microlive 1.0.2__tar.gz → 1.0.4__tar.gz

{microlive-1.0.2 → microlive-1.0.4}/.gitignore

@@ -85,3 +85,4 @@ writing/
 docs/paper_microlive_12112025/
 merged
 tests/
+video_youtube/

{microlive-1.0.2 → microlive-1.0.4}/PKG-INFO

@@ -1,19 +1,76 @@
 Metadata-Version: 2.4
 Name: microlive
-Version: 1.0.2
+Version: 1.0.4
 Summary: Live-cell microscopy image analysis and single-molecule measurements
 Project-URL: Homepage, https://github.com/ningzhaoAnschutz/microlive
 Project-URL: Documentation, https://github.com/ningzhaoAnschutz/microlive/blob/main/docs/user_guide.md
 Project-URL: Repository, https://github.com/ningzhaoAnschutz/microlive
 Project-URL: Issues, https://github.com/ningzhaoAnschutz/microlive/issues
 Project-URL: Changelog, https://github.com/ningzhaoAnschutz/microlive/releases
+Author: Luis U. Aguilera, William S. Raymond, Rhiannon M. Sears, Nathan L. Nowling, Brian Munsky, Ning Zhao
 License-Expression: GPL-3.0-or-later
 License-File: LICENSE
+Keywords: PyQt5,bioimaging,cellpose,image-analysis,live-cell,microscopy,particle-tracking,single-molecule,tracking
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: X11 Applications :: Qt
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: OS Independent
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Requires-Python: >=3.10
+Requires-Dist: big-fish>=0.6
+Requires-Dist: bioio-lif>=1.2
+Requires-Dist: bioio>=1.0
+Requires-Dist: biopython>=1.81
+Requires-Dist: brokenaxes
+Requires-Dist: cellpose>=3.0
+Requires-Dist: dask
+Requires-Dist: dna-features-viewer>=3.1
+Requires-Dist: fpdf>=1.7
+Requires-Dist: imagecodecs
+Requires-Dist: imageio>=2.31
+Requires-Dist: joblib>=1.3
+Requires-Dist: joypy
+Requires-Dist: matplotlib-scalebar
+Requires-Dist: matplotlib>=3.7
+Requires-Dist: natsort
+Requires-Dist: numba>=0.58
+Requires-Dist: numpy<2.0,>=1.24
+Requires-Dist: opencv-python-headless>=4.8
+Requires-Dist: openpyxl>=3.1
+Requires-Dist: pandas>=2.0
+Requires-Dist: pillow>=10.0
+Requires-Dist: psutil
+Requires-Dist: pydantic>=2.0
+Requires-Dist: pyqt5>=5.15
+Requires-Dist: pystackreg>=0.2
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: readlif>=0.6
+Requires-Dist: roifile
+Requires-Dist: scikit-image>=0.21
+Requires-Dist: scikit-learn>=1.3
+Requires-Dist: scipy>=1.10
+Requires-Dist: seaborn>=0.12
+Requires-Dist: snapgene-reader>=0.1
+Requires-Dist: statsmodels>=0.14
+Requires-Dist: tifffile>=2023.7
+Requires-Dist: tqdm>=4.66
+Requires-Dist: trackpy>=0.6
 Provides-Extra: dev
 Requires-Dist: black>=23.0; extra == 'dev'
 Requires-Dist: build; extra == 'dev'
 Requires-Dist: isort>=5.12; extra == 'dev'
 Requires-Dist: mypy>=1.5; extra == 'dev'
+Requires-Dist: pdoc; extra == 'dev'
 Requires-Dist: pytest-qt>=4.0; extra == 'dev'
 Requires-Dist: pytest>=7.0; extra == 'dev'
 Requires-Dist: ruff>=0.1; extra == 'dev'

{microlive-1.0.2 → microlive-1.0.4}/microlive/__init__.py

@@ -23,7 +23,7 @@ Authors:
     Nathan L. Nowling, Brian Munsky, Ning Zhao
 """
 
-__version__ = "1.0.2"
+__version__ = "1.0.4"
 __author__ = "Luis U. Aguilera, William S. Raymond, Rhiannon M. Sears, Nathan L. Nowling, Brian Munsky, Ning Zhao"
 
 # Package name (for backward compatibility)
@@ -41,4 +41,10 @@ name = 'microlive'
 __all__ = [
     "__version__",
     "__author__",
+    # Submodules (listed for pdoc documentation discovery)
+    "microscopy",
+    "imports",
+    "pipelines",
+    "utils",
+    "gui",
 ]

{microlive-1.0.2 → microlive-1.0.4}/microlive/gui/app.py

@@ -2102,38 +2102,68 @@ class GUI(QMainWindow):
                     except Exception:
                         print(f"Error parsing JSON ImageDescription metadata: {desc_text}")
                 else:
-                    # OME-XML metadata
-                    try:
-                        root = ET.fromstring(desc_text)
-                        ns = {'ome': root.tag.split('}')[0].strip('{')}
-                        pixels = root.find('.//ome:Pixels', ns)
-                        if pixels is not None:
-                            attrib = pixels.attrib
-                            if 'PhysicalSizeX' in attrib:
-                                voxel_x_nm = float(attrib['PhysicalSizeX']) * 1000.0
-                            if 'PhysicalSizeY' in attrib:
-                                voxel_y_nm = float(attrib['PhysicalSizeY']) * 1000.0
-                            if 'PhysicalSizeZ' in attrib:
-                                voxel_z_nm = float(attrib['PhysicalSizeZ']) * 1000.0
-                            if 'TimeIncrement' in attrib:
-                                dt_seconds = float(attrib['TimeIncrement'])
-                            channel_elems = pixels.findall('ome:Channel', ns)
-                            detected_channel_names = [ch.attrib.get('Name') for ch in channel_elems if 'Name' in ch.attrib]
-                    except ET.ParseError:
-                        print("Error parsing OME-XML ImageDescription metadata")
+                    # Check if it's ImageJ format (starts with "ImageJ=")
+                    if desc_stripped.startswith('ImageJ='):
+                        # Parse ImageJ metadata
+                        # ImageJ doesn't store XY pixel size in description, only spacing (Z)
+                        # We'll try to get pixel size from XResolution tag later
+                        pass  # ImageJ metadata doesn't contain pixel size in description
+                    elif desc_stripped.startswith('<') or desc_stripped.startswith('<?xml'):
+                        # OME-XML metadata (starts with < or <?xml)
+                        try:
+                            root = ET.fromstring(desc_text)
+                            ns = {'ome': root.tag.split('}')[0].strip('{')}
+                            pixels = root.find('.//ome:Pixels', ns)
+                            if pixels is not None:
+                                attrib = pixels.attrib
+                                if 'PhysicalSizeX' in attrib:
+                                    voxel_x_nm = float(attrib['PhysicalSizeX']) * 1000.0
+                                if 'PhysicalSizeY' in attrib:
+                                    voxel_y_nm = float(attrib['PhysicalSizeY']) * 1000.0
+                                if 'PhysicalSizeZ' in attrib:
+                                    voxel_z_nm = float(attrib['PhysicalSizeZ']) * 1000.0
+                                if 'TimeIncrement' in attrib:
+                                    dt_seconds = float(attrib['TimeIncrement'])
+                                channel_elems = pixels.findall('ome:Channel', ns)
+                                detected_channel_names = [ch.attrib.get('Name') for ch in channel_elems if 'Name' in ch.attrib]
+                        except ET.ParseError:
+                            # Not valid XML - that's okay, will try XResolution tags
+                            pass
             else:
                 print("No ImageDescription found in TIFF metadata.")
+            # Try to get pixel size from XResolution tag if not found yet
             if voxel_x_nm is None:
                 x_res = page0.tags.get('XResolution')
                 if x_res:
                     num, den = x_res.value
-                    voxel_x_nm = float(num) / float(den) * 1000.0
+                    resolution = float(num) / float(den)  # pixels per unit
+                    # Check ResolutionUnit: 1=None, 2=inch, 3=centimeter
+                    res_unit = page0.tags.get('ResolutionUnit')
+                    res_unit_val = res_unit.value if res_unit else 1
+                    if resolution > 0:
+                        # XResolution is pixels per unit, so pixel size = 1/XResolution
+                        pixel_size_in_unit = 1.0 / resolution
+                        if res_unit_val == 2:  # inch
+                            candidate_nm = pixel_size_in_unit * 25400 * 1000  # inch to nm
+                        elif res_unit_val == 3:  # centimeter
+                            candidate_nm = pixel_size_in_unit * 10000 * 1000  # cm to nm
+                        else:  # None or unknown - assume µm for microscopy images
+                            candidate_nm = pixel_size_in_unit * 1000  # µm to nm
+                        # Sanity check: microscopy pixel sizes are typically 10-5000 nm
+                        # Reject values outside this range as likely corrupted/invalid
+                        if 10 <= candidate_nm <= 5000:
+                            voxel_x_nm = candidate_nm
             if voxel_z_nm is None:
                 z_res = page0.tags.get('ZResolution')
                 if z_res:
                     num, den = z_res.value
-                    voxel_z_nm = float(num) / float(den) * 1000.0
-        # If essential metadata is missing, prompt user (as per original logic)
+                    resolution = float(num) / float(den)
+                    if resolution > 0:
+                        candidate_nm = (1.0 / resolution) * 1000  # assume µm
+                        # Sanity check for Z: 50-10000 nm is reasonable
+                        if 50 <= candidate_nm <= 10000:
+                            voxel_z_nm = candidate_nm
+        # If essential metadata is missing, prompt user only for what's missing
         missing = []
         if voxel_x_nm is None:
             missing.append("voxel size X (nm)")
@@ -2142,10 +2172,7 @@ class GUI(QMainWindow):
         if dt_seconds is None:
             missing.append("time increment (s)")
         if missing:
-            voxel_x_nm = None
-            voxel_z_nm = None
-            dt_seconds = None
-            missing = ["voxel size X (nm)", "voxel size Z (nm)", "time increment (s)"]
+            # Only prompt for what's actually missing, keep found values
             self.ask_for_metadata_from_user(missing)
         # Set voxel sizes and time interval if available
         if voxel_x_nm is not None:
@@ -2823,6 +2850,105 @@ class GUI(QMainWindow):
             # Reset current indices
             self.current_frame = 0
             self.current_channel = 0
+            
+            # Reset merged mode
+            self.merged_mode = False
+
+    def close_all_files(self):
+        """
+        Remove all loaded files (LIF and TIFF) from the tree and free their memory.
+        Clears all data and resets the GUI to its initial empty state.
+        """
+        # Get all top-level items count
+        num_files = self.image_tree.topLevelItemCount()
+        if num_files == 0:
+            return
+        
+        # Clear all loaded file data
+        self.loaded_lif_files.clear()
+        
+        # Remove all items from tree view
+        self.image_tree.clear()
+        
+        # Clear core data
+        self.image_stack = None
+        self.data_folder_path = None
+        self.colocalization_results = None
+        self.current_total_plots = None
+        
+        # Use unified reset for all tabs and state
+        self.reset_all_state()
+        
+        # Clear info labels
+        labels_to_clear = [
+            'file_label', 'frames_label', 'z_scales_label',
+            'y_pixels_label', 'x_pixels_label', 'channels_label',
+            'voxel_yx_size_label', 'voxel_z_nm_label',
+            'bit_depth_label', 'time_interval_label',
+            'laser_lines_label', 'intensities_label', 'wave_ranges_label'
+        ]
+        for lbl_name in labels_to_clear:
+            if hasattr(self, lbl_name):
+                getattr(self, lbl_name).setText("")
+        
+        # Clear channel controls
+        if hasattr(self, 'channelControlsTabs'):
+            self.channelControlsTabs.clear()
+        
+        # Clear channel buttons
+        for btn_list in [getattr(self, 'channel_buttons_display', []),
+                        getattr(self, 'channel_buttons_tracking', []),
+                        getattr(self, 'channel_buttons_tracking_vis', []),
+                        getattr(self, 'segmentation_channel_buttons', [])]:
+            for btn in btn_list:
+                if btn:
+                    btn.setParent(None)
+        
+        # Reset button lists
+        self.channel_buttons_display = []
+        self.channel_buttons_tracking = []
+        if hasattr(self, 'channel_buttons_tracking_vis'):
+            self.channel_buttons_tracking_vis = []
+        if hasattr(self, 'segmentation_channel_buttons'):
+            self.segmentation_channel_buttons = []
+        
+        # Clear channel checkboxes for correlation
+        if hasattr(self, 'channel_checkboxes'):
+            for cb in self.channel_checkboxes:
+                if cb:
+                    cb.setParent(None)
+            self.channel_checkboxes = []
+        
+        # Clear combo boxes
+        if hasattr(self, 'intensity_channel_combo'):
+            self.intensity_channel_combo.clear()
+        if hasattr(self, 'time_course_channel_combo'):
+            self.time_course_channel_combo.clear()
+        if hasattr(self, 'channel_combo_box_1'):
+            self.channel_combo_box_1.clear()
+        if hasattr(self, 'channel_combo_box_2'):
+            self.channel_combo_box_2.clear()
+        
+        # Disable controls
+        if hasattr(self, 'time_slider_display'):
+            self.time_slider_display.setEnabled(False)
+            self.time_slider_display.setValue(0)
+        if hasattr(self, 'play_button_display'):
+            self.play_button_display.setEnabled(False)
+        if hasattr(self, 'time_slider_tracking'):
+            self.time_slider_tracking.setValue(0)
+        if hasattr(self, 'time_slider_tracking_vis'):
+            self.time_slider_tracking_vis.setValue(0)
+        
+        # Stop any playing timers
+        self.stop_all_playback()
+        
+        # Reset current indices
+        self.current_frame = 0
+        self.current_channel = 0
+        
+        # Reset merged mode
+        self.merged_mode = False
 
     def on_tree_current_item_changed(self, current, previous):
         """
@@ -2913,7 +3039,7 @@ class GUI(QMainWindow):
 
     def merge_color_channels(self):
         if self.image_stack is None:
-            QMessageBox.information(self, "Merge Error", "No image loaded to merge channels.")
+            # Silently return if no image - this can happen when closing files in merge mode
             return
         merged_img = self.compute_merged_image()
         if merged_img is None:
@@ -3145,10 +3271,15 @@ class GUI(QMainWindow):
         self.image_tree.itemClicked.connect(self.on_tree_item_clicked)
         self.image_tree.currentItemChanged.connect(self.on_tree_current_item_changed)
         display_right_layout.addWidget(self.image_tree)
-        # Close file button
+        # Close file buttons (using horizontal layout for both buttons)
+        close_buttons_layout = QHBoxLayout()
         self.close_file_button = QPushButton("Close File", self)
         self.close_file_button.clicked.connect(self.close_selected_file)
-        display_right_layout.addWidget(self.close_file_button)
+        close_buttons_layout.addWidget(self.close_file_button)
+        self.close_all_files_button = QPushButton("Close All", self)
+        self.close_all_files_button.clicked.connect(self.close_all_files)
+        close_buttons_layout.addWidget(self.close_all_files_button)
+        display_right_layout.addLayout(close_buttons_layout)
         # Visualization controls
         self.control_panel_image_properties(display_right_layout)
         # Group box for image info
@@ -6164,9 +6295,8 @@ class GUI(QMainWindow):
         # (Cellpose masks are labeled, not suitable for photobleaching mask input)
         if has_cellpose_mask and not has_segmentation_mask:
             mode = 'entire_image'
-            # Inform user that we're using entire_image mode
-            QMessageBox.information(self, "Using Entire Image", 
-                                    "Cellpose masks detected. Photobleaching will be calculated using the entire image.")
+            # Inform user via status bar (non-blocking)
+            self.statusBar().showMessage("Cellpose detected: using entire image for photobleaching calculation.", 5000)
         
         self.photobleaching_mode = mode
         radius = self.radius_spinbox.value()
@@ -8106,7 +8236,7 @@ class GUI(QMainWindow):
         if self.image_stack is None:
             QMessageBox.warning(self, "No Image Loaded", "Please load an image first.")
             return
-        if not hasattr(self, 'user_selected_threshold') or self.user_selected_threshold <= 0:
+        if not hasattr(self, 'user_selected_threshold') or self.user_selected_threshold is None or self.user_selected_threshold <= 0:
             QMessageBox.warning(self, "Tracking Aborted", "Threshold is zero; please adjust the threshold slider before running tracking.")
             return
         

microlive-1.0.4/microlive/gui/main.py

@@ -0,0 +1,86 @@
+"""Entry point for MicroLive GUI application.
+
+This module provides the command-line entry point for launching
+the MicroLive graphical user interface.
+
+Usage:
+    $ microlive
+    
+Or programmatically:
+    from microlive.gui.main import main
+    main()
+"""
+
+import sys
+import os
+
+
+def main():
+    """Launch the MicroLive GUI application."""
+    # Ensure proper Qt platform on macOS
+    if sys.platform == "darwin":
+        os.environ.setdefault("QT_MAC_WANTS_LAYER", "1")
+    
+    # Import Qt after environment setup
+    from PyQt5.QtWidgets import QApplication
+    from PyQt5.QtGui import QIcon, QFont, QPalette, QColor
+    from PyQt5.QtCore import Qt
+    import matplotlib.pyplot as plt
+    
+    # Import the main application window
+    from .app import GUI
+    
+    # Get icon path
+    from ..utils.resources import get_icon_path
+    
+    # Create application
+    app = QApplication(sys.argv)
+    app.setStyle('Fusion')
+    
+    # Set modern font based on platform
+    if sys.platform == 'win32':
+        app.setFont(QFont("Segoe UI", 11))
+    elif sys.platform == 'darwin':
+        app.setFont(QFont("SF Pro", 11))
+    else:
+        app.setFont(QFont("Inter", 11))
+    
+    # Set dark matplotlib style
+    plt.style.use('dark_background')
+    
+    # Set dark palette for the application
+    palette = QPalette()
+    palette.setColor(QPalette.Window, QColor(53, 53, 53))
+    palette.setColor(QPalette.WindowText, Qt.white)
+    palette.setColor(QPalette.Base, QColor(35, 35, 35))
+    palette.setColor(QPalette.AlternateBase, QColor(53, 53, 53))
+    palette.setColor(QPalette.ToolTipBase, Qt.white)
+    palette.setColor(QPalette.ToolTipText, Qt.white)
+    palette.setColor(QPalette.Text, Qt.white)
+    palette.setColor(QPalette.Button, QColor(53, 53, 53))
+    palette.setColor(QPalette.ButtonText, Qt.white)
+    palette.setColor(QPalette.BrightText, Qt.red)
+    palette.setColor(QPalette.Highlight, QColor(142, 45, 197).lighter())
+    palette.setColor(QPalette.HighlightedText, Qt.black)
+    app.setPalette(palette)
+    
+    # Set application metadata
+    app.setApplicationName("MicroLive")
+    app.setApplicationDisplayName("MicroLive")
+    app.setOrganizationName("Zhao Lab")
+    
+    # Set application icon
+    icon_path = get_icon_path()
+    if icon_path and icon_path.exists():
+        app.setWindowIcon(QIcon(str(icon_path)))
+    
+    # Create and show main window
+    window = GUI(icon_path=icon_path)
+    window.show()
+    
+    # Run event loop
+    sys.exit(app.exec_())
+
+
+if __name__ == "__main__":
+    main()

{microlive-1.0.2 → microlive-1.0.4}/pyproject.toml

@@ -8,9 +8,6 @@ dynamic = ["version"]
 description = "Live-cell microscopy image analysis and single-molecule measurements"
 readme = "README.md"
 license = "GPL-3.0-or-later"
-
-[tool.hatch.version]
-path = "microlive/__init__.py"
 requires-python = ">=3.10"
 authors = [
     { name = "Luis U. Aguilera" },
@@ -115,6 +112,7 @@ dev = [
     "ruff>=0.1",
     "build",
     "twine",
+    "pdoc",
 ]
 notebooks = [
     "jupyter>=1.0",
@@ -137,6 +135,9 @@ Changelog = "https://github.com/ningzhaoAnschutz/microlive/releases"
 # Build Configuration
 # =============================================================================
 
+[tool.hatch.version]
+path = "microlive/__init__.py"
+
 [tool.hatch.build.targets.wheel]
 packages = ["microlive"]
 exclude = [

microlive-1.0.2/microlive/gui/main.py

@@ -1,54 +0,0 @@
-"""Entry point for MicroLive GUI application.
-
-This module provides the command-line entry point for launching
-the MicroLive graphical user interface.
-
-Usage:
-    $ microlive
-    
-Or programmatically:
-    from microlive.gui.main import main
-    main()
-"""
-
-import sys
-import os
-
-
-def main():
-    """Launch the MicroLive GUI application."""
-    # Ensure proper Qt platform on macOS
-    if sys.platform == "darwin":
-        os.environ.setdefault("QT_MAC_WANTS_LAYER", "1")
-    
-    # Import Qt after environment setup
-    from PyQt5.QtWidgets import QApplication
-    from PyQt5.QtGui import QIcon
-    
-    # Import the main application window
-    from .app import GUI
-    
-    # Get icon path
-    from ..utils.resources import get_icon_path
-    
-    # Create application
-    app = QApplication(sys.argv)
-    app.setApplicationName("MicroLive")
-    app.setApplicationVersion("1.0.0")
-    app.setOrganizationName("Zhao Lab")
-    
-    # Set application icon
-    icon_path = get_icon_path()
-    if icon_path and icon_path.exists():
-        app.setWindowIcon(QIcon(str(icon_path)))
-    
-    # Create and show main window
-    window = GUI(icon_path=icon_path)
-    window.show()
-    
-    # Run event loop
-    sys.exit(app.exec_())
-
-
-if __name__ == "__main__":
-    main()