max_times, origin_times, FrameToMin=0.5)
 	# This would process the events considering left censorship and convert survival times to minutes.
 	
 	"""
@@ -189,6 +189,7 @@ def compute_survival(df, class_of_interest, t_event, t_reference=None, FrameToMi
 	assert class_of_interest in cols,"The requested class cannot be found in the dataframe..."
 	assert t_event in cols,"The event time cannot be found in the dataframe..."
 	left_censored = False
+	first_detections = None
 
 	if not pairs:
 		groupby_cols = ['position','TRACK_ID']
@@ -209,10 +210,7 @@ def compute_survival(df, class_of_interest, t_event, t_reference=None, FrameToMi
 		assert t_reference in cols,"The reference time cannot be found in the dataframe..."
 		first_detections = df.groupby(groupby_cols)[t_reference].max().values
 	
-
-	print(f"{classes=} {event_times=} {max_times=} {first_detections=}")
 	events, survival_times = switch_to_events(classes, event_times, max_times, origin_times=first_detections, left_censored=left_censored, FrameToMin=FrameToMin, cut_observation_time=cut_observation_time)
-	print(f"{events=} {survival_times=}")
 
 	ks = KaplanMeierFitter()
 	if len(events)>0:

celldetective-1.5.0b3/celldetective/exceptions.py

@@ -0,0 +1,11 @@
+class QueryError(Exception):
+    """Base class for query-related errors."""
+
+class EmptyQueryError(QueryError):
+    pass
+
+class MissingColumnsError(QueryError):
+    def __init__(self, missing_cols):
+        msg = f"The following columns are missing from the DataFrame: {missing_cols}"
+        super().__init__(msg)
+        self.missing_cols = missing_cols