Small fix

Reviewed-on: #2

config/app_config.yaml

@@ -12,12 +12,28 @@ image_repository:
 models:
   default_base_model: yolov8s-seg.pt
   models_directory: data/models
+  base_model_choices:
+  - yolov8s-seg.pt
+  - yolo11s-seg.pt
 training:
   default_epochs: 100
   default_batch_size: 16
-  default_imgsz: 640
+  default_imgsz: 1024
   default_patience: 50
   default_lr0: 0.01
+  two_stage:
+    enabled: false
+    stage1:
+      epochs: 20
+      lr0: 0.0005
+      patience: 10
+      freeze: 10
+    stage2:
+      epochs: 150
+      lr0: 0.0003
+      patience: 30
+  last_dataset_yaml: /home/martin/code/object_detection/data/datasets/data.yaml
+  last_dataset_dir: /home/martin/code/object_detection/data/datasets
 detection:
   default_confidence: 0.25
   default_iou: 0.45

src/database/db_manager.py

@@ -10,6 +10,14 @@ from typing import List, Dict, Optional, Tuple, Any, Union
 from pathlib import Path
 import csv
 import hashlib
+import yaml
+
+from src.utils.logger import get_logger
+from src.utils.image import Image
+
+IMAGE_EXTENSIONS = tuple(Image.SUPPORTED_EXTENSIONS)
+
+logger = get_logger(__name__)
 
 
 class DatabaseManager:
@@ -30,18 +38,48 @@ class DatabaseManager:
         # Create directory if it doesn't exist
         Path(self.db_path).parent.mkdir(parents=True, exist_ok=True)
 
-        # Read schema file and execute
-        schema_path = Path(__file__).parent / "schema.sql"
-        with open(schema_path, "r") as f:
-            schema_sql = f.read()
-
         conn = self.get_connection()
         try:
+            # Check if annotations table needs migration
+            self._migrate_annotations_table(conn)
+
+            # Read schema file and execute
+            schema_path = Path(__file__).parent / "schema.sql"
+            with open(schema_path, "r") as f:
+                schema_sql = f.read()
+
             conn.executescript(schema_sql)
             conn.commit()
         finally:
             conn.close()
 
+    def _migrate_annotations_table(self, conn: sqlite3.Connection) -> None:
+        """
+        Migrate annotations table from old schema (class_name) to new schema (class_id).
+        """
+        cursor = conn.cursor()
+
+        # Check if annotations table exists
+        cursor.execute(
+            "SELECT name FROM sqlite_master WHERE type='table' AND name='annotations'"
+        )
+        if not cursor.fetchone():
+            # Table doesn't exist yet, no migration needed
+            return
+
+        # Check if table has old schema (class_name column)
+        cursor.execute("PRAGMA table_info(annotations)")
+        columns = {row[1]: row for row in cursor.fetchall()}
+
+        if "class_name" in columns and "class_id" not in columns:
+            # Old schema detected, need to migrate
+            print("Migrating annotations table to new schema with class_id...")
+
+            # Drop old annotations table (assuming no critical data since this is a new feature)
+            cursor.execute("DROP TABLE IF EXISTS annotations")
+            conn.commit()
+            print("Old annotations table dropped, will be recreated with new schema")
+
     def get_connection(self) -> sqlite3.Connection:
         """Get database connection with proper settings."""
         conn = sqlite3.connect(self.db_path)
@@ -413,6 +451,25 @@ class DatabaseManager:
             filters["model_id"] = model_id
         return self.get_detections(filters)
 
+    def delete_detections_for_image(
+        self, image_id: int, model_id: Optional[int] = None
+    ) -> int:
+        """Delete detections tied to a specific image and optional model."""
+        conn = self.get_connection()
+        try:
+            cursor = conn.cursor()
+            if model_id is not None:
+                cursor.execute(
+                    "DELETE FROM detections WHERE image_id = ? AND model_id = ?",
+                    (image_id, model_id),
+                )
+            else:
+                cursor.execute("DELETE FROM detections WHERE image_id = ?", (image_id,))
+            conn.commit()
+            return cursor.rowcount
+        finally:
+            conn.close()
+
     def delete_detections_for_model(self, model_id: int) -> int:
         """Delete all detections for a specific model."""
         conn = self.get_connection()
@@ -593,25 +650,38 @@ class DatabaseManager:
     def add_annotation(
         self,
         image_id: int,
-        class_name: str,
+        class_id: int,
         bbox: Tuple[float, float, float, float],
         annotator: str,
         segmentation_mask: Optional[List[List[float]]] = None,
         verified: bool = False,
     ) -> int:
-        """Add manual annotation."""
+        """
+        Add manual annotation.
+
+        Args:
+            image_id: ID of the image
+            class_id: ID of the object class (foreign key to object_classes)
+            bbox: Bounding box coordinates (normalized 0-1)
+            annotator: Name of person/tool creating annotation
+            segmentation_mask: Polygon coordinates for segmentation
+            verified: Whether annotation has been verified
+
+        Returns:
+            ID of the inserted annotation
+        """
         conn = self.get_connection()
         try:
             cursor = conn.cursor()
             x_min, y_min, x_max, y_max = bbox
             cursor.execute(
                 """
-                INSERT INTO annotations (image_id, class_name, x_min, y_min, x_max, y_max, segmentation_mask, annotator, verified)
+                INSERT INTO annotations (image_id, class_id, x_min, y_min, x_max, y_max, segmentation_mask, annotator, verified)
                 VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)
                 """,
                 (
                     image_id,
-                    class_name,
+                    class_id,
                     x_min,
                     y_min,
                     x_max,
@@ -627,15 +697,378 @@ class DatabaseManager:
             conn.close()
 
     def get_annotations_for_image(self, image_id: int) -> List[Dict]:
-        """Get all annotations for an image."""
+        """
+        Get all annotations for an image with class information.
+
+        Args:
+            image_id: ID of the image
+
+        Returns:
+            List of annotation dictionaries with joined class information
+        """
         conn = self.get_connection()
         try:
             cursor = conn.cursor()
-            cursor.execute("SELECT * FROM annotations WHERE image_id = ?", (image_id,))
+            cursor.execute(
+                """
+                SELECT
+                    a.*,
+                    c.class_name,
+                    c.color as class_color,
+                    c.description as class_description
+                FROM annotations a
+                JOIN object_classes c ON a.class_id = c.id
+                WHERE a.image_id = ?
+                ORDER BY a.created_at DESC
+                """,
+                (image_id,),
+            )
+            annotations = []
+            for row in cursor.fetchall():
+                ann = dict(row)
+                if ann.get("segmentation_mask"):
+                    ann["segmentation_mask"] = json.loads(ann["segmentation_mask"])
+                annotations.append(ann)
+            return annotations
+        finally:
+            conn.close()
+
+    def delete_annotation(self, annotation_id: int) -> bool:
+        """
+        Delete a manual annotation by ID.
+
+        Args:
+            annotation_id: ID of the annotation to delete
+
+        Returns:
+            True if an annotation was deleted, False otherwise.
+        """
+        conn = self.get_connection()
+        try:
+            cursor = conn.cursor()
+            cursor.execute("DELETE FROM annotations WHERE id = ?", (annotation_id,))
+            conn.commit()
+            return cursor.rowcount > 0
+        finally:
+            conn.close()
+
+    # ==================== Object Class Operations ====================
+
+    def get_object_classes(self) -> List[Dict]:
+        """
+        Get all object classes.
+
+        Returns:
+            List of object class dictionaries
+        """
+        conn = self.get_connection()
+        try:
+            cursor = conn.cursor()
+            cursor.execute("SELECT * FROM object_classes ORDER BY class_name")
             return [dict(row) for row in cursor.fetchall()]
         finally:
             conn.close()
 
+    def get_object_class_by_id(self, class_id: int) -> Optional[Dict]:
+        """Get object class by ID."""
+        conn = self.get_connection()
+        try:
+            cursor = conn.cursor()
+            cursor.execute("SELECT * FROM object_classes WHERE id = ?", (class_id,))
+            row = cursor.fetchone()
+            return dict(row) if row else None
+        finally:
+            conn.close()
+
+    def get_object_class_by_name(self, class_name: str) -> Optional[Dict]:
+        """Get object class by name."""
+        conn = self.get_connection()
+        try:
+            cursor = conn.cursor()
+            cursor.execute(
+                "SELECT * FROM object_classes WHERE class_name = ?", (class_name,)
+            )
+            row = cursor.fetchone()
+            return dict(row) if row else None
+        finally:
+            conn.close()
+
+    def add_object_class(
+        self, class_name: str, color: str, description: Optional[str] = None
+    ) -> int:
+        """
+        Add a new object class.
+
+        Args:
+            class_name: Name of the object class
+            color: Hex color code (e.g., '#FF0000')
+            description: Optional description
+
+        Returns:
+            ID of the inserted object class
+        """
+        conn = self.get_connection()
+        try:
+            cursor = conn.cursor()
+            cursor.execute(
+                """
+                INSERT INTO object_classes (class_name, color, description)
+                VALUES (?, ?, ?)
+                """,
+                (class_name, color, description),
+            )
+            conn.commit()
+            return cursor.lastrowid
+        except sqlite3.IntegrityError:
+            # Class already exists
+            existing = self.get_object_class_by_name(class_name)
+            return existing["id"] if existing else None
+        finally:
+            conn.close()
+
+    def update_object_class(
+        self,
+        class_id: int,
+        class_name: Optional[str] = None,
+        color: Optional[str] = None,
+        description: Optional[str] = None,
+    ) -> bool:
+        """
+        Update an object class.
+
+        Args:
+            class_id: ID of the class to update
+            class_name: New class name (optional)
+            color: New color (optional)
+            description: New description (optional)
+
+        Returns:
+            True if updated, False otherwise
+        """
+        conn = self.get_connection()
+        try:
+            updates = {}
+            if class_name is not None:
+                updates["class_name"] = class_name
+            if color is not None:
+                updates["color"] = color
+            if description is not None:
+                updates["description"] = description
+
+            if not updates:
+                return False
+
+            set_clauses = [f"{key} = ?" for key in updates.keys()]
+            params = list(updates.values()) + [class_id]
+
+            query = f"UPDATE object_classes SET {', '.join(set_clauses)} WHERE id = ?"
+            cursor = conn.cursor()
+            cursor.execute(query, params)
+            conn.commit()
+            return cursor.rowcount > 0
+        finally:
+            conn.close()
+
+    def delete_object_class(self, class_id: int) -> bool:
+        """
+        Delete an object class.
+
+        Args:
+            class_id: ID of the class to delete
+
+        Returns:
+            True if deleted, False otherwise
+        """
+        conn = self.get_connection()
+        try:
+            cursor = conn.cursor()
+            cursor.execute("DELETE FROM object_classes WHERE id = ?", (class_id,))
+            conn.commit()
+            return cursor.rowcount > 0
+        finally:
+            conn.close()
+
+    # ==================== Dataset Utilities ====================
+
+    def compose_data_yaml(
+        self,
+        dataset_root: str,
+        output_path: Optional[str] = None,
+        splits: Optional[Dict[str, str]] = None,
+    ) -> str:
+        """
+        Compose a YOLO data.yaml file based on dataset folders and database metadata.
+
+        Args:
+            dataset_root: Base directory containing the dataset structure.
+            output_path: Optional output path; defaults to <dataset_root>/data.yaml.
+            splits: Optional mapping overriding train/val/test image directories (relative
+                to dataset_root or absolute paths).
+
+        Returns:
+            Path to the generated YAML file.
+        """
+        dataset_root_path = Path(dataset_root).expanduser()
+        if not dataset_root_path.exists():
+            raise ValueError(f"Dataset root does not exist: {dataset_root_path}")
+        dataset_root_path = dataset_root_path.resolve()
+
+        split_map: Dict[str, str] = {key: "" for key in ("train", "val", "test")}
+        if splits:
+            for key, value in splits.items():
+                if key in split_map and value:
+                    split_map[key] = value
+
+        inferred = self._infer_split_dirs(dataset_root_path)
+        for key in split_map:
+            if not split_map[key]:
+                split_map[key] = inferred.get(key, "")
+
+        for required in ("train", "val"):
+            if not split_map[required]:
+                raise ValueError(
+                    "Unable to determine %s image directory under %s. Provide it "
+                    "explicitly via the 'splits' argument."
+                    % (required, dataset_root_path)
+                )
+
+        yaml_splits: Dict[str, str] = {}
+        for key, value in split_map.items():
+            if not value:
+                continue
+            yaml_splits[key] = self._normalize_split_value(value, dataset_root_path)
+
+        class_names = self._fetch_annotation_class_names()
+        if not class_names:
+            class_names = [cls["class_name"] for cls in self.get_object_classes()]
+        if not class_names:
+            raise ValueError("No object classes available to populate data.yaml")
+
+        names_map = {idx: name for idx, name in enumerate(class_names)}
+        payload: Dict[str, Any] = {
+            "path": dataset_root_path.as_posix(),
+            "train": yaml_splits["train"],
+            "val": yaml_splits["val"],
+            "names": names_map,
+            "nc": len(class_names),
+        }
+        if yaml_splits.get("test"):
+            payload["test"] = yaml_splits["test"]
+
+        output_path_obj = (
+            Path(output_path).expanduser()
+            if output_path
+            else dataset_root_path / "data.yaml"
+        )
+        output_path_obj.parent.mkdir(parents=True, exist_ok=True)
+
+        with open(output_path_obj, "w", encoding="utf-8") as handle:
+            yaml.safe_dump(payload, handle, sort_keys=False)
+
+        logger.info(f"Generated data.yaml at {output_path_obj}")
+        return output_path_obj.as_posix()
+
+    def _fetch_annotation_class_names(self) -> List[str]:
+        """Return class names referenced by annotations (ordered by class ID)."""
+        conn = self.get_connection()
+        try:
+            cursor = conn.cursor()
+            cursor.execute(
+                """
+                SELECT DISTINCT c.id, c.class_name
+                FROM annotations a
+                JOIN object_classes c ON a.class_id = c.id
+                ORDER BY c.id
+                """
+            )
+            rows = cursor.fetchall()
+            return [row["class_name"] for row in rows]
+        finally:
+            conn.close()
+
+    def _infer_split_dirs(self, dataset_root: Path) -> Dict[str, str]:
+        """Infer train/val/test image directories relative to dataset_root."""
+        patterns = {
+            "train": [
+                "train/images",
+                "training/images",
+                "images/train",
+                "images/training",
+                "train",
+                "training",
+            ],
+            "val": [
+                "val/images",
+                "validation/images",
+                "images/val",
+                "images/validation",
+                "val",
+                "validation",
+            ],
+            "test": [
+                "test/images",
+                "testing/images",
+                "images/test",
+                "images/testing",
+                "test",
+                "testing",
+            ],
+        }
+
+        inferred: Dict[str, str] = {key: "" for key in patterns}
+        for split_name, options in patterns.items():
+            for relative in options:
+                candidate = (dataset_root / relative).resolve()
+                if (
+                    candidate.exists()
+                    and candidate.is_dir()
+                    and self._directory_has_images(candidate)
+                ):
+                    try:
+                        inferred[split_name] = candidate.relative_to(
+                            dataset_root
+                        ).as_posix()
+                    except ValueError:
+                        inferred[split_name] = candidate.as_posix()
+                    break
+        return inferred
+
+    def _normalize_split_value(self, split_value: str, dataset_root: Path) -> str:
+        """Validate and normalize a split directory to a YAML-friendly string."""
+        split_path = Path(split_value).expanduser()
+        if not split_path.is_absolute():
+            split_path = (dataset_root / split_path).resolve()
+        else:
+            split_path = split_path.resolve()
+
+        if not split_path.exists() or not split_path.is_dir():
+            raise ValueError(f"Split directory not found: {split_path}")
+
+        if not self._directory_has_images(split_path):
+            raise ValueError(f"No images found under {split_path}")
+
+        try:
+            return split_path.relative_to(dataset_root).as_posix()
+        except ValueError:
+            return split_path.as_posix()
+
+    @staticmethod
+    def _directory_has_images(directory: Path, max_checks: int = 2000) -> bool:
+        """Return True if directory tree contains at least one image file."""
+        checked = 0
+        try:
+            for file_path in directory.rglob("*"):
+                if not file_path.is_file():
+                    continue
+                if file_path.suffix.lower() in IMAGE_EXTENSIONS:
+                    return True
+                checked += 1
+                if checked >= max_checks:
+                    break
+        except Exception:
+            return False
+        return False
+
     @staticmethod
     def calculate_checksum(file_path: str) -> str:
         """Calculate MD5 checksum of a file."""

src/database/schema.sql

@@ -44,11 +44,27 @@ CREATE TABLE IF NOT EXISTS detections (
     FOREIGN KEY (model_id) REFERENCES models (id) ON DELETE CASCADE
 );
 
--- Annotations table: stores manual annotations (future feature)
+-- Object classes table: stores annotation class definitions with colors
+CREATE TABLE IF NOT EXISTS object_classes (
+    id INTEGER PRIMARY KEY AUTOINCREMENT,
+    class_name TEXT NOT NULL UNIQUE,
+    color TEXT NOT NULL,  -- Hex color code (e.g., '#FF0000')
+    created_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP,
+    description TEXT
+);
+
+-- Insert default object classes
+INSERT OR IGNORE INTO object_classes (class_name, color, description) VALUES
+    ('cell', '#FF0000', 'Cell object'),
+    ('nucleus', '#00FF00', 'Cell nucleus'),
+    ('mitochondria', '#0000FF', 'Mitochondria'),
+    ('vesicle', '#FFFF00', 'Vesicle');
+
+-- Annotations table: stores manual annotations
 CREATE TABLE IF NOT EXISTS annotations (
     id INTEGER PRIMARY KEY AUTOINCREMENT,
     image_id INTEGER NOT NULL,
-    class_name TEXT NOT NULL,
+    class_id INTEGER NOT NULL,
     x_min REAL NOT NULL CHECK(x_min >= 0 AND x_min <= 1),
     y_min REAL NOT NULL CHECK(y_min >= 0 AND y_min <= 1),
     x_max REAL NOT NULL CHECK(x_max >= 0 AND x_max <= 1),
@@ -57,7 +73,8 @@ CREATE TABLE IF NOT EXISTS annotations (
     annotator TEXT,
     created_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP,
     verified BOOLEAN DEFAULT 0,
-    FOREIGN KEY (image_id) REFERENCES images (id) ON DELETE CASCADE
+    FOREIGN KEY (image_id) REFERENCES images (id) ON DELETE CASCADE,
+    FOREIGN KEY (class_id) REFERENCES object_classes (id) ON DELETE CASCADE
 );
 
 -- Create indexes for performance optimization
@@ -69,4 +86,6 @@ CREATE INDEX IF NOT EXISTS idx_detections_confidence ON detections(confidence);
 CREATE INDEX IF NOT EXISTS idx_images_relative_path ON images(relative_path);
 CREATE INDEX IF NOT EXISTS idx_images_added_at ON images(added_at);
 CREATE INDEX IF NOT EXISTS idx_annotations_image_id ON annotations(image_id);
-CREATE INDEX IF NOT EXISTS idx_models_created_at ON models(created_at);
+CREATE INDEX IF NOT EXISTS idx_annotations_class_id ON annotations(class_id);
+CREATE INDEX IF NOT EXISTS idx_models_created_at ON models(created_at);
+CREATE INDEX IF NOT EXISTS idx_object_classes_class_name ON object_classes(class_name);

src/gui/main_window.py

@@ -13,7 +13,7 @@ from PySide6.QtWidgets import (
     QVBoxLayout,
     QLabel,
 )
-from PySide6.QtCore import Qt, QTimer
+from PySide6.QtCore import Qt, QTimer, QSettings
 from PySide6.QtGui import QAction, QKeySequence
 
 from src.database.db_manager import DatabaseManager
@@ -52,8 +52,8 @@ class MainWindow(QMainWindow):
         self._create_tab_widget()
         self._create_status_bar()
 
-        # Center window on screen
+        # Restore window geometry or center window on screen
-        self._center_window()
+        self._restore_window_state()
 
         logger.info("Main window initialized")
 
@@ -156,6 +156,24 @@ class MainWindow(QMainWindow):
             (screen.width() - size.width()) // 2, (screen.height() - size.height()) // 2
         )
 
+    def _restore_window_state(self):
+        """Restore window geometry from settings or center window."""
+        settings = QSettings("microscopy_app", "object_detection")
+        geometry = settings.value("main_window/geometry")
+
+        if geometry:
+            self.restoreGeometry(geometry)
+            logger.debug("Restored window geometry from settings")
+        else:
+            self._center_window()
+            logger.debug("Centered window on screen")
+
+    def _save_window_state(self):
+        """Save window geometry to settings."""
+        settings = QSettings("microscopy_app", "object_detection")
+        settings.setValue("main_window/geometry", self.saveGeometry())
+        logger.debug("Saved window geometry to settings")
+
     def _show_settings(self):
         """Show settings dialog."""
         logger.info("Opening settings dialog")
@@ -276,6 +294,15 @@ class MainWindow(QMainWindow):
         )
 
         if reply == QMessageBox.Yes:
+            # Save window state before closing
+            self._save_window_state()
+
+            # Persist tab state and stop background work before exit
+            if hasattr(self, "training_tab"):
+                self.training_tab.shutdown()
+            if hasattr(self, "annotation_tab"):
+                self.annotation_tab.save_state()
+
             logger.info("Application closing")
             event.accept()
         else:

src/gui/tabs/annotation_tab.py

@@ -1,6 +1,6 @@
 """
 Annotation tab for the microscopy object detection application.
-Future feature for manual annotation.
+Manual annotation with pen tool and object class management.
 """
 
 from PySide6.QtWidgets import (
@@ -12,6 +12,7 @@ from PySide6.QtWidgets import (
     QPushButton,
     QFileDialog,
     QMessageBox,
+    QSplitter,
 )
 from PySide6.QtCore import Qt, QSettings
 from pathlib import Path
@@ -20,13 +21,13 @@ from src.database.db_manager import DatabaseManager
 from src.utils.config_manager import ConfigManager
 from src.utils.image import Image, ImageLoadError
 from src.utils.logger import get_logger
-from src.gui.widgets import ImageDisplayWidget
+from src.gui.widgets import AnnotationCanvasWidget, AnnotationToolsWidget
 
 logger = get_logger(__name__)
 
 
 class AnnotationTab(QWidget):
-    """Annotation tab placeholder (future feature)."""
+    """Annotation tab for manual image annotation."""
 
     def __init__(
         self, db_manager: DatabaseManager, config_manager: ConfigManager, parent=None
@@ -36,6 +37,10 @@ class AnnotationTab(QWidget):
         self.config_manager = config_manager
         self.current_image = None
         self.current_image_path = None
+        self.current_image_id = None
+        self.current_annotations = []
+        # IDs of annotations currently selected on the canvas (multi-select)
+        self.selected_annotation_ids = []
 
         self._setup_ui()
 
@@ -43,6 +48,75 @@ class AnnotationTab(QWidget):
         """Setup user interface."""
         layout = QVBoxLayout()
 
+        # Main horizontal splitter to divide left (image) and right (controls)
+        self.main_splitter = QSplitter(Qt.Horizontal)
+        self.main_splitter.setHandleWidth(10)
+
+        # { Left splitter for image display and zoom info
+        self.left_splitter = QSplitter(Qt.Vertical)
+        self.left_splitter.setHandleWidth(10)
+
+        # Annotation canvas section
+        canvas_group = QGroupBox("Annotation Canvas")
+        canvas_layout = QVBoxLayout()
+
+        # Use the AnnotationCanvasWidget
+        self.annotation_canvas = AnnotationCanvasWidget()
+        self.annotation_canvas.zoom_changed.connect(self._on_zoom_changed)
+        self.annotation_canvas.annotation_drawn.connect(self._on_annotation_drawn)
+        # Selection of existing polylines (when tool is not in drawing mode)
+        self.annotation_canvas.annotation_selected.connect(self._on_annotation_selected)
+        canvas_layout.addWidget(self.annotation_canvas)
+
+        canvas_group.setLayout(canvas_layout)
+        self.left_splitter.addWidget(canvas_group)
+
+        # Controls info
+        controls_info = QLabel(
+            "Zoom: Mouse wheel or +/- keys | Drawing: Enable pen and drag mouse"
+        )
+        controls_info.setStyleSheet("QLabel { color: #888; font-style: italic; }")
+        self.left_splitter.addWidget(controls_info)
+        # }
+
+        # { Right splitter for annotation tools and controls
+        self.right_splitter = QSplitter(Qt.Vertical)
+        self.right_splitter.setHandleWidth(10)
+
+        # Annotation tools section
+        self.annotation_tools = AnnotationToolsWidget(self.db_manager)
+        self.annotation_tools.polyline_enabled_changed.connect(
+            self.annotation_canvas.set_polyline_enabled
+        )
+        self.annotation_tools.polyline_pen_color_changed.connect(
+            self.annotation_canvas.set_polyline_pen_color
+        )
+        self.annotation_tools.polyline_pen_width_changed.connect(
+            self.annotation_canvas.set_polyline_pen_width
+        )
+        # Show / hide bounding boxes
+        self.annotation_tools.show_bboxes_changed.connect(
+            self.annotation_canvas.set_show_bboxes
+        )
+        # RDP simplification controls
+        self.annotation_tools.simplify_on_finish_changed.connect(
+            self._on_simplify_on_finish_changed
+        )
+        self.annotation_tools.simplify_epsilon_changed.connect(
+            self._on_simplify_epsilon_changed
+        )
+        # Class selection and class-color changes
+        self.annotation_tools.class_selected.connect(self._on_class_selected)
+        self.annotation_tools.class_color_changed.connect(self._on_class_color_changed)
+        self.annotation_tools.clear_annotations_requested.connect(
+            self._on_clear_annotations
+        )
+        # Delete selected annotation on canvas
+        self.annotation_tools.delete_selected_annotation_requested.connect(
+            self._on_delete_selected_annotation
+        )
+        self.right_splitter.addWidget(self.annotation_tools)
+
         # Image loading section
         load_group = QGroupBox("Image Loading")
         load_layout = QVBoxLayout()
@@ -53,7 +127,6 @@ class AnnotationTab(QWidget):
         self.load_image_btn.clicked.connect(self._load_image)
         button_layout.addWidget(self.load_image_btn)
         button_layout.addStretch()
-
         load_layout.addLayout(button_layout)
 
         # Image info label
@@ -61,43 +134,22 @@ class AnnotationTab(QWidget):
         load_layout.addWidget(self.image_info_label)
 
         load_group.setLayout(load_layout)
-        layout.addWidget(load_group)
+        self.right_splitter.addWidget(load_group)
+        # }
 
-        # Image display section
+        # Add both splitters to the main horizontal splitter
-        display_group = QGroupBox("Image Display")
+        self.main_splitter.addWidget(self.left_splitter)
-        display_layout = QVBoxLayout()
+        self.main_splitter.addWidget(self.right_splitter)
 
-        # Use the reusable ImageDisplayWidget
+        # Set initial sizes: 75% for left (image), 25% for right (controls)
-        self.image_display_widget = ImageDisplayWidget()
+        self.main_splitter.setSizes([750, 250])
-        self.image_display_widget.zoom_changed.connect(self._on_zoom_changed)
-        display_layout.addWidget(self.image_display_widget)
-
-        display_group.setLayout(display_layout)
-        layout.addWidget(display_group)
-
-        # Future features info
-        info_group = QGroupBox("Annotation Tool (Future Feature)")
-        info_layout = QVBoxLayout()
-        info_label = QLabel(
-            "Full annotation functionality will be implemented in future version.\n\n"
-            "Planned Features:\n"
-            "- Drawing tools for bounding boxes\n"
-            "- Class label assignment\n"
-            "- Export annotations to YOLO format\n"
-            "- Annotation verification"
-        )
-        info_layout.addWidget(info_label)
-        info_group.setLayout(info_layout)
-
-        layout.addWidget(info_group)
-
-        # Zoom controls info
-        zoom_info = QLabel("Zoom: Mouse wheel or +/- keys to zoom in/out")
-        zoom_info.setStyleSheet("QLabel { color: #888; font-style: italic; }")
-        layout.addWidget(zoom_info)
 
+        layout.addWidget(self.main_splitter)
         self.setLayout(layout)
 
+        # Restore splitter positions from settings
+        self._restore_state()
+
     def _load_image(self):
         """Load and display an image file."""
         # Get last opened directory from QSettings
@@ -116,7 +168,7 @@ class AnnotationTab(QWidget):
             self,
             "Select Image",
             start_dir,
-            "Images (*.jpg *.jpeg *.png *.tif *.tiff *.bmp)",
+            "Images (*" + " *".join(Image.SUPPORTED_EXTENSIONS) + ")",
         )
 
         if not file_path:
@@ -132,13 +184,25 @@ class AnnotationTab(QWidget):
                 "annotation_tab/last_directory", str(Path(file_path).parent)
             )
 
-            # Display image using the ImageDisplayWidget
+            # Get or create image in database
-            self.image_display_widget.load_image(self.current_image)
+            relative_path = str(Path(file_path).name)  # Simplified for now
+            self.current_image_id = self.db_manager.get_or_create_image(
+                relative_path,
+                Path(file_path).name,
+                self.current_image.width,
+                self.current_image.height,
+            )
+
+            # Display image using the AnnotationCanvasWidget
+            self.annotation_canvas.load_image(self.current_image)
+
+            # Load and display any existing annotations for this image
+            self._load_annotations_for_current_image()
 
             # Update info label
             self._update_image_info()
 
-            logger.info(f"Loaded image: {file_path}")
+            logger.info(f"Loaded image: {file_path} (DB ID: {self.current_image_id})")
 
         except ImageLoadError as e:
             logger.error(f"Failed to load image: {e}")
@@ -155,7 +219,7 @@ class AnnotationTab(QWidget):
             self.image_info_label.setText("No image loaded")
             return
 
-        zoom_percentage = self.image_display_widget.get_zoom_percentage()
+        zoom_percentage = self.annotation_canvas.get_zoom_percentage()
         info_text = (
             f"File: {Path(self.current_image_path).name}\n"
             f"Size: {self.current_image.width}x{self.current_image.height} pixels\n"
@@ -168,9 +232,335 @@ class AnnotationTab(QWidget):
         self.image_info_label.setText(info_text)
 
     def _on_zoom_changed(self, zoom_scale: float):
-        """Handle zoom level changes from the image display widget."""
+        """Handle zoom level changes from the annotation canvas."""
         self._update_image_info()
 
+    def _on_annotation_drawn(self, points: list):
+        """
+        Handle when an annotation stroke is drawn.
+
+        Saves the new annotation directly to the database and refreshes the
+        on-canvas display of annotations for the current image.
+        """
+        # Ensure we have an image loaded and in the DB
+        if not self.current_image or not self.current_image_id:
+            logger.warning("Annotation drawn but no image loaded")
+            QMessageBox.warning(
+                self,
+                "No Image",
+                "Please load an image before drawing annotations.",
+            )
+            return
+
+        current_class = self.annotation_tools.get_current_class()
+
+        if not current_class:
+            logger.warning("Annotation drawn but no object class selected")
+            QMessageBox.warning(
+                self,
+                "No Class Selected",
+                "Please select an object class before drawing annotations.",
+            )
+            return
+
+        if not points:
+            logger.warning("Annotation drawn with no points, ignoring")
+            return
+
+        # points are [(x_norm, y_norm), ...]
+        xs = [p[0] for p in points]
+        ys = [p[1] for p in points]
+        x_min, x_max = min(xs), max(xs)
+        y_min, y_max = min(ys), max(ys)
+
+        # Store segmentation mask in [y_norm, x_norm] format to match DB
+        db_polyline = [[float(y), float(x)] for (x, y) in points]
+
+        try:
+            annotation_id = self.db_manager.add_annotation(
+                image_id=self.current_image_id,
+                class_id=current_class["id"],
+                bbox=(x_min, y_min, x_max, y_max),
+                annotator="manual",
+                segmentation_mask=db_polyline,
+                verified=False,
+            )
+
+            logger.info(
+                f"Saved annotation (ID: {annotation_id}) for class "
+                f"'{current_class['class_name']}' "
+                f"Bounding box: ({x_min:.3f}, {y_min:.3f}) to ({x_max:.3f}, {y_max:.3f})\n"
+                f"with {len(points)} polyline points"
+            )
+
+            # Reload annotations from DB and redraw (respecting current class filter)
+            self._load_annotations_for_current_image()
+
+        except Exception as e:
+            logger.error(f"Failed to save annotation: {e}")
+            QMessageBox.critical(self, "Error", f"Failed to save annotation:\n{str(e)}")
+
+    def _on_annotation_selected(self, annotation_ids):
+        """
+        Handle selection of existing annotations on the canvas.
+
+        Args:
+            annotation_ids: List of selected annotation IDs, or None/empty if cleared.
+        """
+        if not annotation_ids:
+            self.selected_annotation_ids = []
+            self.annotation_tools.set_has_selected_annotation(False)
+            logger.debug("Annotation selection cleared on canvas")
+            return
+
+        # Normalize to a unique, sorted list of integer IDs
+        ids = sorted({int(aid) for aid in annotation_ids if isinstance(aid, int)})
+        self.selected_annotation_ids = ids
+        self.annotation_tools.set_has_selected_annotation(bool(ids))
+        logger.debug(f"Annotations selected on canvas: IDs={ids}")
+
+    def _on_simplify_on_finish_changed(self, enabled: bool):
+        """Update canvas simplify-on-finish flag from tools widget."""
+        self.annotation_canvas.simplify_on_finish = enabled
+        logger.debug(f"Annotation simplification on finish set to {enabled}")
+
+    def _on_simplify_epsilon_changed(self, epsilon: float):
+        """Update canvas RDP epsilon from tools widget."""
+        self.annotation_canvas.simplify_epsilon = float(epsilon)
+        logger.debug(f"Annotation simplification epsilon set to {epsilon}")
+
+    def _on_class_color_changed(self):
+        """
+        Handle changes to the selected object's class color.
+
+        When the user updates a class color in the tools widget, reload the
+        annotations for the current image so that all polylines are redrawn
+        using the updated per-class colors.
+        """
+        if not self.current_image_id:
+            return
+
+        logger.debug(
+            f"Class color changed; reloading annotations for image ID {self.current_image_id}"
+        )
+        self._load_annotations_for_current_image()
+
+    def _on_class_selected(self, class_data):
+        """
+        Handle when an object class is selected or cleared.
+
+        When a specific class is selected, only annotations of that class are drawn.
+        When the selection is cleared ("-- Select Class --"), all annotations are shown.
+        """
+        if class_data:
+            logger.debug(f"Object class selected: {class_data['class_name']}")
+        else:
+            logger.debug(
+                'No class selected ("-- Select Class --"), showing all annotations'
+            )
+
+        # Changing the class filter invalidates any previous selection
+        self.selected_annotation_ids = []
+        self.annotation_tools.set_has_selected_annotation(False)
+
+        # Whenever the selection changes, update which annotations are visible
+        self._redraw_annotations_for_current_filter()
+
+    def _on_clear_annotations(self):
+        """Handle clearing all annotations."""
+        self.annotation_canvas.clear_annotations()
+        # Clear in-memory state and selection, but keep DB entries unchanged
+        self.current_annotations = []
+        self.selected_annotation_ids = []
+        self.annotation_tools.set_has_selected_annotation(False)
+        logger.info("Cleared all annotations")
+
+    def _on_delete_selected_annotation(self):
+        """Handle deleting the currently selected annotation(s) (if any)."""
+        if not self.selected_annotation_ids:
+            QMessageBox.information(
+                self,
+                "No Selection",
+                "No annotation is currently selected.",
+            )
+            return
+
+        count = len(self.selected_annotation_ids)
+        if count == 1:
+            question = "Are you sure you want to delete the selected annotation?"
+            title = "Delete Annotation"
+        else:
+            question = (
+                f"Are you sure you want to delete the {count} selected annotations?"
+            )
+            title = "Delete Annotations"
+
+        reply = QMessageBox.question(
+            self,
+            title,
+            question,
+            QMessageBox.Yes | QMessageBox.No,
+            QMessageBox.No,
+        )
+        if reply != QMessageBox.Yes:
+            return
+
+        failed_ids = []
+        try:
+            for ann_id in self.selected_annotation_ids:
+                try:
+                    deleted = self.db_manager.delete_annotation(ann_id)
+                    if not deleted:
+                        failed_ids.append(ann_id)
+                except Exception as e:
+                    logger.error(f"Failed to delete annotation ID {ann_id}: {e}")
+                    failed_ids.append(ann_id)
+
+            if failed_ids:
+                QMessageBox.warning(
+                    self,
+                    "Partial Failure",
+                    "Some annotations could not be deleted:\n"
+                    + ", ".join(str(a) for a in failed_ids),
+                )
+            else:
+                logger.info(
+                    f"Deleted {count} annotation(s): "
+                    + ", ".join(str(a) for a in self.selected_annotation_ids)
+                )
+
+            # Clear selection and reload annotations for the current image from DB
+            self.selected_annotation_ids = []
+            self.annotation_tools.set_has_selected_annotation(False)
+            self._load_annotations_for_current_image()
+
+        except Exception as e:
+            logger.error(f"Failed to delete annotations: {e}")
+            QMessageBox.critical(
+                self,
+                "Error",
+                f"Failed to delete annotations:\n{str(e)}",
+            )
+
+    def _load_annotations_for_current_image(self):
+        """
+        Load all annotations for the current image from the database and
+        redraw them on the canvas, honoring the currently selected class
+        filter (if any).
+        """
+        if not self.current_image_id:
+            self.current_annotations = []
+            self.annotation_canvas.clear_annotations()
+            self.selected_annotation_ids = []
+            self.annotation_tools.set_has_selected_annotation(False)
+            return
+
+        try:
+            self.current_annotations = self.db_manager.get_annotations_for_image(
+                self.current_image_id
+            )
+            # New annotations loaded; reset any selection
+            self.selected_annotation_ids = []
+            self.annotation_tools.set_has_selected_annotation(False)
+            self._redraw_annotations_for_current_filter()
+        except Exception as e:
+            logger.error(
+                f"Failed to load annotations for image {self.current_image_id}: {e}"
+            )
+            QMessageBox.critical(
+                self,
+                "Error",
+                f"Failed to load annotations for this image:\n{str(e)}",
+            )
+
+    def _redraw_annotations_for_current_filter(self):
+        """
+        Redraw annotations for the current image, optionally filtered by the
+        currently selected object class.
+        """
+        # Clear current on-canvas annotations but keep the image
+        self.annotation_canvas.clear_annotations()
+
+        if not self.current_annotations:
+            return
+
+        current_class = self.annotation_tools.get_current_class()
+        selected_class_id = current_class["id"] if current_class else None
+
+        drawn_count = 0
+        for ann in self.current_annotations:
+            # Filter by class if one is selected
+            if (
+                selected_class_id is not None
+                and ann.get("class_id") != selected_class_id
+            ):
+                continue
+
+            if ann.get("segmentation_mask"):
+                polyline = ann["segmentation_mask"]
+                color = ann.get("class_color", "#FF0000")
+
+                self.annotation_canvas.draw_saved_polyline(
+                    polyline,
+                    color,
+                    width=3,
+                    annotation_id=ann["id"],
+                )
+                self.annotation_canvas.draw_saved_bbox(
+                    [ann["x_min"], ann["y_min"], ann["x_max"], ann["y_max"]],
+                    color,
+                    width=3,
+                )
+                drawn_count += 1
+
+        logger.info(
+            f"Displayed {drawn_count} annotation(s) for current image with "
+            f"{'no class filter' if selected_class_id is None else f'class_id={selected_class_id}'}"
+        )
+
+    def _restore_state(self):
+        """Restore splitter positions from settings."""
+        settings = QSettings("microscopy_app", "object_detection")
+
+        # Restore main splitter state
+        main_state = settings.value("annotation_tab/main_splitter_state")
+        if main_state:
+            self.main_splitter.restoreState(main_state)
+            logger.debug("Restored main splitter state")
+
+        # Restore left splitter state
+        left_state = settings.value("annotation_tab/left_splitter_state")
+        if left_state:
+            self.left_splitter.restoreState(left_state)
+            logger.debug("Restored left splitter state")
+
+        # Restore right splitter state
+        right_state = settings.value("annotation_tab/right_splitter_state")
+        if right_state:
+            self.right_splitter.restoreState(right_state)
+            logger.debug("Restored right splitter state")
+
+    def save_state(self):
+        """Save splitter positions to settings."""
+        settings = QSettings("microscopy_app", "object_detection")
+
+        # Save main splitter state
+        settings.setValue(
+            "annotation_tab/main_splitter_state", self.main_splitter.saveState()
+        )
+
+        # Save left splitter state
+        settings.setValue(
+            "annotation_tab/left_splitter_state", self.left_splitter.saveState()
+        )
+
+        # Save right splitter state
+        settings.setValue(
+            "annotation_tab/right_splitter_state", self.right_splitter.saveState()
+        )
+
+        logger.debug("Saved annotation tab splitter states")
+
     def refresh(self):
         """Refresh the tab."""
         pass

src/gui/tabs/detection_tab.py

@@ -20,12 +20,14 @@ from PySide6.QtWidgets import (
 )
 from PySide6.QtCore import Qt, QThread, Signal
 from pathlib import Path
+from typing import Optional
 
 from src.database.db_manager import DatabaseManager
 from src.utils.config_manager import ConfigManager
 from src.utils.logger import get_logger
 from src.utils.file_utils import get_image_files
 from src.model.inference import InferenceEngine
+from src.utils.image import Image
 
 
 logger = get_logger(__name__)
@@ -147,30 +149,66 @@ class DetectionTab(QWidget):
         self.model_combo.currentIndexChanged.connect(self._on_model_changed)
 
     def _load_models(self):
-        """Load available models from database."""
+        """Load available models from database and local storage."""
         try:
-            models = self.db_manager.get_models()
             self.model_combo.clear()
+            models = self.db_manager.get_models()
+            has_models = False
 
-            if not models:
+            known_paths = set()
-                self.model_combo.addItem("No models available", None)
-                self._set_buttons_enabled(False)
-                return
 
-            # Add base model option
+            # Add base model option first (always available)
             base_model = self.config_manager.get(
                 "models.default_base_model", "yolov8s-seg.pt"
             )
-            self.model_combo.addItem(
+            if base_model:
-                f"Base Model ({base_model})", {"id": 0, "path": base_model}
+                base_data = {
-            )
+                    "id": 0,
+                    "path": base_model,
+                    "model_name": Path(base_model).stem or "Base Model",
+                    "model_version": "pretrained",
+                    "base_model": base_model,
+                    "source": "base",
+                }
+                self.model_combo.addItem(f"Base Model ({base_model})", base_data)
+                known_paths.add(self._normalize_model_path(base_model))
+                has_models = True
 
-            # Add trained models
+            # Add trained models from database
             for model in models:
                 display_name = f"{model['model_name']} v{model['model_version']}"
-                self.model_combo.addItem(display_name, model)
+                model_data = {**model, "path": model.get("model_path")}
+                normalized = self._normalize_model_path(model_data.get("path"))
+                if normalized:
+                    known_paths.add(normalized)
+                self.model_combo.addItem(display_name, model_data)
+                has_models = True
 
-            self._set_buttons_enabled(True)
+            # Discover local model files not yet in the database
+            local_models = self._discover_local_models()
+            for model_path in local_models:
+                normalized = self._normalize_model_path(model_path)
+                if normalized in known_paths:
+                    continue
+
+                display_name = f"Local Model ({Path(model_path).stem})"
+                model_data = {
+                    "id": None,
+                    "path": str(model_path),
+                    "model_name": Path(model_path).stem,
+                    "model_version": "local",
+                    "base_model": Path(model_path).stem,
+                    "source": "local",
+                }
+                self.model_combo.addItem(display_name, model_data)
+                known_paths.add(normalized)
+                has_models = True
+
+            if not has_models:
+                self.model_combo.addItem("No models available", None)
+                self._set_buttons_enabled(False)
+            else:
+                self._set_buttons_enabled(True)
 
         except Exception as e:
             logger.error(f"Error loading models: {e}")
@@ -199,7 +237,7 @@ class DetectionTab(QWidget):
             self,
             "Select Image",
             start_dir,
-            "Images (*.jpg *.jpeg *.png *.tif *.tiff *.bmp)",
+            "Images (*" + " *".join(Image.SUPPORTED_EXTENSIONS) + ")",
         )
 
         if not file_path:
@@ -249,25 +287,39 @@ class DetectionTab(QWidget):
                 QMessageBox.warning(self, "No Model", "Please select a model first.")
                 return
 
-            model_path = model_data["path"]
+            model_path = model_data.get("path")
-            model_id = model_data["id"]
+            if not model_path:
+                QMessageBox.warning(
+                    self, "Invalid Model", "Selected model is missing a file path."
+                )
+                return
 
-            # Ensure we have a valid model ID (create entry for base model if needed)
+            if not Path(model_path).exists():
-            if model_id == 0:
+                QMessageBox.critical(
-                # Create database entry for base model
+                    self,
-                base_model = self.config_manager.get(
+                    "Model Not Found",
-                    "models.default_base_model", "yolov8s-seg.pt"
+                    f"The selected model file could not be found:\n{model_path}",
-                )
-                model_id = self.db_manager.add_model(
-                    model_name="Base Model",
-                    model_version="pretrained",
-                    model_path=base_model,
-                    base_model=base_model,
                 )
+                return
+
+            model_id = model_data.get("id")
+
+            # Ensure we have a database entry for the selected model
+            if model_id in (None, 0):
+                model_id = self._ensure_model_record(model_data)
+                if not model_id:
+                    QMessageBox.critical(
+                        self,
+                        "Model Registration Failed",
+                        "Unable to register the selected model in the database.",
+                    )
+                    return
+
+            normalized_model_path = self._normalize_model_path(model_path) or model_path
 
             # Create inference engine
             self.inference_engine = InferenceEngine(
-                model_path, self.db_manager, model_id
+                normalized_model_path, self.db_manager, model_id
             )
 
             # Get confidence threshold
@@ -338,6 +390,76 @@ class DetectionTab(QWidget):
         self.batch_btn.setEnabled(enabled)
         self.model_combo.setEnabled(enabled)
 
+    def _discover_local_models(self) -> list:
+        """Scan the models directory for standalone .pt files."""
+        models_dir = self.config_manager.get_models_directory()
+        if not models_dir:
+            return []
+
+        models_path = Path(models_dir)
+        if not models_path.exists():
+            return []
+
+        try:
+            return sorted(
+                [p for p in models_path.rglob("*.pt") if p.is_file()],
+                key=lambda p: str(p).lower(),
+            )
+        except Exception as e:
+            logger.warning(f"Error discovering local models: {e}")
+            return []
+
+    def _normalize_model_path(self, path_value) -> str:
+        """Return a normalized absolute path string for comparison."""
+        if not path_value:
+            return ""
+        try:
+            return str(Path(path_value).resolve())
+        except Exception:
+            return str(path_value)
+
+    def _ensure_model_record(self, model_data: dict) -> Optional[int]:
+        """Ensure a database record exists for the selected model."""
+        model_path = model_data.get("path")
+        if not model_path:
+            return None
+
+        normalized_target = self._normalize_model_path(model_path)
+
+        try:
+            existing_models = self.db_manager.get_models()
+            for model in existing_models:
+                existing_path = model.get("model_path")
+                if not existing_path:
+                    continue
+                normalized_existing = self._normalize_model_path(existing_path)
+                if (
+                    normalized_existing == normalized_target
+                    or existing_path == model_path
+                ):
+                    return model["id"]
+
+            model_name = (
+                model_data.get("model_name") or Path(model_path).stem or "Custom Model"
+            )
+            model_version = (
+                model_data.get("model_version") or model_data.get("source") or "local"
+            )
+            base_model = model_data.get(
+                "base_model",
+                self.config_manager.get("models.default_base_model", "yolov8s-seg.pt"),
+            )
+
+            return self.db_manager.add_model(
+                model_name=model_name,
+                model_version=model_version,
+                model_path=normalized_target,
+                base_model=base_model,
+            )
+        except Exception as e:
+            logger.error(f"Failed to ensure model record for {model_path}: {e}")
+            return None
+
     def refresh(self):
         """Refresh the tab."""
         self._load_models()

src/gui/tabs/results_tab.py

@@ -1,15 +1,39 @@
 """
-Results tab for the microscopy object detection application.
+Results tab for browsing stored detections and visualizing overlays.
 """
 
-from PySide6.QtWidgets import QWidget, QVBoxLayout, QLabel, QGroupBox
+from pathlib import Path
+from typing import Dict, List, Optional
+
+from PySide6.QtWidgets import (
+    QWidget,
+    QVBoxLayout,
+    QHBoxLayout,
+    QLabel,
+    QGroupBox,
+    QPushButton,
+    QSplitter,
+    QTableWidget,
+    QTableWidgetItem,
+    QHeaderView,
+    QAbstractItemView,
+    QMessageBox,
+    QCheckBox,
+)
+from PySide6.QtCore import Qt
 
 from src.database.db_manager import DatabaseManager
 from src.utils.config_manager import ConfigManager
+from src.utils.logger import get_logger
+from src.utils.image import Image, ImageLoadError
+from src.gui.widgets import AnnotationCanvasWidget
+
+
+logger = get_logger(__name__)
 
 
 class ResultsTab(QWidget):
-    """Results tab placeholder."""
+    """Results tab showing detection history and preview overlays."""
 
     def __init__(
         self, db_manager: DatabaseManager, config_manager: ConfigManager, parent=None
@@ -18,29 +42,398 @@ class ResultsTab(QWidget):
         self.db_manager = db_manager
         self.config_manager = config_manager
 
+        self.detection_summary: List[Dict] = []
+        self.current_selection: Optional[Dict] = None
+        self.current_image: Optional[Image] = None
+        self.current_detections: List[Dict] = []
+        self._image_path_cache: Dict[str, str] = {}
+
         self._setup_ui()
+        self.refresh()
 
     def _setup_ui(self):
         """Setup user interface."""
         layout = QVBoxLayout()
 
-        group = QGroupBox("Results")
+        # Splitter for list + preview
-        group_layout = QVBoxLayout()
+        splitter = QSplitter(Qt.Horizontal)
-        label = QLabel(
-            "Results viewer will be implemented here.\n\n"
-            "Features:\n"
-            "- Detection history browser\n"
-            "- Advanced filtering\n"
-            "- Statistics dashboard\n"
-            "- Export functionality"
-        )
-        group_layout.addWidget(label)
-        group.setLayout(group_layout)
 
-        layout.addWidget(group)
+        # Left pane: detection list
-        layout.addStretch()
+        left_container = QWidget()
+        left_layout = QVBoxLayout()
+        left_layout.setContentsMargins(0, 0, 0, 0)
+
+        controls_layout = QHBoxLayout()
+        self.refresh_btn = QPushButton("Refresh")
+        self.refresh_btn.clicked.connect(self.refresh)
+        controls_layout.addWidget(self.refresh_btn)
+        controls_layout.addStretch()
+        left_layout.addLayout(controls_layout)
+
+        self.results_table = QTableWidget(0, 5)
+        self.results_table.setHorizontalHeaderLabels(
+            ["Image", "Model", "Detections", "Classes", "Last Updated"]
+        )
+        self.results_table.horizontalHeader().setSectionResizeMode(
+            0, QHeaderView.Stretch
+        )
+        self.results_table.horizontalHeader().setSectionResizeMode(
+            1, QHeaderView.Stretch
+        )
+        self.results_table.horizontalHeader().setSectionResizeMode(
+            2, QHeaderView.ResizeToContents
+        )
+        self.results_table.horizontalHeader().setSectionResizeMode(
+            3, QHeaderView.Stretch
+        )
+        self.results_table.horizontalHeader().setSectionResizeMode(
+            4, QHeaderView.ResizeToContents
+        )
+        self.results_table.setSelectionBehavior(QAbstractItemView.SelectRows)
+        self.results_table.setSelectionMode(QAbstractItemView.SingleSelection)
+        self.results_table.setEditTriggers(QAbstractItemView.NoEditTriggers)
+        self.results_table.itemSelectionChanged.connect(self._on_result_selected)
+
+        left_layout.addWidget(self.results_table)
+        left_container.setLayout(left_layout)
+
+        # Right pane: preview canvas and controls
+        right_container = QWidget()
+        right_layout = QVBoxLayout()
+        right_layout.setContentsMargins(0, 0, 0, 0)
+
+        preview_group = QGroupBox("Detection Preview")
+        preview_layout = QVBoxLayout()
+
+        self.preview_canvas = AnnotationCanvasWidget()
+        self.preview_canvas.set_polyline_enabled(False)
+        self.preview_canvas.set_show_bboxes(True)
+        preview_layout.addWidget(self.preview_canvas)
+
+        toggles_layout = QHBoxLayout()
+        self.show_masks_checkbox = QCheckBox("Show Masks")
+        self.show_masks_checkbox.setChecked(False)
+        self.show_masks_checkbox.stateChanged.connect(self._apply_detection_overlays)
+        self.show_bboxes_checkbox = QCheckBox("Show Bounding Boxes")
+        self.show_bboxes_checkbox.setChecked(True)
+        self.show_bboxes_checkbox.stateChanged.connect(self._toggle_bboxes)
+        self.show_confidence_checkbox = QCheckBox("Show Confidence")
+        self.show_confidence_checkbox.setChecked(False)
+        self.show_confidence_checkbox.stateChanged.connect(
+            self._apply_detection_overlays
+        )
+        toggles_layout.addWidget(self.show_masks_checkbox)
+        toggles_layout.addWidget(self.show_bboxes_checkbox)
+        toggles_layout.addWidget(self.show_confidence_checkbox)
+        toggles_layout.addStretch()
+        preview_layout.addLayout(toggles_layout)
+
+        self.summary_label = QLabel("Select a detection result to preview.")
+        self.summary_label.setWordWrap(True)
+        preview_layout.addWidget(self.summary_label)
+
+        preview_group.setLayout(preview_layout)
+        right_layout.addWidget(preview_group)
+        right_container.setLayout(right_layout)
+
+        splitter.addWidget(left_container)
+        splitter.addWidget(right_container)
+        splitter.setStretchFactor(0, 1)
+        splitter.setStretchFactor(1, 2)
+
+        layout.addWidget(splitter)
         self.setLayout(layout)
 
     def refresh(self):
-        """Refresh the tab."""
+        """Refresh the detection list and preview."""
-        pass
+        self._load_detection_summary()
+        self._populate_results_table()
+        self.current_selection = None
+        self.current_image = None
+        self.current_detections = []
+        self.preview_canvas.clear()
+        self.summary_label.setText("Select a detection result to preview.")
+
+    def _load_detection_summary(self):
+        """Load latest detection summaries grouped by image + model."""
+        try:
+            detections = self.db_manager.get_detections(limit=500)
+            summary_map: Dict[tuple, Dict] = {}
+
+            for det in detections:
+                key = (det["image_id"], det["model_id"])
+                metadata = det.get("metadata") or {}
+                entry = summary_map.setdefault(
+                    key,
+                    {
+                        "image_id": det["image_id"],
+                        "model_id": det["model_id"],
+                        "image_path": det.get("image_path"),
+                        "image_filename": det.get("image_filename")
+                        or det.get("image_path"),
+                        "model_name": det.get("model_name", ""),
+                        "model_version": det.get("model_version", ""),
+                        "last_detected": det.get("detected_at"),
+                        "count": 0,
+                        "classes": set(),
+                        "source_path": metadata.get("source_path"),
+                        "repository_root": metadata.get("repository_root"),
+                    },
+                )
+
+                entry["count"] += 1
+                if det.get("detected_at") and (
+                    not entry.get("last_detected")
+                    or str(det.get("detected_at")) > str(entry.get("last_detected"))
+                ):
+                    entry["last_detected"] = det.get("detected_at")
+                if det.get("class_name"):
+                    entry["classes"].add(det["class_name"])
+                if metadata.get("source_path") and not entry.get("source_path"):
+                    entry["source_path"] = metadata.get("source_path")
+                if metadata.get("repository_root") and not entry.get("repository_root"):
+                    entry["repository_root"] = metadata.get("repository_root")
+
+            self.detection_summary = sorted(
+                summary_map.values(),
+                key=lambda x: str(x.get("last_detected") or ""),
+                reverse=True,
+            )
+        except Exception as e:
+            logger.error(f"Failed to load detection summary: {e}")
+            QMessageBox.critical(
+                self,
+                "Error",
+                f"Failed to load detection results:\n{str(e)}",
+            )
+            self.detection_summary = []
+
+    def _populate_results_table(self):
+        """Populate the table widget with detection summaries."""
+        self.results_table.setRowCount(len(self.detection_summary))
+
+        for row, entry in enumerate(self.detection_summary):
+            model_label = f"{entry['model_name']} {entry['model_version']}".strip()
+            class_list = (
+                ", ".join(sorted(entry["classes"])) if entry["classes"] else "-"
+            )
+
+            items = [
+                QTableWidgetItem(entry.get("image_filename", "")),
+                QTableWidgetItem(model_label),
+                QTableWidgetItem(str(entry.get("count", 0))),
+                QTableWidgetItem(class_list),
+                QTableWidgetItem(str(entry.get("last_detected") or "")),
+            ]
+
+            for col, item in enumerate(items):
+                item.setData(Qt.UserRole, row)
+                self.results_table.setItem(row, col, item)
+
+        self.results_table.clearSelection()
+
+    def _on_result_selected(self):
+        """Handle selection changes in the detection table."""
+        selected_items = self.results_table.selectedItems()
+        if not selected_items:
+            return
+
+        row = selected_items[0].data(Qt.UserRole)
+        if row is None or row >= len(self.detection_summary):
+            return
+
+        entry = self.detection_summary[row]
+        if (
+            self.current_selection
+            and self.current_selection.get("image_id") == entry["image_id"]
+            and self.current_selection.get("model_id") == entry["model_id"]
+        ):
+            return
+
+        self.current_selection = entry
+
+        image_path = self._resolve_image_path(entry)
+        if not image_path:
+            QMessageBox.warning(
+                self,
+                "Image Not Found",
+                "Unable to locate the image file for this detection.",
+            )
+            return
+
+        try:
+            self.current_image = Image(image_path)
+            self.preview_canvas.load_image(self.current_image)
+        except ImageLoadError as e:
+            logger.error(f"Failed to load image '{image_path}': {e}")
+            QMessageBox.critical(
+                self,
+                "Image Error",
+                f"Failed to load image for preview:\n{str(e)}",
+            )
+            return
+
+        self._load_detections_for_selection(entry)
+        self._apply_detection_overlays()
+        self._update_summary_label(entry)
+
+    def _load_detections_for_selection(self, entry: Dict):
+        """Load detection records for the selected image/model pair."""
+        self.current_detections = []
+        if not entry:
+            return
+
+        try:
+            filters = {"image_id": entry["image_id"], "model_id": entry["model_id"]}
+            self.current_detections = self.db_manager.get_detections(filters)
+        except Exception as e:
+            logger.error(f"Failed to load detections for preview: {e}")
+            QMessageBox.critical(
+                self,
+                "Error",
+                f"Failed to load detections for this image:\n{str(e)}",
+            )
+            self.current_detections = []
+
+    def _apply_detection_overlays(self):
+        """Draw detections onto the preview canvas based on current toggles."""
+        self.preview_canvas.clear_annotations()
+        self.preview_canvas.set_show_bboxes(self.show_bboxes_checkbox.isChecked())
+
+        if not self.current_detections or not self.current_image:
+            return
+
+        for det in self.current_detections:
+            color = self._get_class_color(det.get("class_name"))
+
+            if self.show_masks_checkbox.isChecked() and det.get("segmentation_mask"):
+                mask_points = self._convert_mask(det["segmentation_mask"])
+                if mask_points:
+                    self.preview_canvas.draw_saved_polyline(mask_points, color)
+
+            bbox = [
+                det.get("x_min"),
+                det.get("y_min"),
+                det.get("x_max"),
+                det.get("y_max"),
+            ]
+            if all(v is not None for v in bbox):
+                label = None
+                if self.show_confidence_checkbox.isChecked():
+                    confidence = det.get("confidence")
+                    if confidence is not None:
+                        label = f"{confidence:.2f}"
+                self.preview_canvas.draw_saved_bbox(bbox, color, label=label)
+
+    def _convert_mask(self, mask_points: List[List[float]]) -> List[List[float]]:
+        """Convert stored [x, y] masks to [y, x] format for the canvas."""
+        converted = []
+        for point in mask_points:
+            if len(point) >= 2:
+                x, y = point[0], point[1]
+                converted.append([y, x])
+        return converted
+
+    def _toggle_bboxes(self):
+        """Update bounding box visibility on the canvas."""
+        self.preview_canvas.set_show_bboxes(self.show_bboxes_checkbox.isChecked())
+        # Re-render to respect show/hide when toggled
+        self._apply_detection_overlays()
+
+    def _update_summary_label(self, entry: Dict):
+        """Display textual summary for the selected detection run."""
+        classes = ", ".join(sorted(entry.get("classes", []))) or "-"
+        summary_text = (
+            f"Image: {entry.get('image_filename', 'unknown')}\n"
+            f"Model: {entry.get('model_name', '')} {entry.get('model_version', '')}\n"
+            f"Detections: {entry.get('count', 0)}\n"
+            f"Classes: {classes}\n"
+            f"Last Updated: {entry.get('last_detected', 'n/a')}"
+        )
+        self.summary_label.setText(summary_text)
+
+    def _resolve_image_path(self, entry: Dict) -> Optional[str]:
+        """Resolve an image path using metadata, cache, and repository hints."""
+        relative_path = entry.get("image_path") if entry else None
+        cache_key = relative_path or entry.get("source_path")
+        if cache_key and cache_key in self._image_path_cache:
+            cached = Path(self._image_path_cache[cache_key])
+            if cached.exists():
+                return self._image_path_cache[cache_key]
+            del self._image_path_cache[cache_key]
+
+        candidates = []
+        source_path = entry.get("source_path") if entry else None
+        if source_path:
+            candidates.append(Path(source_path))
+
+        repo_roots = []
+        if entry.get("repository_root"):
+            repo_roots.append(entry["repository_root"])
+        config_repo = self.config_manager.get_image_repository_path()
+        if config_repo:
+            repo_roots.append(config_repo)
+
+        for root in repo_roots:
+            if relative_path:
+                candidates.append(Path(root) / relative_path)
+
+        if relative_path:
+            candidates.append(Path(relative_path))
+
+        for candidate in candidates:
+            try:
+                if candidate and candidate.exists():
+                    resolved = str(candidate.resolve())
+                    if cache_key:
+                        self._image_path_cache[cache_key] = resolved
+                    return resolved
+            except Exception:
+                continue
+
+        # Fallback: search by filename in known roots
+        filename = Path(relative_path).name if relative_path else None
+        if filename:
+            search_roots = [Path(root) for root in repo_roots if root]
+            if not search_roots:
+                search_roots = [Path("data")]
+            match = self._search_in_roots(filename, search_roots)
+            if match:
+                resolved = str(match.resolve())
+                if cache_key:
+                    self._image_path_cache[cache_key] = resolved
+                return resolved
+
+        return None
+
+    def _search_in_roots(self, filename: str, roots: List[Path]) -> Optional[Path]:
+        """Search for a file name within a list of root directories."""
+        for root in roots:
+            try:
+                if not root.exists():
+                    continue
+                for candidate in root.rglob(filename):
+                    return candidate
+            except Exception as e:
+                logger.debug(f"Error searching for {filename} in {root}: {e}")
+        return None
+
+    def _get_class_color(self, class_name: Optional[str]) -> str:
+        """Return consistent color hex for a class name."""
+        if not class_name:
+            return "#FF6B6B"
+
+        color_map = self.config_manager.get_bbox_colors()
+        if class_name in color_map:
+            return color_map[class_name]
+
+        # Deterministic fallback color based on hash
+        palette = [
+            "#FF6B6B",
+            "#4ECDC4",
+            "#FFD166",
+            "#1D3557",
+            "#F4A261",
+            "#E76F51",
+        ]
+        return palette[hash(class_name) % len(palette)]

src/gui/widgets/__init__.py

@@ -1,5 +1,7 @@
 """GUI widgets for the microscopy object detection application."""
 
 from src.gui.widgets.image_display_widget import ImageDisplayWidget
+from src.gui.widgets.annotation_canvas_widget import AnnotationCanvasWidget
+from src.gui.widgets.annotation_tools_widget import AnnotationToolsWidget
 
-__all__ = ["ImageDisplayWidget"]
+__all__ = ["ImageDisplayWidget", "AnnotationCanvasWidget", "AnnotationToolsWidget"]

src/gui/widgets/annotation_canvas_widget.py

@@ -0,0 +1,931 @@
+"""
+Annotation canvas widget for drawing annotations on images.
+Currently supports polyline drawing tool with color selection for manual annotation.
+"""
+
+import numpy as np
+import math
+
+from PySide6.QtWidgets import QWidget, QVBoxLayout, QLabel, QScrollArea
+from PySide6.QtGui import (
+    QPixmap,
+    QImage,
+    QPainter,
+    QPen,
+    QColor,
+    QKeyEvent,
+    QMouseEvent,
+    QPaintEvent,
+    QPolygonF,
+)
+from PySide6.QtCore import Qt, QEvent, Signal, QPoint, QPointF, QRect
+from typing import Any, Dict, List, Optional, Tuple
+
+from src.utils.image import Image, ImageLoadError
+from src.utils.logger import get_logger
+
+logger = get_logger(__name__)
+
+
+def perpendicular_distance(
+    point: Tuple[float, float],
+    start: Tuple[float, float],
+    end: Tuple[float, float],
+) -> float:
+    """Perpendicular distance from `point` to the line defined by `start`->`end`."""
+    (x, y), (x1, y1), (x2, y2) = point, start, end
+    dx = x2 - x1
+    dy = y2 - y1
+    if dx == 0.0 and dy == 0.0:
+        return math.hypot(x - x1, y - y1)
+    num = abs(dy * x - dx * y + x2 * y1 - y2 * x1)
+    den = math.hypot(dx, dy)
+    return num / den
+
+
+def rdp(points: List[Tuple[float, float]], epsilon: float) -> List[Tuple[float, float]]:
+    """
+    Recursive Ramer-Douglas-Peucker (RDP) polyline simplification.
+
+    Args:
+        points: List of (x, y) points.
+        epsilon: Maximum allowed perpendicular distance in pixels.
+
+    Returns:
+        Simplified list of (x, y) points including first and last.
+    """
+    if len(points) <= 2:
+        return list(points)
+
+    start = points[0]
+    end = points[-1]
+    max_dist = -1.0
+    index = -1
+
+    for i in range(1, len(points) - 1):
+        d = perpendicular_distance(points[i], start, end)
+        if d > max_dist:
+            max_dist = d
+            index = i
+
+    if max_dist > epsilon:
+        # Recursive split
+        left = rdp(points[: index + 1], epsilon)
+        right = rdp(points[index:], epsilon)
+        # Concatenate but avoid duplicate at split point
+        return left[:-1] + right
+
+    # Keep only start and end
+    return [start, end]
+
+
+def simplify_polyline(
+    points: List[Tuple[float, float]], epsilon: float
+) -> List[Tuple[float, float]]:
+    """
+    Simplify a polyline with RDP while preserving closure semantics.
+
+    If the polyline is closed (first == last), the duplicate last point is removed
+    before simplification and then re-added after simplification.
+    """
+    if not points:
+        return []
+
+    pts = [(float(x), float(y)) for x, y in points]
+    closed = False
+
+    if len(pts) >= 2 and pts[0] == pts[-1]:
+        closed = True
+        pts = pts[:-1]  # remove duplicate last for simplification
+
+    if len(pts) <= 2:
+        simplified = list(pts)
+    else:
+        simplified = rdp(pts, epsilon)
+
+    if closed and simplified:
+        if simplified[0] != simplified[-1]:
+            simplified.append(simplified[0])
+
+    return simplified
+
+
+class AnnotationCanvasWidget(QWidget):
+    """
+    Widget for displaying images and drawing annotations with zoom and drawing tools.
+
+    Features:
+    - Display images with zoom functionality
+    - Polyline tool for drawing annotations
+    - Configurable pen color and width
+    - Mouse-based drawing interface
+    - Zoom in/out with mouse wheel and keyboard
+
+    Signals:
+        zoom_changed: Emitted when zoom level changes (float zoom_scale)
+        annotation_drawn: Emitted when a new stroke is completed (list of points)
+    """
+
+    zoom_changed = Signal(float)
+    annotation_drawn = Signal(list)  # List of (x, y) points in normalized coordinates
+    # Emitted when the user selects an existing polyline on the canvas.
+    # Carries the associated annotation_id (int) or None if selection is cleared
+    annotation_selected = Signal(object)
+
+    def __init__(self, parent=None):
+        """Initialize the annotation canvas widget."""
+        super().__init__(parent)
+
+        self.current_image = None
+        self.original_pixmap = None
+        self.annotation_pixmap = None  # Overlay for annotations
+        self.zoom_scale = 1.0
+        self.zoom_min = 0.1
+        self.zoom_max = 10.0
+        self.zoom_step = 0.1
+        self.zoom_wheel_step = 0.15
+
+        # Drawing / interaction state
+        self.is_drawing = False
+        self.polyline_enabled = False
+        self.polyline_pen_color = QColor(255, 0, 0, 128)  # Default red with 50% alpha
+        self.polyline_pen_width = 3
+        self.show_bboxes: bool = True  # Control visibility of bounding boxes
+
+        # Current stroke and stored polylines (in image coordinates, pixel units)
+        self.current_stroke: List[Tuple[float, float]] = []
+        self.polylines: List[List[Tuple[float, float]]] = []
+        self.stroke_meta: List[Dict[str, Any]] = []  # per-polyline style (color, width)
+        # Optional DB annotation_id for each stored polyline (None for temporary / unsaved)
+        self.polyline_annotation_ids: List[Optional[int]] = []
+        # Indices in self.polylines of the currently selected polylines (multi-select)
+        self.selected_polyline_indices: List[int] = []
+
+        # Stored bounding boxes in normalized coordinates (x_min, y_min, x_max, y_max)
+        self.bboxes: List[List[float]] = []
+        self.bbox_meta: List[Dict[str, Any]] = []  # per-bbox style (color, width)
+
+        # Legacy collection of strokes in normalized coordinates (kept for API compatibility)
+        self.all_strokes: List[dict] = []
+
+        # RDP simplification parameters (in pixels)
+        self.simplify_on_finish: bool = True
+        self.simplify_epsilon: float = 2.0
+        self.sample_threshold: float = 2.0  # minimum movement to sample a new point
+
+        self._setup_ui()
+
+    def _setup_ui(self):
+        """Setup user interface."""
+        layout = QVBoxLayout()
+        layout.setContentsMargins(0, 0, 0, 0)
+
+        # Scroll area for canvas
+        self.scroll_area = QScrollArea()
+        self.scroll_area.setWidgetResizable(True)
+        self.scroll_area.setMinimumHeight(400)
+
+        self.canvas_label = QLabel("No image loaded")
+        self.canvas_label.setAlignment(Qt.AlignCenter)
+        self.canvas_label.setStyleSheet(
+            "QLabel { background-color: #2b2b2b; color: #888; }"
+        )
+        self.canvas_label.setScaledContents(False)
+        self.canvas_label.setMouseTracking(True)
+
+        self.scroll_area.setWidget(self.canvas_label)
+        self.scroll_area.viewport().installEventFilter(self)
+
+        layout.addWidget(self.scroll_area)
+        self.setLayout(layout)
+
+        self.setFocusPolicy(Qt.StrongFocus)
+
+    def load_image(self, image: Image):
+        """
+        Load and display an image.
+
+        Args:
+            image: Image object to display
+        """
+        self.current_image = image
+        self.zoom_scale = 1.0
+        self.clear_annotations()
+        self._display_image()
+        logger.debug(
+            f"Loaded image into annotation canvas: {image.width}x{image.height}"
+        )
+
+    def clear(self):
+        """Clear the displayed image and all annotations."""
+        self.current_image = None
+        self.original_pixmap = None
+        self.annotation_pixmap = None
+        self.zoom_scale = 1.0
+        self.clear_annotations()
+        self.canvas_label.setText("No image loaded")
+        self.canvas_label.setPixmap(QPixmap())
+
+    def clear_annotations(self):
+        """Clear all drawn annotations."""
+        self.all_strokes = []
+        self.current_stroke = []
+        self.polylines = []
+        self.stroke_meta = []
+        self.polyline_annotation_ids = []
+        self.selected_polyline_indices = []
+        self.bboxes = []
+        self.bbox_meta = []
+        self.is_drawing = False
+        if self.annotation_pixmap:
+            self.annotation_pixmap.fill(Qt.transparent)
+            self._update_display()
+
+    def _display_image(self):
+        """Display the current image in the canvas."""
+        if self.current_image is None:
+            return
+
+        try:
+            # Get image data in a format compatible with Qt
+            if self.current_image.channels in (3, 4):
+                image_data = self.current_image.get_rgb()
+                height, width = image_data.shape[:2]
+            else:
+                image_data = self.current_image.get_grayscale()
+                height, width = image_data.shape
+
+            image_data = np.ascontiguousarray(image_data)
+            bytes_per_line = image_data.strides[0]
+
+            qimage = QImage(
+                image_data.data,
+                width,
+                height,
+                bytes_per_line,
+                self.current_image.qtimage_format,
+            ).copy()  # Copy so Qt owns the buffer even after numpy array goes out of scope
+
+            self.original_pixmap = QPixmap.fromImage(qimage)
+
+            # Create transparent overlay for annotations
+            self.annotation_pixmap = QPixmap(self.original_pixmap.size())
+            self.annotation_pixmap.fill(Qt.transparent)
+
+            self._apply_zoom()
+
+        except Exception as e:
+            logger.error(f"Error displaying image: {e}")
+            raise ImageLoadError(f"Failed to display image: {str(e)}")
+
+    def _apply_zoom(self):
+        """Apply current zoom level to the displayed image."""
+        if self.original_pixmap is None:
+            return
+
+        scaled_width = int(self.original_pixmap.width() * self.zoom_scale)
+        scaled_height = int(self.original_pixmap.height() * self.zoom_scale)
+
+        # Scale both image and annotations
+        scaled_image = self.original_pixmap.scaled(
+            scaled_width,
+            scaled_height,
+            Qt.KeepAspectRatio,
+            (
+                Qt.SmoothTransformation
+                if self.zoom_scale >= 1.0
+                else Qt.FastTransformation
+            ),
+        )
+
+        scaled_annotations = self.annotation_pixmap.scaled(
+            scaled_width,
+            scaled_height,
+            Qt.KeepAspectRatio,
+            (
+                Qt.SmoothTransformation
+                if self.zoom_scale >= 1.0
+                else Qt.FastTransformation
+            ),
+        )
+
+        # Composite image and annotations
+        combined = QPixmap(scaled_image.size())
+        painter = QPainter(combined)
+        painter.drawPixmap(0, 0, scaled_image)
+        painter.drawPixmap(0, 0, scaled_annotations)
+        painter.end()
+
+        self.canvas_label.setPixmap(combined)
+        self.canvas_label.setScaledContents(False)
+        self.canvas_label.adjustSize()
+
+        self.zoom_changed.emit(self.zoom_scale)
+
+    def _update_display(self):
+        """Update display after drawing."""
+        self._apply_zoom()
+
+    def set_polyline_enabled(self, enabled: bool):
+        """Enable or disable polyline tool."""
+        self.polyline_enabled = enabled
+        if enabled:
+            self.canvas_label.setCursor(Qt.CrossCursor)
+        else:
+            self.canvas_label.setCursor(Qt.ArrowCursor)
+
+    def set_polyline_pen_color(self, color: QColor):
+        """Set polyline pen color."""
+        self.polyline_pen_color = color
+
+    def set_polyline_pen_width(self, width: int):
+        """Set polyline pen width."""
+        self.polyline_pen_width = max(1, width)
+
+    def get_zoom_percentage(self) -> int:
+        """Get current zoom level as percentage."""
+        return int(self.zoom_scale * 100)
+
+    def zoom_in(self):
+        """Zoom in on the image."""
+        if self.original_pixmap is None:
+            return
+        new_scale = self.zoom_scale + self.zoom_step
+        if new_scale <= self.zoom_max:
+            self.zoom_scale = new_scale
+            self._apply_zoom()
+
+    def zoom_out(self):
+        """Zoom out from the image."""
+        if self.original_pixmap is None:
+            return
+        new_scale = self.zoom_scale - self.zoom_step
+        if new_scale >= self.zoom_min:
+            self.zoom_scale = new_scale
+            self._apply_zoom()
+
+    def reset_zoom(self):
+        """Reset zoom to 100%."""
+        if self.original_pixmap is None:
+            return
+        self.zoom_scale = 1.0
+        self._apply_zoom()
+
+    def _canvas_to_image_coords(self, pos: QPoint) -> Optional[Tuple[int, int]]:
+        """Convert canvas coordinates to image coordinates, accounting for zoom and centering."""
+        if self.original_pixmap is None or self.canvas_label.pixmap() is None:
+            return None
+
+        # Get the displayed pixmap size (after zoom)
+        displayed_pixmap = self.canvas_label.pixmap()
+        displayed_width = displayed_pixmap.width()
+        displayed_height = displayed_pixmap.height()
+
+        # Calculate offset due to label centering (label might be larger than pixmap)
+        label_width = self.canvas_label.width()
+        label_height = self.canvas_label.height()
+        offset_x = max(0, (label_width - displayed_width) // 2)
+        offset_y = max(0, (label_height - displayed_height) // 2)
+
+        # Adjust position for offset and convert to image coordinates
+        x = (pos.x() - offset_x) / self.zoom_scale
+        y = (pos.y() - offset_y) / self.zoom_scale
+
+        # Check bounds
+        if (
+            0 <= x < self.original_pixmap.width()
+            and 0 <= y < self.original_pixmap.height()
+        ):
+            return (int(x), int(y))
+        return None
+
+    def _find_polyline_at(
+        self, img_x: float, img_y: float, threshold_px: float = 5.0
+    ) -> Optional[int]:
+        """
+        Find index of polyline whose geometry is within threshold_px of (img_x, img_y).
+        Returns the index in self.polylines, or None if none is close enough.
+        """
+        best_index: Optional[int] = None
+        best_dist: float = float("inf")
+
+        for idx, polyline in enumerate(self.polylines):
+            if len(polyline) < 2:
+                continue
+
+            # Quick bounding-box check to skip obviously distant polylines
+            xs = [p[0] for p in polyline]
+            ys = [p[1] for p in polyline]
+            if img_x < min(xs) - threshold_px or img_x > max(xs) + threshold_px:
+                continue
+            if img_y < min(ys) - threshold_px or img_y > max(ys) + threshold_px:
+                continue
+
+            # Precise distance to all segments
+            for (x1, y1), (x2, y2) in zip(polyline[:-1], polyline[1:]):
+                d = perpendicular_distance(
+                    (img_x, img_y), (float(x1), float(y1)), (float(x2), float(y2))
+                )
+                if d < best_dist:
+                    best_dist = d
+                    best_index = idx
+
+        if best_index is not None and best_dist <= threshold_px:
+            return best_index
+        return None
+
+    def _image_to_normalized_coords(self, x: int, y: int) -> Tuple[float, float]:
+        """Convert image coordinates to normalized coordinates (0-1)."""
+        if self.original_pixmap is None:
+            return (0.0, 0.0)
+
+        norm_x = x / self.original_pixmap.width()
+        norm_y = y / self.original_pixmap.height()
+        return (norm_x, norm_y)
+
+    def _add_polyline(
+        self,
+        img_points: List[Tuple[float, float]],
+        color: QColor,
+        width: int,
+        annotation_id: Optional[int] = None,
+    ):
+        """Store a polyline in image coordinates and redraw annotations."""
+        if not img_points or len(img_points) < 2:
+            return
+
+        # Ensure all points are tuples of floats
+        normalized_points = [(float(x), float(y)) for x, y in img_points]
+        self.polylines.append(normalized_points)
+        self.stroke_meta.append({"color": QColor(color), "width": int(width)})
+        self.polyline_annotation_ids.append(annotation_id)
+
+        self._redraw_annotations()
+
+    def _redraw_annotations(self):
+        """Redraw all stored polylines and (optionally) bounding boxes onto the annotation pixmap."""
+        if self.annotation_pixmap is None:
+            return
+
+        # Clear existing overlay
+        self.annotation_pixmap.fill(Qt.transparent)
+
+        painter = QPainter(self.annotation_pixmap)
+
+        # Draw polylines
+        for idx, (polyline, meta) in enumerate(zip(self.polylines, self.stroke_meta)):
+            pen_color: QColor = meta.get("color", self.polyline_pen_color)
+            width: int = meta.get("width", self.polyline_pen_width)
+
+            if idx in self.selected_polyline_indices:
+                # Highlight selected polylines in a distinct color / width
+                highlight_color = QColor(255, 255, 0, 200)  # yellow, semi-opaque
+                pen = QPen(
+                    highlight_color,
+                    width + 1,
+                    Qt.SolidLine,
+                    Qt.RoundCap,
+                    Qt.RoundJoin,
+                )
+            else:
+                pen = QPen(
+                    pen_color,
+                    width,
+                    Qt.SolidLine,
+                    Qt.RoundCap,
+                    Qt.RoundJoin,
+                )
+
+            painter.setPen(pen)
+            # Use QPolygonF for efficient polygon rendering (single call vs N-1 calls)
+            # drawPolygon() automatically closes the shape, ensuring proper visual closure
+            polygon = QPolygonF([QPointF(x, y) for x, y in polyline])
+            painter.drawPolygon(polygon)
+
+        # Draw bounding boxes (dashed) if enabled
+        if self.show_bboxes and self.original_pixmap is not None and self.bboxes:
+            img_width = float(self.original_pixmap.width())
+            img_height = float(self.original_pixmap.height())
+
+            for bbox, meta in zip(self.bboxes, self.bbox_meta):
+                if len(bbox) != 4:
+                    continue
+
+                x_min_norm, y_min_norm, x_max_norm, y_max_norm = bbox
+                x_min = int(x_min_norm * img_width)
+                y_min = int(y_min_norm * img_height)
+                x_max = int(x_max_norm * img_width)
+                y_max = int(y_max_norm * img_height)
+
+                rect_width = x_max - x_min
+                rect_height = y_max - y_min
+
+                pen_color: QColor = meta.get("color", QColor(255, 0, 0, 128))
+                width: int = meta.get("width", self.polyline_pen_width)
+                pen = QPen(
+                    pen_color,
+                    width,
+                    Qt.DashLine,
+                    Qt.SquareCap,
+                    Qt.MiterJoin,
+                )
+                painter.setPen(pen)
+                painter.drawRect(x_min, y_min, rect_width, rect_height)
+
+                label_text = meta.get("label")
+                if label_text:
+                    painter.save()
+                    font = painter.font()
+                    font.setPointSizeF(max(10.0, width + 4))
+                    painter.setFont(font)
+                    metrics = painter.fontMetrics()
+                    text_width = metrics.horizontalAdvance(label_text)
+                    text_height = metrics.height()
+                    padding = 4
+                    bg_width = text_width + padding * 2
+                    bg_height = text_height + padding * 2
+                    canvas_width = self.original_pixmap.width()
+                    canvas_height = self.original_pixmap.height()
+                    bg_x = max(0, min(x_min, canvas_width - bg_width))
+                    bg_y = y_min - bg_height
+                    if bg_y < 0:
+                        bg_y = min(y_min, canvas_height - bg_height)
+                        bg_y = max(0, bg_y)
+                    background_rect = QRect(bg_x, bg_y, bg_width, bg_height)
+                    background_color = QColor(pen_color)
+                    background_color.setAlpha(220)
+                    painter.fillRect(background_rect, background_color)
+                    text_color = QColor(0, 0, 0)
+                    if background_color.lightness() < 128:
+                        text_color = QColor(255, 255, 255)
+                    painter.setPen(text_color)
+                    painter.drawText(
+                        background_rect.adjusted(padding, padding, -padding, -padding),
+                        Qt.AlignLeft | Qt.AlignVCenter,
+                        label_text,
+                    )
+                    painter.restore()
+
+        painter.end()
+
+        self._update_display()
+
+    def mousePressEvent(self, event: QMouseEvent):
+        """Handle mouse press events for drawing and selecting polylines."""
+        if self.annotation_pixmap is None:
+            super().mousePressEvent(event)
+            return
+
+        # Map click to image coordinates
+        label_pos = self.canvas_label.mapFromGlobal(event.globalPos())
+        img_coords = self._canvas_to_image_coords(label_pos)
+
+        # Left button + drawing tool enabled -> start a new stroke
+        if event.button() == Qt.LeftButton and self.polyline_enabled:
+            if img_coords:
+                self.is_drawing = True
+                self.current_stroke = [(float(img_coords[0]), float(img_coords[1]))]
+            return
+
+        # Left button + drawing tool disabled -> attempt selection of existing polyline
+        if event.button() == Qt.LeftButton and not self.polyline_enabled:
+            if img_coords:
+                idx = self._find_polyline_at(float(img_coords[0]), float(img_coords[1]))
+                if idx is not None:
+                    if event.modifiers() & Qt.ShiftModifier:
+                        # Multi-select mode: add to current selection (if not already selected)
+                        if idx not in self.selected_polyline_indices:
+                            self.selected_polyline_indices.append(idx)
+                    else:
+                        # Single-select mode: replace current selection
+                        self.selected_polyline_indices = [idx]
+
+                    # Build list of selected annotation IDs (ignore None entries)
+                    selected_ids: List[int] = []
+                    for sel_idx in self.selected_polyline_indices:
+                        if 0 <= sel_idx < len(self.polyline_annotation_ids):
+                            ann_id = self.polyline_annotation_ids[sel_idx]
+                            if isinstance(ann_id, int):
+                                selected_ids.append(ann_id)
+
+                    if selected_ids:
+                        self.annotation_selected.emit(selected_ids)
+                    else:
+                        # No valid DB-backed annotations in selection
+                        self.annotation_selected.emit(None)
+                else:
+                    # Clicked on empty space -> clear selection
+                    self.selected_polyline_indices = []
+                    self.annotation_selected.emit(None)
+
+                self._redraw_annotations()
+            return
+
+        # Fallback for other buttons / cases
+        super().mousePressEvent(event)
+
+    def mouseMoveEvent(self, event: QMouseEvent):
+        """Handle mouse move events for drawing."""
+        if (
+            not self.is_drawing
+            or not self.polyline_enabled
+            or self.annotation_pixmap is None
+        ):
+            super().mouseMoveEvent(event)
+            return
+
+        # Get accurate position using global coordinates
+        label_pos = self.canvas_label.mapFromGlobal(event.globalPos())
+        img_coords = self._canvas_to_image_coords(label_pos)
+
+        if img_coords and len(self.current_stroke) > 0:
+            last_point = self.current_stroke[-1]
+            dx = img_coords[0] - last_point[0]
+            dy = img_coords[1] - last_point[1]
+
+            # Only sample a new point if we moved enough pixels
+            if math.hypot(dx, dy) < self.sample_threshold:
+                return
+
+            # Draw line from last point to current point for interactive feedback
+            painter = QPainter(self.annotation_pixmap)
+            pen = QPen(
+                self.polyline_pen_color,
+                self.polyline_pen_width,
+                Qt.SolidLine,
+                Qt.RoundCap,
+                Qt.RoundJoin,
+            )
+            painter.setPen(pen)
+            painter.drawLine(
+                int(last_point[0]),
+                int(last_point[1]),
+                int(img_coords[0]),
+                int(img_coords[1]),
+            )
+            painter.end()
+
+            self.current_stroke.append((float(img_coords[0]), float(img_coords[1])))
+            self._update_display()
+
+    def mouseReleaseEvent(self, event: QMouseEvent):
+        """Handle mouse release events to complete a stroke."""
+        if not self.is_drawing or event.button() != Qt.LeftButton:
+            super().mouseReleaseEvent(event)
+            return
+
+        self.is_drawing = False
+
+        if len(self.current_stroke) > 1 and self.original_pixmap is not None:
+            # Ensure the stroke is closed by connecting end -> start
+            raw_points = list(self.current_stroke)
+            if raw_points[0] != raw_points[-1]:
+                raw_points.append(raw_points[0])
+
+            # Optional RDP simplification (in image pixel space)
+            if self.simplify_on_finish:
+                simplified = simplify_polyline(raw_points, self.simplify_epsilon)
+            else:
+                simplified = raw_points
+
+            if len(simplified) >= 2:
+                # Store polyline and redraw all annotations
+                self._add_polyline(
+                    simplified, self.polyline_pen_color, self.polyline_pen_width
+                )
+
+                # Convert to normalized coordinates for metadata + signal
+                normalized_stroke = [
+                    self._image_to_normalized_coords(int(x), int(y))
+                    for (x, y) in simplified
+                ]
+                self.all_strokes.append(
+                    {
+                        "points": normalized_stroke,
+                        "color": self.polyline_pen_color.name(),
+                        "alpha": self.polyline_pen_color.alpha(),
+                        "width": self.polyline_pen_width,
+                    }
+                )
+
+                # Emit signal with normalized coordinates
+                self.annotation_drawn.emit(normalized_stroke)
+                logger.debug(
+                    f"Completed stroke with {len(simplified)} points "
+                    f"(normalized len={len(normalized_stroke)})"
+                )
+
+        self.current_stroke = []
+
+    def get_all_strokes(self) -> List[dict]:
+        """Get all drawn strokes with metadata."""
+        return self.all_strokes
+
+    def get_annotation_parameters(self) -> Optional[List[Dict[str, Any]]]:
+        """
+        Get all annotation parameters including bounding box and polyline.
+
+        Returns:
+            List of dictionaries, each containing:
+            - 'bbox': [x_min, y_min, x_max, y_max] in normalized image coordinates
+            - 'polyline': List of [y_norm, x_norm] points describing the polygon
+        """
+        if self.original_pixmap is None or not self.polylines:
+            return None
+
+        img_width = float(self.original_pixmap.width())
+        img_height = float(self.original_pixmap.height())
+
+        params: List[Dict[str, Any]] = []
+
+        for idx, polyline in enumerate(self.polylines):
+            if len(polyline) < 2:
+                continue
+
+            xs = [p[0] for p in polyline]
+            ys = [p[1] for p in polyline]
+
+            x_min_norm = min(xs) / img_width
+            x_max_norm = max(xs) / img_width
+            y_min_norm = min(ys) / img_height
+            y_max_norm = max(ys) / img_height
+
+            # Store polyline as [y_norm, x_norm] to match DB convention and
+            # the expectations of draw_saved_polyline().
+            normalized_polyline = [
+                [y / img_height, x / img_width] for (x, y) in polyline
+            ]
+
+            logger.debug(
+                f"Polyline {idx}: {len(polyline)} points, "
+                f"bbox=({x_min_norm:.3f}, {y_min_norm:.3f})-({x_max_norm:.3f}, {y_max_norm:.3f})"
+            )
+
+            params.append(
+                {
+                    "bbox": [x_min_norm, y_min_norm, x_max_norm, y_max_norm],
+                    "polyline": normalized_polyline,
+                }
+            )
+
+        return params or None
+
+    def draw_saved_polyline(
+        self,
+        polyline: List[List[float]],
+        color: str,
+        width: int = 3,
+        annotation_id: Optional[int] = None,
+    ):
+        """
+        Draw a polyline from database coordinates onto the annotation canvas.
+
+        Args:
+            polyline: List of [x, y] coordinate pairs in normalized coordinates (0-1)
+            color: Color hex string (e.g., '#FF0000')
+            width: Line width in pixels
+        """
+        if not self.annotation_pixmap or not self.original_pixmap:
+            logger.warning("Cannot draw polyline: no image loaded")
+            return
+
+        if len(polyline) < 2:
+            logger.warning("Polyline has less than 2 points, cannot draw")
+            return
+
+        # Convert normalized coordinates to image coordinates
+        # Polyline is stored as [[y_norm, x_norm], ...] (row_norm, col_norm format)
+        img_width = self.original_pixmap.width()
+        img_height = self.original_pixmap.height()
+
+        logger.debug(f"Loading polyline with {len(polyline)} points")
+        logger.debug(f"  Image size: {img_width}x{img_height}")
+        logger.debug(f"  First 3 normalized points from DB: {polyline[:3]}")
+
+        img_coords: List[Tuple[float, float]] = []
+        for y_norm, x_norm in polyline:
+            x = float(x_norm * img_width)
+            y = float(y_norm * img_height)
+            img_coords.append((x, y))
+
+        logger.debug(f"  First 3 pixel coords: {img_coords[:3]}")
+
+        # Store and redraw using common pipeline
+        pen_color = QColor(color)
+        pen_color.setAlpha(128)  # Add semi-transparency
+        self._add_polyline(img_coords, pen_color, width, annotation_id=annotation_id)
+
+        # Store in all_strokes for consistency (uses normalized coordinates)
+        self.all_strokes.append(
+            {"points": polyline, "color": color, "alpha": 128, "width": width}
+        )
+
+        logger.debug(
+            f"Drew saved polyline with {len(polyline)} points in color {color}"
+        )
+
+    def draw_saved_bbox(
+        self,
+        bbox: List[float],
+        color: str,
+        width: int = 3,
+        label: Optional[str] = None,
+    ):
+        """
+        Draw a bounding box from database coordinates onto the annotation canvas.
+
+        Args:
+            bbox: Bounding box as [x_min_norm, y_min_norm, x_max_norm, y_max_norm]
+                  in normalized coordinates (0-1)
+            color: Color hex string (e.g., '#FF0000')
+            width: Line width in pixels
+            label: Optional text label to render near the bounding box
+        """
+        if not self.annotation_pixmap or not self.original_pixmap:
+            logger.warning("Cannot draw bounding box: no image loaded")
+            return
+
+        if len(bbox) != 4:
+            logger.warning(
+                f"Invalid bounding box format: expected 4 values, got {len(bbox)}"
+            )
+            return
+
+        # Convert normalized coordinates to image coordinates (for logging/debug)
+        img_width = self.original_pixmap.width()
+        img_height = self.original_pixmap.height()
+
+        x_min_norm, y_min_norm, x_max_norm, y_max_norm = bbox
+        x_min = int(x_min_norm * img_width)
+        y_min = int(y_min_norm * img_height)
+        x_max = int(x_max_norm * img_width)
+        y_max = int(y_max_norm * img_height)
+
+        logger.debug(f"Drawing bounding box: {bbox}")
+        logger.debug(f"  Image size: {img_width}x{img_height}")
+        logger.debug(f"  Pixel coords: ({x_min}, {y_min}) to ({x_max}, {y_max})")
+
+        # Store bounding box (normalized) and its style; actual drawing happens
+        # in _redraw_annotations() together with all polylines.
+        pen_color = QColor(color)
+        pen_color.setAlpha(128)  # Add semi-transparency
+        self.bboxes.append(
+            [float(x_min_norm), float(y_min_norm), float(x_max_norm), float(y_max_norm)]
+        )
+        self.bbox_meta.append({"color": pen_color, "width": int(width), "label": label})
+
+        # Store in all_strokes for consistency
+        self.all_strokes.append(
+            {"bbox": bbox, "color": color, "alpha": 128, "width": width, "label": label}
+        )
+
+        # Redraw overlay (polylines + all bounding boxes)
+        self._redraw_annotations()
+        logger.debug(f"Drew saved bounding box in color {color}")
+
+    def set_show_bboxes(self, show: bool):
+        """
+        Enable or disable drawing of bounding boxes.
+
+        Args:
+            show: If True, draw bounding boxes; if False, hide them.
+        """
+        self.show_bboxes = bool(show)
+        logger.debug(f"Set show_bboxes to {self.show_bboxes}")
+        self._redraw_annotations()
+
+    def keyPressEvent(self, event: QKeyEvent):
+        """Handle keyboard events for zooming."""
+        if event.key() in (Qt.Key_Plus, Qt.Key_Equal):
+            self.zoom_in()
+            event.accept()
+        elif event.key() == Qt.Key_Minus:
+            self.zoom_out()
+            event.accept()
+        elif event.key() == Qt.Key_0 and event.modifiers() == Qt.ControlModifier:
+            self.reset_zoom()
+            event.accept()
+        else:
+            super().keyPressEvent(event)
+
+    def eventFilter(self, obj, event: QEvent) -> bool:
+        """Event filter to capture wheel events for zooming."""
+        if event.type() == QEvent.Wheel:
+            wheel_event = event
+            if self.original_pixmap is not None:
+                delta = wheel_event.angleDelta().y()
+
+                if delta > 0:
+                    new_scale = self.zoom_scale + self.zoom_wheel_step
+                    if new_scale <= self.zoom_max:
+                        self.zoom_scale = new_scale
+                        self._apply_zoom()
+                else:
+                    new_scale = self.zoom_scale - self.zoom_wheel_step
+                    if new_scale >= self.zoom_min:
+                        self.zoom_scale = new_scale
+                        self._apply_zoom()
+
+                return True
+
+        return super().eventFilter(obj, event)

src/gui/widgets/annotation_tools_widget.py

@@ -0,0 +1,478 @@
+"""
+Annotation tools widget for controlling annotation parameters.
+Includes polyline tool, color picker, class selection, and annotation management.
+"""
+
+from PySide6.QtWidgets import (
+    QWidget,
+    QVBoxLayout,
+    QHBoxLayout,
+    QLabel,
+    QGroupBox,
+    QPushButton,
+    QComboBox,
+    QSpinBox,
+    QDoubleSpinBox,
+    QCheckBox,
+    QColorDialog,
+    QInputDialog,
+    QMessageBox,
+)
+from PySide6.QtGui import QColor, QIcon, QPixmap, QPainter
+from PySide6.QtCore import Qt, Signal
+from typing import Optional, Dict
+
+from src.database.db_manager import DatabaseManager
+from src.utils.logger import get_logger
+
+logger = get_logger(__name__)
+
+
+class AnnotationToolsWidget(QWidget):
+    """
+    Widget for annotation tool controls.
+
+    Features:
+    - Enable/disable polyline tool
+    - Color selection for polyline pen
+    - Object class selection
+    - Add new object classes
+    - Pen width control
+    - Clear annotations
+
+    Signals:
+        polyline_enabled_changed: Emitted when polyline tool is enabled/disabled (bool)
+        polyline_pen_color_changed: Emitted when polyline pen color changes (QColor)
+        polyline_pen_width_changed: Emitted when polyline pen width changes (int)
+        class_selected: Emitted when object class is selected (dict)
+        clear_annotations_requested: Emitted when clear button is pressed
+    """
+
+    polyline_enabled_changed = Signal(bool)
+    polyline_pen_color_changed = Signal(QColor)
+    polyline_pen_width_changed = Signal(int)
+    simplify_on_finish_changed = Signal(bool)
+    simplify_epsilon_changed = Signal(float)
+    # Toggle visibility of bounding boxes on the canvas
+    show_bboxes_changed = Signal(bool)
+    class_selected = Signal(dict)
+    class_color_changed = Signal()
+    clear_annotations_requested = Signal()
+    # Request deletion of the currently selected annotation on the canvas
+    delete_selected_annotation_requested = Signal()
+
+    def __init__(self, db_manager: DatabaseManager, parent=None):
+        """
+        Initialize annotation tools widget.
+
+        Args:
+            db_manager: Database manager instance
+            parent: Parent widget
+        """
+        super().__init__(parent)
+        self.db_manager = db_manager
+        self.polyline_enabled = False
+        self.current_color = QColor(255, 0, 0, 128)  # Red with 50% alpha
+        self.current_class = None
+
+        self._setup_ui()
+        self._load_object_classes()
+
+    def _setup_ui(self):
+        """Setup user interface."""
+        layout = QVBoxLayout()
+
+        # Polyline Tool Group
+        polyline_group = QGroupBox("Polyline Tool")
+        polyline_layout = QVBoxLayout()
+
+        # Enable/Disable polyline tool
+        button_layout = QHBoxLayout()
+        self.polyline_toggle_btn = QPushButton("Start Drawing Polyline")
+        self.polyline_toggle_btn.setCheckable(True)
+        self.polyline_toggle_btn.clicked.connect(self._on_polyline_toggle)
+        button_layout.addWidget(self.polyline_toggle_btn)
+        polyline_layout.addLayout(button_layout)
+
+        # Polyline pen width control
+        width_layout = QHBoxLayout()
+        width_layout.addWidget(QLabel("Pen Width:"))
+        self.polyline_pen_width_spin = QSpinBox()
+        self.polyline_pen_width_spin.setMinimum(1)
+        self.polyline_pen_width_spin.setMaximum(20)
+        self.polyline_pen_width_spin.setValue(3)
+        self.polyline_pen_width_spin.valueChanged.connect(
+            self._on_polyline_pen_width_changed
+        )
+        width_layout.addWidget(self.polyline_pen_width_spin)
+        width_layout.addStretch()
+        polyline_layout.addLayout(width_layout)
+
+        # Simplification controls (RDP)
+        simplify_layout = QHBoxLayout()
+        self.simplify_checkbox = QCheckBox("Simplify on finish")
+        self.simplify_checkbox.setChecked(True)
+        self.simplify_checkbox.stateChanged.connect(self._on_simplify_toggle)
+        simplify_layout.addWidget(self.simplify_checkbox)
+
+        simplify_layout.addWidget(QLabel("epsilon (px):"))
+        self.eps_spin = QDoubleSpinBox()
+        self.eps_spin.setRange(0.0, 1000.0)
+        self.eps_spin.setSingleStep(0.5)
+        self.eps_spin.setValue(2.0)
+        self.eps_spin.valueChanged.connect(self._on_eps_change)
+        simplify_layout.addWidget(self.eps_spin)
+        simplify_layout.addStretch()
+        polyline_layout.addLayout(simplify_layout)
+
+        polyline_group.setLayout(polyline_layout)
+        layout.addWidget(polyline_group)
+
+        # Object Class Group
+        class_group = QGroupBox("Object Class")
+        class_layout = QVBoxLayout()
+
+        # Class selection dropdown
+        self.class_combo = QComboBox()
+        self.class_combo.currentIndexChanged.connect(self._on_class_selected)
+        class_layout.addWidget(self.class_combo)
+
+        # Add / manage classes
+        class_button_layout = QHBoxLayout()
+        self.add_class_btn = QPushButton("Add New Class")
+        self.add_class_btn.clicked.connect(self._on_add_class)
+        class_button_layout.addWidget(self.add_class_btn)
+
+        self.refresh_classes_btn = QPushButton("Refresh")
+        self.refresh_classes_btn.clicked.connect(self._load_object_classes)
+        class_button_layout.addWidget(self.refresh_classes_btn)
+        class_layout.addLayout(class_button_layout)
+
+        # Class color (associated with selected object class)
+        color_layout = QHBoxLayout()
+        color_layout.addWidget(QLabel("Class Color:"))
+        self.color_btn = QPushButton()
+        self.color_btn.setFixedSize(40, 30)
+        self.color_btn.clicked.connect(self._on_color_picker)
+        self._update_color_button()
+        color_layout.addWidget(self.color_btn)
+        color_layout.addStretch()
+        class_layout.addLayout(color_layout)
+
+        # Selected class info
+        self.class_info_label = QLabel("No class selected")
+        self.class_info_label.setWordWrap(True)
+        self.class_info_label.setStyleSheet(
+            "QLabel { color: #888; font-style: italic; }"
+        )
+        class_layout.addWidget(self.class_info_label)
+
+        class_group.setLayout(class_layout)
+        layout.addWidget(class_group)
+
+        # Actions Group
+        actions_group = QGroupBox("Actions")
+        actions_layout = QVBoxLayout()
+
+        # Show / hide bounding boxes
+        self.show_bboxes_checkbox = QCheckBox("Show bounding boxes")
+        self.show_bboxes_checkbox.setChecked(True)
+        self.show_bboxes_checkbox.stateChanged.connect(self._on_show_bboxes_toggle)
+        actions_layout.addWidget(self.show_bboxes_checkbox)
+
+        self.clear_btn = QPushButton("Clear All Annotations")
+        self.clear_btn.clicked.connect(self._on_clear_annotations)
+        actions_layout.addWidget(self.clear_btn)
+
+        # Delete currently selected annotation (enabled when a selection exists)
+        self.delete_selected_btn = QPushButton("Delete Selected Annotation")
+        self.delete_selected_btn.clicked.connect(self._on_delete_selected_annotation)
+        self.delete_selected_btn.setEnabled(False)
+        actions_layout.addWidget(self.delete_selected_btn)
+
+        actions_group.setLayout(actions_layout)
+        layout.addWidget(actions_group)
+
+        layout.addStretch()
+        self.setLayout(layout)
+
+    def _update_color_button(self):
+        """Update the color button appearance with current color."""
+        pixmap = QPixmap(40, 30)
+        pixmap.fill(self.current_color)
+
+        # Add border
+        painter = QPainter(pixmap)
+        painter.setPen(Qt.black)
+        painter.drawRect(0, 0, pixmap.width() - 1, pixmap.height() - 1)
+        painter.end()
+
+        self.color_btn.setIcon(QIcon(pixmap))
+        self.color_btn.setStyleSheet(f"background-color: {self.current_color.name()};")
+
+    def _load_object_classes(self):
+        """Load object classes from database and populate combo box."""
+        try:
+            classes = self.db_manager.get_object_classes()
+
+            # Clear and repopulate combo box
+            self.class_combo.clear()
+            self.class_combo.addItem("-- Select Class / Show All --", None)
+
+            for cls in classes:
+                self.class_combo.addItem(cls["class_name"], cls)
+
+            logger.debug(f"Loaded {len(classes)} object classes")
+
+        except Exception as e:
+            logger.error(f"Error loading object classes: {e}")
+            QMessageBox.warning(
+                self, "Error", f"Failed to load object classes:\n{str(e)}"
+            )
+
+    def _on_polyline_toggle(self, checked: bool):
+        """Handle polyline tool enable/disable."""
+        self.polyline_enabled = checked
+
+        if checked:
+            self.polyline_toggle_btn.setText("Stop Drawing Polyline")
+            self.polyline_toggle_btn.setStyleSheet(
+                "QPushButton { background-color: #4CAF50; }"
+            )
+        else:
+            self.polyline_toggle_btn.setText("Start Drawing Polyline")
+            self.polyline_toggle_btn.setStyleSheet("")
+
+        self.polyline_enabled_changed.emit(self.polyline_enabled)
+        logger.debug(f"Polyline tool {'enabled' if checked else 'disabled'}")
+
+    def _on_polyline_pen_width_changed(self, width: int):
+        """Handle polyline pen width changes."""
+        self.polyline_pen_width_changed.emit(width)
+        logger.debug(f"Polyline pen width changed to {width}")
+
+    def _on_simplify_toggle(self, state: int):
+        """Handle simplify-on-finish checkbox toggle."""
+        enabled = bool(state)
+        self.simplify_on_finish_changed.emit(enabled)
+        logger.debug(f"Simplify on finish set to {enabled}")
+
+    def _on_eps_change(self, val: float):
+        """Handle epsilon (RDP tolerance) value changes."""
+        epsilon = float(val)
+        self.simplify_epsilon_changed.emit(epsilon)
+        logger.debug(f"Simplification epsilon changed to {epsilon}")
+
+    def _on_show_bboxes_toggle(self, state: int):
+        """Handle 'Show bounding boxes' checkbox toggle."""
+        show = bool(state)
+        self.show_bboxes_changed.emit(show)
+        logger.debug(f"Show bounding boxes set to {show}")
+
+    def _on_color_picker(self):
+        """Open color picker dialog and update the selected object's class color."""
+        if not self.current_class:
+            QMessageBox.warning(
+                self,
+                "No Class Selected",
+                "Please select an object class before changing its color.",
+            )
+            return
+
+        # Use current class color (without alpha) as the base
+        base_color = QColor(self.current_class.get("color", self.current_color.name()))
+        color = QColorDialog.getColor(
+            base_color,
+            self,
+            "Select Class Color",
+            QColorDialog.ShowAlphaChannel,  # Allow alpha in UI, but store RGB in DB
+        )
+
+        if not color.isValid():
+            return
+
+        # Normalize to opaque RGB for storage
+        new_color = QColor(color)
+        new_color.setAlpha(255)
+        hex_color = new_color.name()
+
+        try:
+            # Update in database
+            self.db_manager.update_object_class(
+                class_id=self.current_class["id"], color=hex_color
+            )
+        except Exception as e:
+            logger.error(f"Failed to update class color in database: {e}")
+            QMessageBox.critical(
+                self,
+                "Error",
+                f"Failed to update class color in database:\n{str(e)}",
+            )
+            return
+
+        # Update local class data and combo box item data
+        self.current_class["color"] = hex_color
+        current_index = self.class_combo.currentIndex()
+        if current_index >= 0:
+            self.class_combo.setItemData(current_index, dict(self.current_class))
+
+        # Update info label text
+        info_text = f"Class: {self.current_class['class_name']}\nColor: {hex_color}"
+        if self.current_class.get("description"):
+            info_text += f"\nDescription: {self.current_class['description']}"
+        self.class_info_label.setText(info_text)
+
+        # Use semi-transparent version for polyline pen / button preview
+        class_color = QColor(hex_color)
+        class_color.setAlpha(128)
+        self.current_color = class_color
+        self._update_color_button()
+        self.polyline_pen_color_changed.emit(class_color)
+
+        logger.debug(
+            f"Updated class '{self.current_class['class_name']}' color to "
+            f"{hex_color} (polyline pen alpha={class_color.alpha()})"
+        )
+
+        # Notify listeners (e.g., AnnotationTab) so they can reload/redraw
+        self.class_color_changed.emit()
+
+    def _on_class_selected(self, index: int):
+        """Handle object class selection (including '-- Select Class --')."""
+        class_data = self.class_combo.currentData()
+
+        if class_data:
+            self.current_class = class_data
+
+            # Update info label
+            info_text = (
+                f"Class: {class_data['class_name']}\n" f"Color: {class_data['color']}"
+            )
+            if class_data.get("description"):
+                info_text += f"\nDescription: {class_data['description']}"
+
+            self.class_info_label.setText(info_text)
+
+            # Update polyline pen color to match class color with semi-transparency
+            class_color = QColor(class_data["color"])
+            if class_color.isValid():
+                # Add 50% alpha for semi-transparency
+                class_color.setAlpha(128)
+                self.current_color = class_color
+                self._update_color_button()
+                self.polyline_pen_color_changed.emit(class_color)
+
+            self.class_selected.emit(class_data)
+            logger.debug(f"Selected class: {class_data['class_name']}")
+        else:
+            # "-- Select Class --" chosen: clear current class and show all annotations
+            self.current_class = None
+            self.class_info_label.setText("No class selected")
+            self.class_selected.emit(None)
+            logger.debug("Class selection cleared: showing annotations for all classes")
+
+    def _on_add_class(self):
+        """Handle adding a new object class."""
+        # Get class name
+        class_name, ok = QInputDialog.getText(
+            self, "Add Object Class", "Enter class name:"
+        )
+
+        if not ok or not class_name.strip():
+            return
+
+        class_name = class_name.strip()
+
+        # Check if class already exists
+        existing = self.db_manager.get_object_class_by_name(class_name)
+        if existing:
+            QMessageBox.warning(
+                self, "Class Exists", f"A class named '{class_name}' already exists."
+            )
+            return
+
+        # Get color
+        color = QColorDialog.getColor(self.current_color, self, "Select Class Color")
+
+        if not color.isValid():
+            return
+
+        # Get optional description
+        description, ok = QInputDialog.getText(
+            self, "Class Description", "Enter class description (optional):"
+        )
+
+        if not ok:
+            description = None
+
+        # Add to database
+        try:
+            class_id = self.db_manager.add_object_class(
+                class_name, color.name(), description.strip() if description else None
+            )
+
+            logger.info(f"Added new object class: {class_name} (ID: {class_id})")
+
+            # Reload classes and select the new one
+            self._load_object_classes()
+
+            # Find and select the newly added class
+            for i in range(self.class_combo.count()):
+                class_data = self.class_combo.itemData(i)
+                if class_data and class_data.get("id") == class_id:
+                    self.class_combo.setCurrentIndex(i)
+                    break
+
+            QMessageBox.information(
+                self, "Success", f"Class '{class_name}' added successfully!"
+            )
+
+        except Exception as e:
+            logger.error(f"Error adding object class: {e}")
+            QMessageBox.critical(
+                self, "Error", f"Failed to add object class:\n{str(e)}"
+            )
+
+    def _on_clear_annotations(self):
+        """Handle clear annotations button."""
+        reply = QMessageBox.question(
+            self,
+            "Clear Annotations",
+            "Are you sure you want to clear all annotations?",
+            QMessageBox.Yes | QMessageBox.No,
+            QMessageBox.No,
+        )
+
+        if reply == QMessageBox.Yes:
+            self.clear_annotations_requested.emit()
+            logger.debug("Clear annotations requested")
+
+    def _on_delete_selected_annotation(self):
+        """Handle delete selected annotation button."""
+        self.delete_selected_annotation_requested.emit()
+        logger.debug("Delete selected annotation requested")
+
+    def set_has_selected_annotation(self, has_selection: bool):
+        """
+        Enable/disable actions that require a selected annotation.
+
+        Args:
+            has_selection: True if an annotation is currently selected on the canvas.
+        """
+        self.delete_selected_btn.setEnabled(bool(has_selection))
+
+    def get_current_class(self) -> Optional[Dict]:
+        """Get currently selected object class."""
+        return self.current_class
+
+    def get_polyline_pen_color(self) -> QColor:
+        """Get current polyline pen color."""
+        return self.current_color
+
+    def get_polyline_pen_width(self) -> int:
+        """Get current polyline pen width."""
+        return self.polyline_pen_width_spin.value()
+
+    def is_polyline_enabled(self) -> bool:
+        """Check if polyline tool is enabled."""
+        return self.polyline_enabled

src/gui/widgets/image_display_widget.py

@@ -137,7 +137,7 @@ class ImageDisplayWidget(QWidget):
                 height,
                 bytes_per_line,
                 self.current_image.qtimage_format,
-            )
+            ).copy()  # Copy to ensure Qt owns its memory after this scope
 
             # Convert to pixmap
             pixmap = QPixmap.fromImage(qimage)

src/model/inference.py

@@ -5,12 +5,12 @@ Handles detection inference and result storage.
 
 from typing import List, Dict, Optional, Callable
 from pathlib import Path
-from PIL import Image
 import cv2
 import numpy as np
 
 from src.model.yolo_wrapper import YOLOWrapper
 from src.database.db_manager import DatabaseManager
+from src.utils.image import Image
 from src.utils.logger import get_logger
 from src.utils.file_utils import get_relative_path
 
@@ -42,6 +42,7 @@ class InferenceEngine:
         relative_path: str,
         conf: float = 0.25,
         save_to_db: bool = True,
+        repository_root: Optional[str] = None,
     ) -> Dict:
         """
         Detect objects in a single image.
@@ -51,49 +52,79 @@ class InferenceEngine:
             relative_path: Relative path from repository root
             conf: Confidence threshold
             save_to_db: Whether to save results to database
+            repository_root: Base directory used to compute relative_path (if known)
 
         Returns:
             Dictionary with detection results
         """
         try:
+            # Normalize storage path (fall back to absolute path when repo root is unknown)
+            stored_relative_path = relative_path
+            if not repository_root:
+                stored_relative_path = str(Path(image_path).resolve())
+
             # Get image dimensions
-            img = Image.open(image_path)
+            img = Image(image_path)
-            width, height = img.size
+            width = img.width
-            img.close()
+            height = img.height
 
             # Perform detection
             detections = self.yolo.predict(image_path, conf=conf)
 
             # Add/get image in database
             image_id = self.db_manager.get_or_create_image(
-                relative_path=relative_path,
+                relative_path=stored_relative_path,
                 filename=Path(image_path).name,
                 width=width,
                 height=height,
             )
 
-            # Save detections to database
+            inserted_count = 0
-            if save_to_db and detections:
+            deleted_count = 0
-                detection_records = []
-                for det in detections:
-                    # Use normalized bbox from detection
-                    bbox_normalized = det[
-                        "bbox_normalized"
-                    ]  # [x_min, y_min, x_max, y_max]
 
-                    record = {
+            # Save detections to database, replacing any previous results for this image/model
-                        "image_id": image_id,
+            if save_to_db:
-                        "model_id": self.model_id,
+                deleted_count = self.db_manager.delete_detections_for_image(
-                        "class_name": det["class_name"],
+                    image_id, self.model_id
-                        "bbox": tuple(bbox_normalized),
+                )
-                        "confidence": det["confidence"],
+                if detections:
-                        "segmentation_mask": det.get("segmentation_mask"),
+                    detection_records = []
-                        "metadata": {"class_id": det["class_id"]},
+                    for det in detections:
-                    }
+                        # Use normalized bbox from detection
-                    detection_records.append(record)
+                        bbox_normalized = det[
+                            "bbox_normalized"
+                        ]  # [x_min, y_min, x_max, y_max]
 
-                self.db_manager.add_detections_batch(detection_records)
+                        metadata = {
-                logger.info(f"Saved {len(detection_records)} detections to database")
+                            "class_id": det["class_id"],
+                            "source_path": str(Path(image_path).resolve()),
+                        }
+                        if repository_root:
+                            metadata["repository_root"] = str(
+                                Path(repository_root).resolve()
+                            )
+
+                        record = {
+                            "image_id": image_id,
+                            "model_id": self.model_id,
+                            "class_name": det["class_name"],
+                            "bbox": tuple(bbox_normalized),
+                            "confidence": det["confidence"],
+                            "segmentation_mask": det.get("segmentation_mask"),
+                            "metadata": metadata,
+                        }
+                        detection_records.append(record)
+
+                    inserted_count = self.db_manager.add_detections_batch(
+                        detection_records
+                    )
+                    logger.info(
+                        f"Saved {inserted_count} detections to database (replaced {deleted_count})"
+                    )
+                else:
+                    logger.info(
+                        f"Detection run removed {deleted_count} stale entries but produced no new detections"
+                    )
 
             return {
                 "success": True,
@@ -142,7 +173,12 @@ class InferenceEngine:
             rel_path = get_relative_path(image_path, repository_root)
 
             # Perform detection
-            result = self.detect_single(image_path, rel_path, conf)
+            result = self.detect_single(
+                image_path,
+                rel_path,
+                conf=conf,
+                repository_root=repository_root,
+            )
             results.append(result)
 
             # Update progress

src/model/yolo_wrapper.py

@@ -7,6 +7,9 @@ from ultralytics import YOLO
 from pathlib import Path
 from typing import Optional, List, Dict, Callable, Any
 import torch
+import tempfile
+import os
+from src.utils.image import Image
 from src.utils.logger import get_logger
 
 
@@ -55,6 +58,7 @@ class YOLOWrapper:
         save_dir: str = "data/models",
         name: str = "custom_model",
         resume: bool = False,
+        callbacks: Optional[Dict[str, Callable]] = None,
         **kwargs,
     ) -> Dict[str, Any]:
         """
@@ -69,13 +73,15 @@ class YOLOWrapper:
             save_dir: Directory to save trained model
             name: Name for the training run
             resume: Resume training from last checkpoint
+            callbacks: Optional Ultralytics callback dictionary
             **kwargs: Additional training arguments
 
         Returns:
             Dictionary with training results
         """
         if self.model is None:
-            self.load_model()
+            if not self.load_model():
+                raise RuntimeError(f"Failed to load model from {self.model_path}")
 
         try:
             logger.info(f"Starting training: {name}")
@@ -117,7 +123,8 @@ class YOLOWrapper:
             Dictionary with validation metrics
         """
         if self.model is None:
-            self.load_model()
+            if not self.load_model():
+                raise RuntimeError(f"Failed to load model from {self.model_path}")
 
         try:
             logger.info(f"Starting validation on {split} split")
@@ -158,12 +165,15 @@ class YOLOWrapper:
             List of detection dictionaries
         """
         if self.model is None:
-            self.load_model()
+            if not self.load_model():
+                raise RuntimeError(f"Failed to load model from {self.model_path}")
+
+        prepared_source, cleanup_path = self._prepare_source(source)
 
         try:
             logger.info(f"Running inference on {source}")
             results = self.model.predict(
-                source=source,
+                source=prepared_source,
                 conf=conf,
                 iou=iou,
                 save=save,
@@ -180,6 +190,14 @@ class YOLOWrapper:
         except Exception as e:
             logger.error(f"Error during inference: {e}")
             raise
+        finally:
+            if 0:  # cleanup_path:
+                try:
+                    os.remove(cleanup_path)
+                except OSError as cleanup_error:
+                    logger.warning(
+                        f"Failed to delete temporary RGB image {cleanup_path}: {cleanup_error}"
+                    )
 
     def export(
         self, format: str = "onnx", output_path: Optional[str] = None, **kwargs
@@ -196,7 +214,8 @@ class YOLOWrapper:
             Path to exported model
         """
         if self.model is None:
-            self.load_model()
+            if not self.load_model():
+                raise RuntimeError(f"Failed to load model from {self.model_path}")
 
         try:
             logger.info(f"Exporting model to {format} format")
@@ -208,6 +227,38 @@ class YOLOWrapper:
             logger.error(f"Error exporting model: {e}")
             raise
 
+    def _prepare_source(self, source):
+        """Convert single-channel images to RGB temporarily for inference."""
+        cleanup_path = None
+
+        if isinstance(source, (str, Path)):
+            source_path = Path(source)
+            if source_path.is_file():
+                try:
+                    img_obj = Image(source_path)
+                    pil_img = img_obj.pil_image
+                    if len(pil_img.getbands()) == 1:
+                        rgb_img = img_obj.convert_grayscale_to_rgb_preserve_range()
+                    else:
+                        rgb_img = pil_img.convert("RGB")
+
+                    suffix = source_path.suffix or ".png"
+                    tmp = tempfile.NamedTemporaryFile(suffix=suffix, delete=False)
+                    tmp_path = tmp.name
+                    tmp.close()
+                    rgb_img.save(tmp_path)
+                    cleanup_path = tmp_path
+                    logger.info(
+                        f"Converted image {source_path} to RGB for inference at {tmp_path}"
+                    )
+                    return tmp_path, cleanup_path
+                except Exception as convert_error:
+                    logger.warning(
+                        f"Failed to preprocess {source_path} as RGB, continuing with original file: {convert_error}"
+                    )
+
+        return source, cleanup_path
+
     def _format_training_results(self, results) -> Dict[str, Any]:
         """Format training results into dictionary."""
         try:

src/utils/config_manager.py

@@ -7,6 +7,7 @@ import yaml
 from pathlib import Path
 from typing import Any, Dict, Optional
 from src.utils.logger import get_logger
+from src.utils.image import Image
 
 
 logger = get_logger(__name__)
@@ -46,18 +47,15 @@ class ConfigManager:
             "database": {"path": "data/detections.db"},
             "image_repository": {
                 "base_path": "",
-                "allowed_extensions": [
+                "allowed_extensions": Image.SUPPORTED_EXTENSIONS,
-                    ".jpg",
-                    ".jpeg",
-                    ".png",
-                    ".tif",
-                    ".tiff",
-                    ".bmp",
-                ],
             },
             "models": {
                 "default_base_model": "yolov8s-seg.pt",
                 "models_directory": "data/models",
+                "base_model_choices": [
+                    "yolov8s-seg.pt",
+                    "yolov11s-seg.pt",
+                ],
             },
             "training": {
                 "default_epochs": 100,
@@ -65,6 +63,20 @@ class ConfigManager:
                 "default_imgsz": 640,
                 "default_patience": 50,
                 "default_lr0": 0.01,
+                "two_stage": {
+                    "enabled": False,
+                    "stage1": {
+                        "epochs": 20,
+                        "lr0": 0.0005,
+                        "patience": 10,
+                        "freeze": 10,
+                    },
+                    "stage2": {
+                        "epochs": 150,
+                        "lr0": 0.0003,
+                        "patience": 30,
+                    },
+                },
             },
             "detection": {
                 "default_confidence": 0.25,
@@ -214,5 +226,5 @@ class ConfigManager:
     def get_allowed_extensions(self) -> list:
         """Get list of allowed image file extensions."""
         return self.get(
-            "image_repository.allowed_extensions", [".jpg", ".jpeg", ".png"]
+            "image_repository.allowed_extensions", Image.SUPPORTED_EXTENSIONS
         )

src/utils/file_utils.py

@@ -28,7 +28,9 @@ def get_image_files(
         List of absolute paths to image files
     """
     if allowed_extensions is None:
-        allowed_extensions = [".jpg", ".jpeg", ".png", ".tif", ".tiff", ".bmp"]
+        from src.utils.image import Image
+
+        allowed_extensions = Image.SUPPORTED_EXTENSIONS
 
     # Normalize extensions to lowercase
     allowed_extensions = [ext.lower() for ext in allowed_extensions]
@@ -204,7 +206,9 @@ def is_image_file(
         True if file is an image
     """
     if allowed_extensions is None:
-        allowed_extensions = [".jpg", ".jpeg", ".png", ".tif", ".tiff", ".bmp"]
+        from src.utils.image import Image
+
+        allowed_extensions = Image.SUPPORTED_EXTENSIONS
 
     extension = Path(file_path).suffix.lower()
     return extension in [ext.lower() for ext in allowed_extensions]

src/utils/image.py

@@ -277,6 +277,38 @@ class Image:
         """
         return self._channels >= 3
 
+    def convert_grayscale_to_rgb_preserve_range(
+        self,
+    ) -> PILImage.Image:
+        """Convert a single-channel PIL image to RGB while preserving dynamic range.
+
+        Returns:
+            PIL Image in RGB mode with intensities normalized to 0-255.
+        """
+        if self._channels == 3:
+            return self.pil_image
+
+        grayscale = self.data
+        if grayscale.ndim == 3:
+            grayscale = grayscale[:, :, 0]
+
+        original_dtype = grayscale.dtype
+        grayscale = grayscale.astype(np.float32)
+
+        if grayscale.size == 0:
+            return PILImage.new("RGB", self.shape, color=(0, 0, 0))
+
+        if np.issubdtype(original_dtype, np.integer):
+            denom = float(max(np.iinfo(original_dtype).max, 1))
+        else:
+            max_val = float(grayscale.max())
+            denom = max(max_val, 1.0)
+
+        grayscale = np.clip(grayscale / denom, 0.0, 1.0)
+        grayscale_u8 = (grayscale * 255.0).round().astype(np.uint8)
+        rgb_arr = np.repeat(grayscale_u8[:, :, None], 3, axis=2)
+        return PILImage.fromarray(rgb_arr, mode="RGB")
+
     def __repr__(self) -> str:
         """String representation of the Image object."""
         return (

src/utils/image_converters.py

@@ -0,0 +1,160 @@
+import numpy as np
+
+from roifile import ImagejRoi
+from tifffile import TiffFile, TiffWriter
+from pathlib import Path
+
+
+class UT:
+    """
+    Docstring for UT
+
+    Operetta files along with rois drawn in ImageJ
+    """
+
+    def __init__(self, roifile_fn: Path, no_labels: bool):
+        self.roifile_fn = roifile_fn
+        print("is file", self.roifile_fn.is_file())
+        self.rois = None
+        if no_labels:
+            self.rois = ImagejRoi.fromfile(self.roifile_fn)
+            self.stem = self.roifile_fn.stem.split("Roi-")[1]
+        else:
+            self.roifile_fn = roifile_fn / roifile_fn.parts[-1]
+            self.stem = self.roifile_fn.stem
+
+            print(self.roifile_fn)
+
+        print(self.stem)
+        self.image, self.image_props = self._load_images()
+
+    def _load_images(self):
+        """Loading sequence of tif files
+        array sequence is CZYX
+        """
+        print("Loading images:", self.roifile_fn.parent, self.stem)
+        fns = list(self.roifile_fn.parent.glob(f"{self.stem.lower()}*.tif*"))
+        stems = [fn.stem.split(self.stem)[-1] for fn in fns]
+        n_ch = len(set([stem.split("-ch")[-1].split("t")[0] for stem in stems]))
+        n_p = len(set([stem.split("-")[0] for stem in stems]))
+        n_t = len(set([stem.split("t")[1] for stem in stems]))
+
+        with TiffFile(fns[0]) as tif:
+            img = tif.asarray()
+            w, h = img.shape
+            dtype = img.dtype
+            self.image_props = {
+                "channels": n_ch,
+                "planes": n_p,
+                "tiles": n_t,
+                "width": w,
+                "height": h,
+                "dtype": dtype,
+            }
+        print("Image props", self.image_props)
+
+        image_stack = np.zeros((n_ch, n_p, w, h), dtype=dtype)
+        for fn in fns:
+            with TiffFile(fn) as tif:
+                img = tif.asarray()
+                stem = fn.stem.split(self.stem)[-1]
+                ch = int(stem.split("-ch")[-1].split("t")[0])
+                p = int(stem.split("-")[0].split("p")[1])
+                t = int(stem.split("t")[1])
+                print(fn.stem, "ch", ch, "p", p, "t", t)
+                image_stack[ch - 1, p - 1] = img
+
+        print(image_stack.shape)
+
+        return image_stack, self.image_props
+
+    @property
+    def width(self):
+        return self.image_props["width"]
+
+    @property
+    def height(self):
+        return self.image_props["height"]
+
+    @property
+    def nchannels(self):
+        return self.image_props["channels"]
+
+    @property
+    def nplanes(self):
+        return self.image_props["planes"]
+
+    def export_rois(
+        self,
+        path: Path,
+        subfolder: str = "labels",
+        class_index: int = 0,
+    ):
+        """Export rois to a file"""
+        with open(path / subfolder / f"{self.stem}.txt", "w") as f:
+            for i, roi in enumerate(self.rois):
+                rc = roi.subpixel_coordinates
+                if rc is None:
+                    print(
+                        f"No coordinates: {self.roifile_fn}, element {i}, out of {len(self.rois)}"
+                    )
+                    continue
+                xmn, ymn = rc.min(axis=0)
+                xmx, ymx = rc.max(axis=0)
+                xc = (xmn + xmx) / 2
+                yc = (ymn + ymx) / 2
+                bw = xmx - xmn
+                bh = ymx - ymn
+                coords = f"{xc/self.width} {yc/self.height} {bw/self.width} {bh/self.height} "
+                for x, y in rc:
+                    coords += f"{x/self.width} {y/self.height} "
+                f.write(f"{class_index} {coords}\n")
+
+        return
+
+    def export_image(
+        self,
+        path: Path,
+        subfolder: str = "images",
+        plane_mode: str = "max projection",
+        channel: int = 0,
+    ):
+        """Export image to a file"""
+
+        if plane_mode == "max projection":
+            self.image = np.max(self.image[channel], axis=0)
+            print(self.image.shape)
+
+        print(path / subfolder / f"{self.stem}.tif")
+        with TiffWriter(path / subfolder / f"{self.stem}.tif") as tif:
+            tif.write(self.image)
+
+
+if __name__ == "__main__":
+    import argparse
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-i", "--input", nargs="*", type=Path)
+    parser.add_argument("-o", "--output", type=Path)
+    parser.add_argument(
+        "--no-labels",
+        action="store_false",
+        help="Source does not have labels, export only images",
+    )
+    args = parser.parse_args()
+
+    for path in args.input:
+        print("Path:", path)
+        if not args.no_labels:
+            print("No labels")
+            ut = UT(path, args.no_labels)
+            ut.export_image(args.output, plane_mode="max projection", channel=0)
+
+        else:
+            for rfn in Path(path).glob("*.zip"):
+                print("Roi FN:", rfn)
+                ut = UT(rfn, args.no_labels)
+                ut.export_rois(args.output, class_index=0)
+                ut.export_image(args.output, plane_mode="max projection", channel=0)
+
+        print()

tests/show_yolo_seg.py

@@ -0,0 +1,184 @@
+#!/usr/bin/env python3
+"""
+show_yolo_seg.py
+
+Usage:
+    python show_yolo_seg.py /path/to/image.jpg /path/to/labels.txt
+
+Supports:
+ - Segmentation polygons: "class x1 y1 x2 y2 ... xn yn"
+ - YOLO bbox lines as fallback: "class x_center y_center width height"
+Coordinates can be normalized [0..1] or absolute pixels (auto-detected).
+"""
+import sys
+import cv2
+import numpy as np
+import matplotlib.pyplot as plt
+import argparse
+from pathlib import Path
+import random
+
+
+def parse_label_line(line):
+    parts = line.strip().split()
+    if not parts:
+        return None
+    cls = int(float(parts[0]))
+    coords = [float(x) for x in parts[1:]]
+    return cls, coords
+
+
+def coords_are_normalized(coords):
+    # If every coordinate is between 0 and 1 (inclusive-ish), assume normalized
+    if not coords:
+        return False
+    return max(coords) <= 1.001
+
+
+def yolo_bbox_to_xyxy(coords, img_w, img_h):
+    # coords: [xc, yc, w, h] normalized or absolute
+    xc, yc, w, h = coords[:4]
+    if max(coords) <= 1.001:
+        xc *= img_w
+        yc *= img_h
+        w *= img_w
+        h *= img_h
+    x1 = int(round(xc - w / 2))
+    y1 = int(round(yc - h / 2))
+    x2 = int(round(xc + w / 2))
+    y2 = int(round(yc + h / 2))
+    return x1, y1, x2, y2
+
+
+def poly_to_pts(coords, img_w, img_h):
+    # coords: [x1 y1 x2 y2 ...] either normalized or absolute
+    if coords_are_normalized(coords[4:]):
+        coords = [
+            coords[i] * (img_w if i % 2 == 0 else img_h) for i in range(len(coords))
+        ]
+    pts = np.array(coords, dtype=np.int32).reshape(-1, 2)
+    return pts
+
+
+def random_color_for_class(cls):
+    random.seed(cls)  # deterministic per class
+    return tuple(int(x) for x in np.array([random.randint(0, 255) for _ in range(3)]))
+
+
+def draw_annotations(img, labels, alpha=0.4, draw_bbox_for_poly=True):
+    # img: BGR numpy array
+    overlay = img.copy()
+    h, w = img.shape[:2]
+    for cls, coords in labels:
+        if not coords:
+            continue
+        # polygon case (>=6 coordinates)
+        if len(coords) >= 6:
+            color = random_color_for_class(cls)
+
+            x1, y1, x2, y2 = yolo_bbox_to_xyxy(coords[:4], w, h)
+            cv2.rectangle(img, (x1, y1), (x2, y2), color, 2)
+
+            pts = poly_to_pts(coords[4:], w, h)
+            # fill on overlay
+            cv2.fillPoly(overlay, [pts], color)
+            # outline on base image
+            cv2.polylines(img, [pts], isClosed=True, color=color, thickness=2)
+            # put class text at first point
+            x, y = int(pts[0, 0]), int(pts[0, 1]) - 6
+            cv2.putText(
+                img,
+                str(cls),
+                (x, max(6, y)),
+                cv2.FONT_HERSHEY_SIMPLEX,
+                0.6,
+                (255, 255, 255),
+                2,
+                cv2.LINE_AA,
+            )
+
+        # YOLO bbox case (4 coords)
+        elif len(coords) == 4:
+            x1, y1, x2, y2 = yolo_bbox_to_xyxy(coords, w, h)
+            color = random_color_for_class(cls)
+            cv2.rectangle(img, (x1, y1), (x2, y2), color, 2)
+            cv2.putText(
+                img,
+                str(cls),
+                (x1, max(6, y1 - 4)),
+                cv2.FONT_HERSHEY_SIMPLEX,
+                0.6,
+                (255, 255, 255),
+                2,
+                cv2.LINE_AA,
+            )
+        else:
+            # Unknown / invalid format, skip
+            continue
+
+    # blend overlay for filled polygons
+    cv2.addWeighted(overlay, alpha, img, 1 - alpha, 0, img)
+    return img
+
+
+def load_labels_file(label_path):
+    labels = []
+    with open(label_path, "r") as f:
+        for raw in f:
+            line = raw.strip()
+            if not line:
+                continue
+            parsed = parse_label_line(line)
+            if parsed:
+                labels.append(parsed)
+    return labels
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Show YOLO segmentation / polygon annotations"
+    )
+    parser.add_argument("image", type=str, help="Path to image file")
+    parser.add_argument("labels", type=str, help="Path to YOLO label file (polygons)")
+    parser.add_argument(
+        "--alpha", type=float, default=0.4, help="Polygon fill alpha (0..1)"
+    )
+    parser.add_argument(
+        "--no-bbox", action="store_true", help="Don't draw bounding boxes for polygons"
+    )
+    args = parser.parse_args()
+
+    img_path = Path(args.image)
+    lbl_path = Path(args.labels)
+
+    if not img_path.exists():
+        print("Image not found:", img_path)
+        sys.exit(1)
+    if not lbl_path.exists():
+        print("Label file not found:", lbl_path)
+        sys.exit(1)
+
+    img = cv2.imread(str(img_path), cv2.IMREAD_COLOR)
+    if img is None:
+        print("Could not load image:", img_path)
+        sys.exit(1)
+
+    labels = load_labels_file(str(lbl_path))
+    if not labels:
+        print("No labels parsed from", lbl_path)
+        # continue and just show image
+    out = draw_annotations(
+        img.copy(), labels, alpha=args.alpha, draw_bbox_for_poly=(not args.no_bbox)
+    )
+
+    # Convert BGR -> RGB for matplotlib display
+    out_rgb = cv2.cvtColor(out, cv2.COLOR_BGR2RGB)
+    plt.figure(figsize=(10, 10 * out.shape[0] / out.shape[1]))
+    plt.imshow(out_rgb)
+    plt.axis("off")
+    plt.title(f"{img_path.name} ({lbl_path.name})")
+    plt.show()
+
+
+if __name__ == "__main__":
+    main()

tests/test_image.py

@@ -27,7 +27,7 @@ class TestImage:
 
     def test_supported_extensions(self):
         """Test that supported extensions are correctly defined."""
-        expected_extensions = [".jpg", ".jpeg", ".png", ".tif", ".tiff", ".bmp"]
+        expected_extensions = Image.SUPPORTED_EXTENSIONS
         assert Image.SUPPORTED_EXTENSIONS == expected_extensions
 
     def test_image_properties(self, tmp_path):