spacr 0.1.63__py3-none-any.whl → 0.1.75__py3-none-any.whl

spacr/gui_elements.py

@@ -1,6 +1,19 @@
+import os, threading, time, sqlite3
 import tkinter as tk
 from tkinter import ttk
 import tkinter.font as tkFont
+from queue import Queue
+from tkinter import Label
+import numpy as np
+from PIL import Image, ImageOps, ImageTk
+from concurrent.futures import ThreadPoolExecutor
+from skimage.exposure import rescale_intensity
+from IPython.display import display, HTML
+import imageio.v2 as imageio
+from collections import deque
+from skimage.draw import polygon, line
+from skimage.transform import resize
+from scipy.ndimage import binary_fill_holes, label
 
 class spacrDropdownMenu(tk.OptionMenu):
     def __init__(self, parent, variable, options, command=None, **kwargs):
@@ -261,19 +274,1173 @@ class spacrToolTip:
             self.tooltip_window.destroy()
         self.tooltip_window = None
 
+class modify_masks:
+
+    def __init__(self, root, folder_path, scale_factor):
+        self.root = root
+        self.folder_path = folder_path
+        self.scale_factor = scale_factor
+        self.image_filenames = sorted([f for f in os.listdir(folder_path) if f.endswith(('.png', '.jpg', '.jpeg', '.tif', '.tiff'))])
+        self.masks_folder = os.path.join(folder_path, 'masks')
+        self.current_image_index = 0
+        self.initialize_flags()
+        self.canvas_width = self.root.winfo_screenheight() -100
+        self.canvas_height = self.root.winfo_screenheight() -100
+        self.root.configure(bg='black')
+        self.setup_navigation_toolbar()
+        self.setup_mode_toolbar()
+        self.setup_function_toolbar()
+        self.setup_zoom_toolbar()
+        self.setup_canvas()
+        self.load_first_image()
+    
+    ####################################################################################################
+    # Helper functions#
+    ####################################################################################################
+    
+    def update_display(self):
+        if self.zoom_active:
+            self.display_zoomed_image()
+        else:
+            self.display_image()
+    
+    def update_original_mask_from_zoom(self):
+        y0, y1, x0, x1 = self.zoom_y0, self.zoom_y1, self.zoom_x0, self.zoom_x1
+        zoomed_mask_resized = resize(self.zoom_mask, (y1 - y0, x1 - x0), order=0, preserve_range=True).astype(np.uint8)
+        self.mask[y0:y1, x0:x1] = zoomed_mask_resized
+        
+    def update_original_mask(self, zoomed_mask, x0, x1, y0, y1):
+        actual_mask_region = self.mask[y0:y1, x0:x1]
+        target_shape = actual_mask_region.shape
+        resized_mask = resize(zoomed_mask, target_shape, order=0, preserve_range=True).astype(np.uint8)
+        if resized_mask.shape != actual_mask_region.shape:
+            raise ValueError(f"Shape mismatch: resized_mask {resized_mask.shape}, actual_mask_region {actual_mask_region.shape}")
+        self.mask[y0:y1, x0:x1] = np.maximum(actual_mask_region, resized_mask)
+        self.mask = self.mask.copy()
+        self.mask[y0:y1, x0:x1] = np.maximum(self.mask[y0:y1, x0:x1], resized_mask)
+        self.mask = self.mask.copy()
+
+    def get_scaling_factors(self, img_width, img_height, canvas_width, canvas_height):
+        x_scale = img_width / canvas_width
+        y_scale = img_height / canvas_height
+        return x_scale, y_scale
+    
+    def canvas_to_image(self, x_canvas, y_canvas):
+        x_scale, y_scale = self.get_scaling_factors(
+            self.image.shape[1], self.image.shape[0],
+            self.canvas_width, self.canvas_height
+        )
+        x_image = int(x_canvas * x_scale)
+        y_image = int(y_canvas * y_scale)
+        return x_image, y_image
+
+    def apply_zoom_on_enter(self, event):
+        if self.zoom_active and self.zoom_rectangle_start is not None:
+            self.set_zoom_rectangle_end(event)
+        
+    def normalize_image(self, image, lower_quantile, upper_quantile):
+        lower_bound = np.percentile(image, lower_quantile)
+        upper_bound = np.percentile(image, upper_quantile)
+        normalized = np.clip(image, lower_bound, upper_bound)
+        normalized = (normalized - lower_bound) / (upper_bound - lower_bound)
+        max_value = np.iinfo(image.dtype).max
+        normalized = (normalized * max_value).astype(image.dtype)
+        return normalized
+    
+    def resize_arrays(self, img, mask):
+        original_dtype = img.dtype
+        scaled_height = int(img.shape[0] * self.scale_factor)
+        scaled_width = int(img.shape[1] * self.scale_factor)
+        scaled_img = resize(img, (scaled_height, scaled_width), anti_aliasing=True, preserve_range=True)
+        scaled_mask = resize(mask, (scaled_height, scaled_width), order=0, anti_aliasing=False, preserve_range=True)
+        stretched_img = resize(scaled_img, (self.canvas_height, self.canvas_width), anti_aliasing=True, preserve_range=True)
+        stretched_mask = resize(scaled_mask, (self.canvas_height, self.canvas_width), order=0, anti_aliasing=False, preserve_range=True)
+        return stretched_img.astype(original_dtype), stretched_mask.astype(original_dtype)
+    
+    ####################################################################################################
+    #Initiate canvas elements#
+    ####################################################################################################
+    
+    def load_first_image(self):
+        self.image, self.mask = self.load_image_and_mask(self.current_image_index)
+        self.original_size = self.image.shape
+        self.image, self.mask = self.resize_arrays(self.image, self.mask)
+        self.display_image()
+
+    def setup_canvas(self):
+        self.canvas = tk.Canvas(self.root, width=self.canvas_width, height=self.canvas_height, bg='black')
+        self.canvas.pack()
+        self.canvas.bind("<Motion>", self.update_mouse_info)
+
+    def initialize_flags(self):
+        self.zoom_rectangle_start = None
+        self.zoom_rectangle_end = None
+        self.zoom_rectangle_id = None
+        self.zoom_x0 = None
+        self.zoom_y0 = None
+        self.zoom_x1 = None
+        self.zoom_y1 = None
+        self.zoom_mask = None
+        self.zoom_image = None
+        self.zoom_image_orig = None
+        self.zoom_scale = 1
+        self.drawing = False
+        self.zoom_active = False
+        self.magic_wand_active = False
+        self.brush_active = False
+        self.dividing_line_active = False
+        self.dividing_line_coords = []
+        self.current_dividing_line = None
+        self.lower_quantile = tk.StringVar(value="1.0")
+        self.upper_quantile = tk.StringVar(value="99.9")
+        self.magic_wand_tolerance = tk.StringVar(value="1000")
+
+    def update_mouse_info(self, event):
+        x, y = event.x, event.y
+        intensity = "N/A"
+        mask_value = "N/A"
+        pixel_count = "N/A"  
+        if self.zoom_active:
+            if 0 <= x < self.canvas_width and 0 <= y < self.canvas_height:
+                intensity = self.zoom_image_orig[y, x] if self.zoom_image_orig is not None else "N/A"
+                mask_value = self.zoom_mask[y, x] if self.zoom_mask is not None else "N/A"
+        else:
+            if 0 <= x < self.image.shape[1] and 0 <= y < self.image.shape[0]:
+                intensity = self.image[y, x]
+                mask_value = self.mask[y, x]
+        if mask_value != "N/A" and mask_value != 0:
+            pixel_count = np.sum(self.mask == mask_value)
+        self.intensity_label.config(text=f"Intensity: {intensity}")
+        self.mask_value_label.config(text=f"Mask: {mask_value}, Area: {pixel_count}")
+        self.mask_value_label.config(text=f"Mask: {mask_value}")
+        if mask_value != "N/A" and mask_value != 0:
+            self.pixel_count_label.config(text=f"Area: {pixel_count}")
+        else:
+            self.pixel_count_label.config(text="Area: N/A")
+    
+    def setup_navigation_toolbar(self):
+        navigation_toolbar = tk.Frame(self.root, bg='black')
+        navigation_toolbar.pack(side='top', fill='x')
+        prev_btn = tk.Button(navigation_toolbar, text="Previous", command=self.previous_image, bg='black', fg='white')
+        prev_btn.pack(side='left')
+        next_btn = tk.Button(navigation_toolbar, text="Next", command=self.next_image, bg='black', fg='white')
+        next_btn.pack(side='left')
+        save_btn = tk.Button(navigation_toolbar, text="Save", command=self.save_mask, bg='black', fg='white')
+        save_btn.pack(side='left')
+        self.intensity_label = tk.Label(navigation_toolbar, text="Image: N/A", bg='black', fg='white')
+        self.intensity_label.pack(side='right')
+        self.mask_value_label = tk.Label(navigation_toolbar, text="Mask: N/A", bg='black', fg='white')
+        self.mask_value_label.pack(side='right')
+        self.pixel_count_label = tk.Label(navigation_toolbar, text="Area: N/A", bg='black', fg='white')
+        self.pixel_count_label.pack(side='right')
+
+    def setup_mode_toolbar(self):
+        self.mode_toolbar = tk.Frame(self.root, bg='black')
+        self.mode_toolbar.pack(side='top', fill='x')
+        self.draw_btn = tk.Button(self.mode_toolbar, text="Draw", command=self.toggle_draw_mode, bg='black', fg='white')
+        self.draw_btn.pack(side='left')
+        self.magic_wand_btn = tk.Button(self.mode_toolbar, text="Magic Wand", command=self.toggle_magic_wand_mode, bg='black', fg='white')
+        self.magic_wand_btn.pack(side='left')
+        tk.Label(self.mode_toolbar, text="Tolerance:", bg='black', fg='white').pack(side='left')
+        self.tolerance_entry = tk.Entry(self.mode_toolbar, textvariable=self.magic_wand_tolerance, bg='black', fg='white')
+        self.tolerance_entry.pack(side='left')
+        tk.Label(self.mode_toolbar, text="Max Pixels:", bg='black', fg='white').pack(side='left')
+        self.max_pixels_entry = tk.Entry(self.mode_toolbar, bg='black', fg='white')
+        self.max_pixels_entry.insert(0, "1000")
+        self.max_pixels_entry.pack(side='left')
+        self.erase_btn = tk.Button(self.mode_toolbar, text="Erase", command=self.toggle_erase_mode, bg='black', fg='white')
+        self.erase_btn.pack(side='left')
+        self.brush_btn = tk.Button(self.mode_toolbar, text="Brush", command=self.toggle_brush_mode, bg='black', fg='white')
+        self.brush_btn.pack(side='left')
+        self.brush_size_entry = tk.Entry(self.mode_toolbar, bg='black', fg='white')
+        self.brush_size_entry.insert(0, "10")
+        self.brush_size_entry.pack(side='left')
+        tk.Label(self.mode_toolbar, text="Brush Size:", bg='black', fg='white').pack(side='left')
+        self.dividing_line_btn = tk.Button(self.mode_toolbar, text="Dividing Line", command=self.toggle_dividing_line_mode, bg='black', fg='white')
+        self.dividing_line_btn.pack(side='left')
+
+    def setup_function_toolbar(self):
+        self.function_toolbar = tk.Frame(self.root, bg='black')
+        self.function_toolbar.pack(side='top', fill='x')
+        self.fill_btn = tk.Button(self.function_toolbar, text="Fill", command=self.fill_objects, bg='black', fg='white')
+        self.fill_btn.pack(side='left')
+        self.relabel_btn = tk.Button(self.function_toolbar, text="Relabel", command=self.relabel_objects, bg='black', fg='white')
+        self.relabel_btn.pack(side='left')
+        self.clear_btn = tk.Button(self.function_toolbar, text="Clear", command=self.clear_objects, bg='black', fg='white')
+        self.clear_btn.pack(side='left')
+        self.invert_btn = tk.Button(self.function_toolbar, text="Invert", command=self.invert_mask, bg='black', fg='white')
+        self.invert_btn.pack(side='left')
+        remove_small_btn = tk.Button(self.function_toolbar, text="Remove Small", command=self.remove_small_objects, bg='black', fg='white')
+        remove_small_btn.pack(side='left')
+        tk.Label(self.function_toolbar, text="Min Area:", bg='black', fg='white').pack(side='left')
+        self.min_area_entry = tk.Entry(self.function_toolbar, bg='black', fg='white')
+        self.min_area_entry.insert(0, "100")  # Default minimum area
+        self.min_area_entry.pack(side='left')
+
+    def setup_zoom_toolbar(self):
+        self.zoom_toolbar = tk.Frame(self.root, bg='black')
+        self.zoom_toolbar.pack(side='top', fill='x')
+        self.zoom_btn = tk.Button(self.zoom_toolbar, text="Zoom", command=self.toggle_zoom_mode, bg='black', fg='white')
+        self.zoom_btn.pack(side='left')
+        self.normalize_btn = tk.Button(self.zoom_toolbar, text="Apply Normalization", command=self.apply_normalization, bg='black', fg='white')
+        self.normalize_btn.pack(side='left')
+        tk.Label(self.zoom_toolbar, text="Lower Percentile:", bg='black', fg='white').pack(side='left')
+        self.lower_entry = tk.Entry(self.zoom_toolbar, textvariable=self.lower_quantile, bg='black', fg='white')
+        self.lower_entry.pack(side='left')
+        
+        tk.Label(self.zoom_toolbar, text="Upper Percentile:", bg='black', fg='white').pack(side='left')
+        self.upper_entry = tk.Entry(self.zoom_toolbar, textvariable=self.upper_quantile, bg='black', fg='white')
+        self.upper_entry.pack(side='left')
+
+        
+    def load_image_and_mask(self, index):
+        image_path = os.path.join(self.folder_path, self.image_filenames[index])
+        image = imageio.imread(image_path)        
+        mask_path = os.path.join(self.masks_folder, self.image_filenames[index])
+        if os.path.exists(mask_path):
+            print(f'loading mask:{mask_path} for image: {image_path}')
+            mask = imageio.imread(mask_path)
+            if mask.dtype != np.uint8:
+                mask = (mask / np.max(mask) * 255).astype(np.uint8)
+        else:
+            mask = np.zeros(image.shape[:2], dtype=np.uint8)
+            print(f'loaded new mask for image: {image_path}')
+        return image, mask
+    
+    ####################################################################################################
+    # Image Display functions#
+    ####################################################################################################
+    def display_image(self):
+        if self.zoom_rectangle_id is not None:
+            self.canvas.delete(self.zoom_rectangle_id)
+            self.zoom_rectangle_id = None
+        lower_quantile = float(self.lower_quantile.get()) if self.lower_quantile.get() else 1.0
+        upper_quantile = float(self.upper_quantile.get()) if self.upper_quantile.get() else 99.9
+        normalized = self.normalize_image(self.image, lower_quantile, upper_quantile)
+        combined = self.overlay_mask_on_image(normalized, self.mask)
+        self.tk_image = ImageTk.PhotoImage(image=Image.fromarray(combined))
+        self.canvas.create_image(0, 0, anchor='nw', image=self.tk_image)
+
+    def display_zoomed_image(self):
+        if self.zoom_rectangle_start and self.zoom_rectangle_end:
+            # Convert canvas coordinates to image coordinates
+            x0, y0 = self.canvas_to_image(*self.zoom_rectangle_start)
+            x1, y1 = self.canvas_to_image(*self.zoom_rectangle_end)
+            x0, x1 = min(x0, x1), max(x0, x1)
+            y0, y1 = min(y0, y1), max(y0, y1)
+            self.zoom_x0 = x0
+            self.zoom_y0 = y0
+            self.zoom_x1 = x1
+            self.zoom_y1 = y1
+            # Normalize the entire image
+            lower_quantile = float(self.lower_quantile.get()) if self.lower_quantile.get() else 1.0
+            upper_quantile = float(self.upper_quantile.get()) if self.upper_quantile.get() else 99.9
+            normalized_image = self.normalize_image(self.image, lower_quantile, upper_quantile)
+            # Extract the zoomed portion of the normalized image and mask
+            self.zoom_image = normalized_image[y0:y1, x0:x1]
+            self.zoom_image_orig = self.image[y0:y1, x0:x1]
+            self.zoom_mask = self.mask[y0:y1, x0:x1]
+            original_mask_area = self.mask.shape[0] * self.mask.shape[1]
+            zoom_mask_area = self.zoom_mask.shape[0] * self.zoom_mask.shape[1]
+            if original_mask_area > 0:
+                self.zoom_scale = original_mask_area/zoom_mask_area
+            # Resize the zoomed image and mask to fit the canvas
+            canvas_height = self.canvas.winfo_height()
+            canvas_width = self.canvas.winfo_width()
+            
+            if self.zoom_image.size > 0 and canvas_height > 0 and canvas_width > 0:
+                self.zoom_image = resize(self.zoom_image, (canvas_height, canvas_width), preserve_range=True).astype(self.zoom_image.dtype)
+                self.zoom_image_orig = resize(self.zoom_image_orig, (canvas_height, canvas_width), preserve_range=True).astype(self.zoom_image_orig.dtype)
+                #self.zoom_mask = resize(self.zoom_mask, (canvas_height, canvas_width), preserve_range=True).astype(np.uint8)
+                self.zoom_mask = resize(self.zoom_mask, (canvas_height, canvas_width), order=0, preserve_range=True).astype(np.uint8)
+                combined = self.overlay_mask_on_image(self.zoom_image, self.zoom_mask)
+                self.tk_image = ImageTk.PhotoImage(image=Image.fromarray(combined))
+                self.canvas.create_image(0, 0, anchor='nw', image=self.tk_image)
+
+    def overlay_mask_on_image(self, image, mask, alpha=0.5):
+        if len(image.shape) == 2:
+            image = np.stack((image,) * 3, axis=-1)
+        mask = mask.astype(np.int32)
+        max_label = np.max(mask)
+        np.random.seed(0)
+        colors = np.random.randint(0, 255, size=(max_label + 1, 3), dtype=np.uint8)
+        colors[0] = [0, 0, 0]  # background color
+        colored_mask = colors[mask]
+        image_8bit = (image / 256).astype(np.uint8)
+        # Blend the mask and the image with transparency
+        combined_image = np.where(mask[..., None] > 0, 
+                                  np.clip(image_8bit * (1 - alpha) + colored_mask * alpha, 0, 255), 
+                                  image_8bit)
+        # Convert the final image back to uint8
+        combined_image = combined_image.astype(np.uint8)
+        return combined_image
+    
+    ####################################################################################################
+    # Navigation functions#
+    ####################################################################################################
+    
+    def previous_image(self):
+        if self.current_image_index > 0:
+            self.current_image_index -= 1
+            self.initialize_flags()            
+            self.image, self.mask = self.load_image_and_mask(self.current_image_index)
+            self.original_size = self.image.shape
+            self.image, self.mask = self.resize_arrays(self.image, self.mask)
+            self.display_image()
+
+    def next_image(self):
+        if self.current_image_index < len(self.image_filenames) - 1:
+            self.current_image_index += 1
+            self.initialize_flags()            
+            self.image, self.mask = self.load_image_and_mask(self.current_image_index)
+            self.original_size = self.image.shape
+            self.image, self.mask = self.resize_arrays(self.image, self.mask)
+            self.display_image()
+            
+    def save_mask(self):
+        if self.current_image_index < len(self.image_filenames):
+            original_size = self.original_size
+            if self.mask.shape != original_size:
+                resized_mask = resize(self.mask, original_size, order=0, preserve_range=True).astype(np.uint16)
+            else:
+                resized_mask = self.mask
+            resized_mask, _ = label(resized_mask > 0)
+            save_folder = os.path.join(self.folder_path, 'masks')
+            if not os.path.exists(save_folder):
+                os.makedirs(save_folder)
+            image_filename = os.path.splitext(self.image_filenames[self.current_image_index])[0] + '.tif'
+            save_path = os.path.join(save_folder, image_filename)
+
+            print(f"Saving mask to: {save_path}")  # Debug print
+            imageio.imwrite(save_path, resized_mask)
+
+    ####################################################################################################
+    # Zoom Functions #
+    ####################################################################################################
+    def set_zoom_rectangle_start(self, event):
+        if self.zoom_active:
+            self.zoom_rectangle_start = (event.x, event.y)
+    
+    def set_zoom_rectangle_end(self, event):
+        if self.zoom_active:
+            self.zoom_rectangle_end = (event.x, event.y)
+            if self.zoom_rectangle_id is not None:
+                self.canvas.delete(self.zoom_rectangle_id)
+                self.zoom_rectangle_id = None
+            self.display_zoomed_image()  
+            self.canvas.unbind("<Motion>")  
+            self.canvas.unbind("<Button-1>")
+            self.canvas.unbind("<Button-3>")  
+            self.canvas.bind("<Motion>", self.update_mouse_info)
+            
+    def update_zoom_box(self, event):
+        if self.zoom_active and self.zoom_rectangle_start is not None:
+            if self.zoom_rectangle_id is not None:
+                self.canvas.delete(self.zoom_rectangle_id)
+            # Assuming event.x and event.y are already in image coordinates
+            self.zoom_rectangle_end = (event.x, event.y)
+            x0, y0 = self.zoom_rectangle_start
+            x1, y1 = self.zoom_rectangle_end
+            self.zoom_rectangle_id = self.canvas.create_rectangle(x0, y0, x1, y1, outline="red", width=2)
+    
+    ####################################################################################################
+    # Mode activation#
+    ####################################################################################################
+    
+    def toggle_zoom_mode(self):
+        if not self.zoom_active:
+            self.brush_btn.config(text="Brush")
+            self.canvas.unbind("<B1-Motion>")
+            self.canvas.unbind("<B3-Motion>")
+            self.canvas.unbind("<ButtonRelease-1>")
+            self.canvas.unbind("<ButtonRelease-3>")
+            self.zoom_active = True
+            self.drawing = False
+            self.magic_wand_active = False
+            self.erase_active = False
+            self.brush_active = False
+            self.dividing_line_active = False
+            self.draw_btn.config(text="Draw")
+            self.erase_btn.config(text="Erase")
+            self.magic_wand_btn.config(text="Magic Wand")
+            self.zoom_btn.config(text="Zoom ON")
+            self.dividing_line_btn.config(text="Dividing Line")
+            self.canvas.unbind("<Button-1>")
+            self.canvas.unbind("<Button-3>")
+            self.canvas.unbind("<Motion>")
+            self.canvas.bind("<Button-1>", self.set_zoom_rectangle_start)
+            self.canvas.bind("<Button-3>", self.set_zoom_rectangle_end)
+            self.canvas.bind("<Motion>", self.update_zoom_box)
+        else:
+            self.zoom_active = False
+            self.zoom_btn.config(text="Zoom")
+            self.canvas.unbind("<Button-1>")
+            self.canvas.unbind("<Button-3>")
+            self.canvas.unbind("<Motion>")
+            self.zoom_rectangle_start = self.zoom_rectangle_end = None
+            self.zoom_rectangle_id = None
+            self.display_image()
+            self.canvas.bind("<Motion>", self.update_mouse_info)
+            self.zoom_rectangle_start = None
+            self.zoom_rectangle_end = None
+            self.zoom_rectangle_id = None
+            self.zoom_x0 = None
+            self.zoom_y0 = None
+            self.zoom_x1 = None
+            self.zoom_y1 = None
+            self.zoom_mask = None
+            self.zoom_image = None
+            self.zoom_image_orig = None
+
+    def toggle_brush_mode(self):
+        self.brush_active = not self.brush_active
+        if self.brush_active:
+            self.drawing = False
+            self.magic_wand_active = False
+            self.erase_active = False
+            self.brush_btn.config(text="Brush ON")
+            self.draw_btn.config(text="Draw")
+            self.erase_btn.config(text="Erase")
+            self.magic_wand_btn.config(text="Magic Wand")
+            self.canvas.unbind("<Button-1>")
+            self.canvas.unbind("<Button-3>")
+            self.canvas.unbind("<Motion>")
+            self.canvas.bind("<B1-Motion>", self.apply_brush)  # Left click and drag to apply brush
+            self.canvas.bind("<B3-Motion>", self.erase_brush)  # Right click and drag to erase with brush
+            self.canvas.bind("<ButtonRelease-1>", self.apply_brush_release)  # Left button release
+            self.canvas.bind("<ButtonRelease-3>", self.erase_brush_release)  # Right button release
+        else:
+            self.brush_active = False
+            self.brush_btn.config(text="Brush")
+            self.canvas.unbind("<B1-Motion>")
+            self.canvas.unbind("<B3-Motion>")
+            self.canvas.unbind("<ButtonRelease-1>")
+            self.canvas.unbind("<ButtonRelease-3>")
+
+    def image_to_canvas(self, x_image, y_image):
+        x_scale, y_scale = self.get_scaling_factors(
+            self.image.shape[1], self.image.shape[0],
+            self.canvas_width, self.canvas_height
+        )
+        x_canvas = int(x_image / x_scale)
+        y_canvas = int(y_image / y_scale)
+        return x_canvas, y_canvas
+
+    def toggle_dividing_line_mode(self):
+        self.dividing_line_active = not self.dividing_line_active
+        if self.dividing_line_active:
+            self.drawing = False
+            self.magic_wand_active = False
+            self.erase_active = False
+            self.brush_active = False
+            self.draw_btn.config(text="Draw")
+            self.erase_btn.config(text="Erase")
+            self.magic_wand_btn.config(text="Magic Wand")
+            self.brush_btn.config(text="Brush")
+            self.dividing_line_btn.config(text="Dividing Line ON")
+            self.canvas.unbind("<Button-1>")
+            self.canvas.unbind("<ButtonRelease-1>")
+            self.canvas.unbind("<Motion>")
+            self.canvas.bind("<Button-1>", self.start_dividing_line)
+            self.canvas.bind("<ButtonRelease-1>", self.finish_dividing_line)
+            self.canvas.bind("<Motion>", self.update_dividing_line_preview)
+        else:
+            print("Dividing Line Mode: OFF")
+            self.dividing_line_active = False
+            self.dividing_line_btn.config(text="Dividing Line")
+            self.canvas.unbind("<Button-1>")
+            self.canvas.unbind("<ButtonRelease-1>")
+            self.canvas.unbind("<Motion>")
+            self.display_image()
+
+    def start_dividing_line(self, event):
+        if self.dividing_line_active:
+            self.dividing_line_coords = [(event.x, event.y)]
+            self.current_dividing_line = self.canvas.create_line(event.x, event.y, event.x, event.y, fill="red", width=2)
+
+    def finish_dividing_line(self, event):
+        if self.dividing_line_active:
+            self.dividing_line_coords.append((event.x, event.y))
+            if self.zoom_active:
+                self.dividing_line_coords = [self.canvas_to_image(x, y) for x, y in self.dividing_line_coords]
+            self.apply_dividing_line()
+            self.canvas.delete(self.current_dividing_line)
+            self.current_dividing_line = None
+
+    def update_dividing_line_preview(self, event):
+        if self.dividing_line_active and self.dividing_line_coords:
+            x, y = event.x, event.y
+            if self.zoom_active:
+                x, y = self.canvas_to_image(x, y)
+            self.dividing_line_coords.append((x, y))
+            canvas_coords = [(self.image_to_canvas(*pt) if self.zoom_active else pt) for pt in self.dividing_line_coords]
+            flat_canvas_coords = [coord for pt in canvas_coords for coord in pt]
+            self.canvas.coords(self.current_dividing_line, *flat_canvas_coords)
+
+    def apply_dividing_line(self):
+        if self.dividing_line_coords:
+            coords = self.dividing_line_coords
+            if self.zoom_active:
+                coords = [self.canvas_to_image(x, y) for x, y in coords]
+
+            rr, cc = [], []
+            for (x0, y0), (x1, y1) in zip(coords[:-1], coords[1:]):
+                line_rr, line_cc = line(y0, x0, y1, x1)
+                rr.extend(line_rr)
+                cc.extend(line_cc)
+            rr, cc = np.array(rr), np.array(cc)
+
+            mask_copy = self.mask.copy()
+
+            if self.zoom_active:
+                # Update the zoomed mask
+                self.zoom_mask[rr, cc] = 0
+                # Reflect changes to the original mask
+                y0, y1, x0, x1 = self.zoom_y0, self.zoom_y1, self.zoom_x0, self.zoom_x1
+                zoomed_mask_resized_back = resize(self.zoom_mask, (y1 - y0, x1 - x0), order=0, preserve_range=True).astype(np.uint8)
+                self.mask[y0:y1, x0:x1] = zoomed_mask_resized_back
+            else:
+                # Directly update the original mask
+                mask_copy[rr, cc] = 0
+                self.mask = mask_copy
+
+            labeled_mask, num_labels = label(self.mask > 0)
+            self.mask = labeled_mask
+            self.update_display()
+
+            self.dividing_line_coords = []
+            self.canvas.unbind("<Button-1>")
+            self.canvas.unbind("<ButtonRelease-1>")
+            self.canvas.unbind("<Motion>")
+            self.dividing_line_active = False
+            self.dividing_line_btn.config(text="Dividing Line")
+
+    def toggle_draw_mode(self):
+        self.drawing = not self.drawing
+        if self.drawing:
+            self.brush_btn.config(text="Brush")
+            self.canvas.unbind("<B1-Motion>")
+            self.canvas.unbind("<B3-Motion>")
+            self.canvas.unbind("<ButtonRelease-1>")
+            self.canvas.unbind("<ButtonRelease-3>")
+            self.magic_wand_active = False
+            self.erase_active = False
+            self.brush_active = False
+            self.draw_btn.config(text="Draw ON")
+            self.magic_wand_btn.config(text="Magic Wand")
+            self.erase_btn.config(text="Erase")
+            self.draw_coordinates = []
+            self.canvas.unbind("<Button-1>")
+            self.canvas.unbind("<Motion>")
+            self.canvas.bind("<B1-Motion>", self.draw)
+            self.canvas.bind("<ButtonRelease-1>", self.finish_drawing)
+        else:
+            self.drawing = False
+            self.draw_btn.config(text="Draw")
+            self.canvas.unbind("<B1-Motion>")
+            self.canvas.unbind("<ButtonRelease-1>")
+            
+    def toggle_magic_wand_mode(self):
+        self.magic_wand_active = not self.magic_wand_active
+        if self.magic_wand_active:
+            self.brush_btn.config(text="Brush")
+            self.canvas.unbind("<B1-Motion>")
+            self.canvas.unbind("<B3-Motion>")
+            self.canvas.unbind("<ButtonRelease-1>")
+            self.canvas.unbind("<ButtonRelease-3>")
+            self.drawing = False
+            self.erase_active = False
+            self.brush_active = False
+            self.draw_btn.config(text="Draw")
+            self.erase_btn.config(text="Erase")
+            self.magic_wand_btn.config(text="Magic Wand ON")
+            self.canvas.bind("<Button-1>", self.use_magic_wand)
+            self.canvas.bind("<Button-3>", self.use_magic_wand)
+        else:
+            self.magic_wand_btn.config(text="Magic Wand")
+            self.canvas.unbind("<Button-1>")
+            self.canvas.unbind("<Button-3>")
+            
+    def toggle_erase_mode(self):
+        self.erase_active = not self.erase_active
+        if self.erase_active:
+            self.brush_btn.config(text="Brush")
+            self.canvas.unbind("<B1-Motion>")
+            self.canvas.unbind("<B3-Motion>")
+            self.canvas.unbind("<ButtonRelease-1>")
+            self.canvas.unbind("<ButtonRelease-3>")
+            self.erase_btn.config(text="Erase ON")
+            self.canvas.bind("<Button-1>", self.erase_object)
+            self.drawing = False
+            self.magic_wand_active = False
+            self.brush_active = False
+            self.draw_btn.config(text="Draw")
+            self.magic_wand_btn.config(text="Magic Wand")
+        else:
+            self.erase_active = False
+            self.erase_btn.config(text="Erase")
+            self.canvas.unbind("<Button-1>")
+    
+    ####################################################################################################
+    # Mode functions#
+    ####################################################################################################
+    
+    def apply_brush_release(self, event):
+        if hasattr(self, 'brush_path'):
+            for x, y, brush_size in self.brush_path:
+                img_x, img_y = (x, y) if self.zoom_active else self.canvas_to_image(x, y)
+                x0 = max(img_x - brush_size // 2, 0)
+                y0 = max(img_y - brush_size // 2, 0)
+                x1 = min(img_x + brush_size // 2, self.zoom_mask.shape[1] if self.zoom_active else self.mask.shape[1])
+                y1 = min(img_y + brush_size // 2, self.zoom_mask.shape[0] if self.zoom_active else self.mask.shape[0])
+                if self.zoom_active:
+                    self.zoom_mask[y0:y1, x0:x1] = 255
+                    self.update_original_mask_from_zoom()
+                else:
+                    self.mask[y0:y1, x0:x1] = 255
+            del self.brush_path
+            self.canvas.delete("temp_line")
+            self.update_display()
+
+    def erase_brush_release(self, event):
+        if hasattr(self, 'erase_path'):
+            for x, y, brush_size in self.erase_path:
+                img_x, img_y = (x, y) if self.zoom_active else self.canvas_to_image(x, y)
+                x0 = max(img_x - brush_size // 2, 0)
+                y0 = max(img_y - brush_size // 2, 0)
+                x1 = min(img_x + brush_size // 2, self.zoom_mask.shape[1] if self.zoom_active else self.mask.shape[1])
+                y1 = min(img_y + brush_size // 2, self.zoom_mask.shape[0] if self.zoom_active else self.mask.shape[0])
+                if self.zoom_active:
+                    self.zoom_mask[y0:y1, x0:x1] = 0                    
+                    self.update_original_mask_from_zoom()
+                else:
+                    self.mask[y0:y1, x0:x1] = 0
+            del self.erase_path
+            self.canvas.delete("temp_line")
+            self.update_display()
+        
+    def apply_brush(self, event):
+        brush_size = int(self.brush_size_entry.get())
+        x, y = event.x, event.y
+        if not hasattr(self, 'brush_path'):
+            self.brush_path = []
+            self.last_brush_coord = (x, y)
+        if self.last_brush_coord:
+            last_x, last_y = self.last_brush_coord
+            rr, cc = line(last_y, last_x, y, x)
+            for ry, rx in zip(rr, cc):
+                self.brush_path.append((rx, ry, brush_size))
+
+        self.canvas.create_line(self.last_brush_coord[0], self.last_brush_coord[1], x, y, width=brush_size, fill="blue", tag="temp_line")
+        self.last_brush_coord = (x, y)
+
+    def erase_brush(self, event):
+        brush_size = int(self.brush_size_entry.get())
+        x, y = event.x, event.y
+        if not hasattr(self, 'erase_path'):
+            self.erase_path = []
+            self.last_erase_coord = (x, y)
+        if self.last_erase_coord:
+            last_x, last_y = self.last_erase_coord
+            rr, cc = line(last_y, last_x, y, x)
+            for ry, rx in zip(rr, cc):
+                self.erase_path.append((rx, ry, brush_size))
+
+        self.canvas.create_line(self.last_erase_coord[0], self.last_erase_coord[1], x, y, width=brush_size, fill="white", tag="temp_line")
+        self.last_erase_coord = (x, y)
+
+    def erase_object(self, event):
+        x, y = event.x, event.y
+        if self.zoom_active:
+            canvas_x, canvas_y = x, y
+            zoomed_x = int(canvas_x * (self.zoom_image.shape[1] / self.canvas_width))
+            zoomed_y = int(canvas_y * (self.zoom_image.shape[0] / self.canvas_height))
+            orig_x = int(zoomed_x * ((self.zoom_x1 - self.zoom_x0) / self.canvas_width) + self.zoom_x0)
+            orig_y = int(zoomed_y * ((self.zoom_y1 - self.zoom_y0) / self.canvas_height) + self.zoom_y0)
+            if orig_x < 0 or orig_y < 0 or orig_x >= self.image.shape[1] or orig_y >= self.image.shape[0]:
+                print("Point is out of bounds in the original image.")
+                return
+        else:
+            orig_x, orig_y = x, y
+        label_to_remove = self.mask[orig_y, orig_x]
+        if label_to_remove > 0:
+            self.mask[self.mask == label_to_remove] = 0
+        self.update_display()
+            
+    def use_magic_wand(self, event):
+        x, y = event.x, event.y
+        tolerance = int(self.magic_wand_tolerance.get())
+        maximum = int(self.max_pixels_entry.get())
+        action = 'add' if event.num == 1 else 'erase'
+        if self.zoom_active:
+            self.magic_wand_zoomed((x, y), tolerance, action)
+        else:
+            self.magic_wand_normal((x, y), tolerance, action)
+    
+    def apply_magic_wand(self, image, mask, seed_point, tolerance, maximum, action='add'):
+        x, y = seed_point
+        initial_value = image[y, x].astype(np.float32)
+        visited = np.zeros_like(image, dtype=bool)
+        queue = deque([(x, y)])
+        added_pixels = 0
+
+        while queue and added_pixels < maximum:
+            cx, cy = queue.popleft()
+            if visited[cy, cx]:
+                continue
+            visited[cy, cx] = True
+            current_value = image[cy, cx].astype(np.float32)
+
+            if np.linalg.norm(abs(current_value - initial_value)) <= tolerance:
+                if mask[cy, cx] == 0:
+                    added_pixels += 1
+                mask[cy, cx] = 255 if action == 'add' else 0
+
+                if added_pixels >= maximum:
+                    break
+
+                for dx, dy in [(-1, 0), (1, 0), (0, -1), (0, 1)]:
+                    nx, ny = cx + dx, cy + dy
+                    if 0 <= nx < image.shape[1] and 0 <= ny < image.shape[0] and not visited[ny, nx]:
+                        queue.append((nx, ny))
+        return mask
+
+    def magic_wand_normal(self, seed_point, tolerance, action):
+        try:
+            maximum = int(self.max_pixels_entry.get())
+        except ValueError:
+            print("Invalid maximum value; using default of 1000")
+            maximum = 1000 
+        self.mask = self.apply_magic_wand(self.image, self.mask, seed_point, tolerance, maximum, action)
+        self.display_image()
+        
+    def magic_wand_zoomed(self, seed_point, tolerance, action):
+        if self.zoom_image_orig is None or self.zoom_mask is None:
+            print("Zoomed image or mask not initialized")
+            return
+        try:
+            maximum = int(self.max_pixels_entry.get())
+            maximum = maximum * self.zoom_scale
+        except ValueError:
+            print("Invalid maximum value; using default of 1000")
+            maximum = 1000
+            
+        canvas_x, canvas_y = seed_point
+        if canvas_x < 0 or canvas_y < 0 or canvas_x >= self.zoom_image_orig.shape[1] or canvas_y >= self.zoom_image_orig.shape[0]:
+            print("Selected point is out of bounds in the zoomed image.")
+            return
+        
+        self.zoom_mask = self.apply_magic_wand(self.zoom_image_orig, self.zoom_mask, (canvas_x, canvas_y), tolerance, maximum, action)
+        y0, y1, x0, x1 = self.zoom_y0, self.zoom_y1, self.zoom_x0, self.zoom_x1
+        zoomed_mask_resized_back = resize(self.zoom_mask, (y1 - y0, x1 - x0), order=0, preserve_range=True).astype(np.uint8)
+        if action == 'erase':
+            self.mask[y0:y1, x0:x1] = np.where(zoomed_mask_resized_back == 0, 0, self.mask[y0:y1, x0:x1])
+        else:
+            self.mask[y0:y1, x0:x1] = np.where(zoomed_mask_resized_back > 0, zoomed_mask_resized_back, self.mask[y0:y1, x0:x1])
+        self.update_display()
+                
+    def draw(self, event):
+        if self.drawing:
+            x, y = event.x, event.y
+            if self.draw_coordinates:
+                last_x, last_y = self.draw_coordinates[-1]
+                self.current_line = self.canvas.create_line(last_x, last_y, x, y, fill="yellow", width=3)
+            self.draw_coordinates.append((x, y))
+            
+    def draw_on_zoomed_mask(self, draw_coordinates):
+        canvas_height = self.canvas.winfo_height()
+        canvas_width = self.canvas.winfo_width()
+        zoomed_mask = np.zeros((canvas_height, canvas_width), dtype=np.uint8)
+        rr, cc = polygon(np.array(draw_coordinates)[:, 1], np.array(draw_coordinates)[:, 0], shape=zoomed_mask.shape)
+        zoomed_mask[rr, cc] = 255
+        return zoomed_mask
+            
+    def finish_drawing(self, event):
+        if len(self.draw_coordinates) > 2:
+            self.draw_coordinates.append(self.draw_coordinates[0])
+            if self.zoom_active:
+                x0, x1, y0, y1 = self.zoom_x0, self.zoom_x1, self.zoom_y0, self.zoom_y1
+                zoomed_mask = self.draw_on_zoomed_mask(self.draw_coordinates)
+                self.update_original_mask(zoomed_mask, x0, x1, y0, y1)
+            else:
+                rr, cc = polygon(np.array(self.draw_coordinates)[:, 1], np.array(self.draw_coordinates)[:, 0], shape=self.mask.shape)
+                self.mask[rr, cc] = np.maximum(self.mask[rr, cc], 255)
+                self.mask = self.mask.copy()
+            self.canvas.delete(self.current_line)
+            self.draw_coordinates.clear()
+        self.update_display()
+            
+    def finish_drawing_if_active(self, event):
+        if self.drawing and len(self.draw_coordinates) > 2:
+            self.finish_drawing(event)
+
+    ####################################################################################################
+    # Single function butons#
+    ####################################################################################################
+            
+    def apply_normalization(self):
+        self.lower_quantile.set(self.lower_entry.get())
+        self.upper_quantile.set(self.upper_entry.get())
+        self.update_display()
+
+    def fill_objects(self):
+        binary_mask = self.mask > 0
+        filled_mask = binary_fill_holes(binary_mask)
+        self.mask = filled_mask.astype(np.uint8) * 255
+        labeled_mask, _ = label(filled_mask)
+        self.mask = labeled_mask
+        self.update_display()
+
+    def relabel_objects(self):
+        mask = self.mask
+        labeled_mask, num_labels = label(mask > 0)
+        self.mask = labeled_mask
+        self.update_display()
+        
+    def clear_objects(self):
+        self.mask = np.zeros_like(self.mask)
+        self.update_display()
+
+    def invert_mask(self):
+        self.mask = np.where(self.mask > 0, 0, 1)
+        self.relabel_objects()
+        self.update_display()
+        
+    def remove_small_objects(self):
+        try:
+            min_area = int(self.min_area_entry.get())
+        except ValueError:
+            print("Invalid minimum area value; using default of 100")
+            min_area = 100
+
+        labeled_mask, num_labels = label(self.mask > 0)
+        for i in range(1, num_labels + 1):  # Skip background
+            if np.sum(labeled_mask == i) < min_area:
+                self.mask[labeled_mask == i] = 0  # Remove small objects
+        self.update_display()
+
+class ImageApp:
+    def __init__(self, root, db_path, src, image_type=None, channels=None, grid_rows=None, grid_cols=None, image_size=(200, 200), annotation_column='annotate', normalize=False, percentiles=(1,99), measurement=None, threshold=None):
+        self.root = root
+        self.db_path = db_path
+        self.src = src
+        self.index = 0
+        self.grid_rows = grid_rows
+        self.grid_cols = grid_cols
+        self.image_size = image_size
+        self.annotation_column = annotation_column
+        self.image_type = image_type
+        self.channels = channels
+        self.normalize = normalize
+        self.percentiles = percentiles
+        self.images = {}
+        self.pending_updates = {}
+        self.labels = []
+        self.adjusted_to_original_paths = {}
+        self.terminate = False
+        self.update_queue = Queue()
+        self.status_label = Label(self.root, text="", font=("Arial", 12))
+        self.status_label.grid(row=self.grid_rows + 1, column=0, columnspan=self.grid_cols)
+        self.measurement = measurement
+        self.threshold = threshold
+
+        self.filtered_paths_annotations = []
+        self.prefilter_paths_annotations()
+
+        self.db_update_thread = threading.Thread(target=self.update_database_worker)
+        self.db_update_thread.start()
+
+        for i in range(grid_rows * grid_cols):
+            label = Label(root)
+            label.grid(row=i // grid_cols, column=i % grid_cols)
+            self.labels.append(label)
+
+    def prefilter_paths_annotations(self):
+        from .io import _read_and_join_tables
+        from .utils import is_list_of_lists
+
+        if self.measurement and self.threshold is not None:
+            df = _read_and_join_tables(self.db_path)
+            df[self.annotation_column] = None
+            before = len(df)
+
+            if is_list_of_lists(self.measurement):
+                if isinstance(self.threshold, list) or is_list_of_lists(self.threshold):
+                    if len(self.measurement) == len(self.threshold):
+                        for idx, var in enumerate(self.measurement):
+                            df = df[df[var[idx]] > self.threshold[idx]]
+                        after = len(df)
+                    elif len(self.measurement) == len(self.threshold)*2:
+                        th_idx = 0
+                        for idx, var in enumerate(self.measurement):
+                            if idx % 2 != 0:
+                                th_idx += 1
+                                thd = self.threshold
+                                if isinstance(thd, list):
+                                    thd = thd[0]
+                                df[f'threshold_measurement_{idx}'] = df[self.measurement[idx]]/df[self.measurement[idx+1]]
+                                print(f"mean threshold_measurement_{idx}: {np.mean(df['threshold_measurement'])}")
+                                print(f"median threshold measurement: {np.median(df[self.measurement])}")
+                                df = df[df[f'threshold_measurement_{idx}'] > thd]
+                        after = len(df)
+            elif isinstance(self.measurement, list):
+                df['threshold_measurement'] = df[self.measurement[0]]/df[self.measurement[1]]
+                print(f"mean threshold measurement: {np.mean(df['threshold_measurement'])}")
+                print(f"median threshold measurement: {np.median(df[self.measurement])}")
+                df = df[df['threshold_measurement'] > self.threshold]
+                after = len(df)
+                self.measurement = 'threshold_measurement'
+                print(f'Removed: {before-after} rows, retained {after}')
+            else:
+                print(f"mean threshold measurement: {np.mean(df[self.measurement])}")
+                print(f"median threshold measurement: {np.median(df[self.measurement])}")
+                before = len(df)
+                if isinstance(self.threshold, str):
+                    if self.threshold == 'q1':
+                        self.threshold = df[self.measurement].quantile(0.1)
+                    if self.threshold == 'q2':
+                        self.threshold = df[self.measurement].quantile(0.2)
+                    if self.threshold == 'q3':
+                        self.threshold = df[self.measurement].quantile(0.3)
+                    if self.threshold == 'q4':
+                        self.threshold = df[self.measurement].quantile(0.4)
+                    if self.threshold == 'q5':
+                        self.threshold = df[self.measurement].quantile(0.5)
+                    if self.threshold == 'q6':
+                        self.threshold = df[self.measurement].quantile(0.6)
+                    if self.threshold == 'q7':
+                        self.threshold = df[self.measurement].quantile(0.7)
+                    if self.threshold == 'q8':
+                        self.threshold = df[self.measurement].quantile(0.8)
+                    if self.threshold == 'q9':
+                        self.threshold = df[self.measurement].quantile(0.9)
+                print(f"threshold: {self.threshold}")
+
+                df = df[df[self.measurement] > self.threshold]
+                after = len(df)
+                print(f'Removed: {before-after} rows, retained {after}')
+
+            df = df.dropna(subset=['png_path'])
+            if self.image_type:
+                before = len(df)
+                if isinstance(self.image_type, list):
+                    for tpe in self.image_type:
+                        df = df[df['png_path'].str.contains(tpe)]
+                else:
+                    df = df[df['png_path'].str.contains(self.image_type)]
+                after = len(df)
+                print(f'image_type: Removed: {before-after} rows, retained {after}')
+
+            self.filtered_paths_annotations = df[['png_path', self.annotation_column]].values.tolist()
+        else:
+            conn = sqlite3.connect(self.db_path)
+            c = conn.cursor()
+            if self.image_type:
+                c.execute(f"SELECT png_path, {self.annotation_column} FROM png_list WHERE png_path LIKE ?", (f"%{self.image_type}%",))
+            else:
+                c.execute(f"SELECT png_path, {self.annotation_column} FROM png_list")
+            self.filtered_paths_annotations = c.fetchall()
+            conn.close()
+
+    def load_images(self):
+        for label in self.labels:
+            label.config(image='')
+
+        self.images = {}
+        paths_annotations = self.filtered_paths_annotations[self.index:self.index + self.grid_rows * self.grid_cols]
+
+        adjusted_paths = []
+        for path, annotation in paths_annotations:
+            if not path.startswith(self.src):
+                parts = path.split('/data/')
+                if len(parts) > 1:
+                    new_path = os.path.join(self.src, 'data', parts[1])
+                    self.adjusted_to_original_paths[new_path] = path
+                    adjusted_paths.append((new_path, annotation))
+                else:
+                    adjusted_paths.append((path, annotation))
+            else:
+                adjusted_paths.append((path, annotation))
+
+        with ThreadPoolExecutor() as executor:
+            loaded_images = list(executor.map(self.load_single_image, adjusted_paths))
+
+        for i, (img, annotation) in enumerate(loaded_images):
+            if annotation:
+                border_color = 'teal' if annotation == 1 else 'red'
+                img = self.add_colored_border(img, border_width=5, border_color=border_color)
+
+            photo = ImageTk.PhotoImage(img)
+            label = self.labels[i]
+            self.images[label] = photo
+            label.config(image=photo)
+
+            path = adjusted_paths[i][0]
+            label.bind('<Button-1>', self.get_on_image_click(path, label, img))
+            label.bind('<Button-3>', self.get_on_image_click(path, label, img))
+
+        self.root.update()
+
+    def load_single_image(self, path_annotation_tuple):
+        path, annotation = path_annotation_tuple
+        img = Image.open(path)
+        img = self.normalize_image(img, self.normalize, self.percentiles)
+        img = img.convert('RGB')
+        img = self.filter_channels(img)
+        img = img.resize(self.image_size)
+        return img, annotation
+
+    @staticmethod
+    def normalize_image(img, normalize=False, percentiles=(1, 99)):
+        img_array = np.array(img)
+
+        if normalize:
+            if img_array.ndim == 2:  # Grayscale image
+                p2, p98 = np.percentile(img_array, percentiles)
+                img_array = rescale_intensity(img_array, in_range=(p2, p98), out_range=(0, 255))
+            else:  # Color image or multi-channel image
+                for channel in range(img_array.shape[2]):
+                    p2, p98 = np.percentile(img_array[:, :, channel], percentiles)
+                    img_array[:, :, channel] = rescale_intensity(img_array[:, :, channel], in_range=(p2, p98), out_range=(0, 255))
+
+        img_array = np.clip(img_array, 0, 255).astype('uint8')
+
+        return Image.fromarray(img_array)
+    
+    def add_colored_border(self, img, border_width, border_color):
+        top_border = Image.new('RGB', (img.width, border_width), color=border_color)
+        bottom_border = Image.new('RGB', (img.width, border_width), color=border_color)
+        left_border = Image.new('RGB', (border_width, img.height), color=border_color)
+        right_border = Image.new('RGB', (border_width, img.height), color=border_color)
+
+        bordered_img = Image.new('RGB', (img.width + 2 * border_width, img.height + 2 * border_width), color='white')
+        bordered_img.paste(top_border, (border_width, 0))
+        bordered_img.paste(bottom_border, (border_width, img.height + border_width))
+        bordered_img.paste(left_border, (0, border_width))
+        bordered_img.paste(right_border, (img.width + border_width, border_width))
+        bordered_img.paste(img, (border_width, border_width))
+
+        return bordered_img
+    
+    def filter_channels(self, img):
+        r, g, b = img.split()
+        if self.channels:
+            if 'r' not in self.channels:
+                r = r.point(lambda _: 0)
+            if 'g' not in self.channels:
+                g = g.point(lambda _: 0)
+            if 'b' not in self.channels:
+                b = b.point(lambda _: 0)
+
+            if len(self.channels) == 1:
+                channel_img = r if 'r' in self.channels else (g if 'g' in self.channels else b)
+                return ImageOps.grayscale(channel_img)
+
+        return Image.merge("RGB", (r, g, b))
+
+    def get_on_image_click(self, path, label, img):
+        def on_image_click(event):
+            new_annotation = 1 if event.num == 1 else (2 if event.num == 3 else None)
+            
+            original_path = self.adjusted_to_original_paths.get(path, path)
+            
+            if original_path in self.pending_updates and self.pending_updates[original_path] == new_annotation:
+                self.pending_updates[original_path] = None
+                new_annotation = None
+            else:
+                self.pending_updates[original_path] = new_annotation
+            
+            print(f"Image {os.path.split(path)[1]} annotated: {new_annotation}")
+            
+            img_ = img.crop((5, 5, img.width-5, img.height-5))
+            border_fill = 'teal' if new_annotation == 1 else ('red' if new_annotation == 2 else None)
+            img_ = ImageOps.expand(img_, border=5, fill=border_fill) if border_fill else img_
+
+            photo = ImageTk.PhotoImage(img_)
+            self.images[label] = photo
+            label.config(image=photo)
+            self.root.update()
+
+        return on_image_click
+
+    @staticmethod
+    def update_html(text):
+        display(HTML(f"""
+        <script>
+        document.getElementById('unique_id').innerHTML = '{text}';
+        </script>
+        """))
+
+    def update_database_worker(self):
+        conn = sqlite3.connect(self.db_path)
+        c = conn.cursor()
+
+        display(HTML("<div id='unique_id'>Initial Text</div>"))
+
+        while True:
+            if self.terminate:
+                conn.close()
+                break
+
+            if not self.update_queue.empty():
+                ImageApp.update_html("Do not exit, Updating database...")
+                self.status_label.config(text='Do not exit, Updating database...')
+
+                pending_updates = self.update_queue.get()
+                for path, new_annotation in pending_updates.items():
+                    if new_annotation is None:
+                        c.execute(f'UPDATE png_list SET {self.annotation_column} = NULL WHERE png_path = ?', (path,))
+                    else:
+                        c.execute(f'UPDATE png_list SET {self.annotation_column} = ? WHERE png_path = ?', (new_annotation, path))
+                conn.commit()
+
+                ImageApp.update_html('')
+                self.status_label.config(text='')
+                self.root.update()
+            time.sleep(0.1)
+
+    def update_gui_text(self, text):
+        self.status_label.config(text=text)
+        self.root.update()
+
+    def next_page(self):
+        if self.pending_updates:
+            self.update_queue.put(self.pending_updates.copy())
+        self.pending_updates.clear()
+        self.index += self.grid_rows * self.grid_cols
+        self.load_images()
+
+    def previous_page(self):
+        if self.pending_updates:
+            self.update_queue.put(self.pending_updates.copy())
+        self.pending_updates.clear()
+        self.index -= self.grid_rows * self.grid_cols
+        if self.index < 0:
+            self.index = 0
+        self.load_images()
+
+    def shutdown(self):
+        self.terminate = True
+        self.update_queue.put(self.pending_updates.copy())
+        self.pending_updates.clear()
+        self.db_update_thread.join()
+        self.root.quit()
+        self.root.destroy()
+        print(f'Quit application')
+
 def create_menu_bar(root):
-    from .app_annotate import initiate_annotation_app_root
-    from .app_make_masks import initiate_mask_app_root
     from .gui_utils import load_app
+    from .gui_core import initiate_root
 
     gui_apps = {
-        "Mask": 'mask',
-        "Measure": 'measure',
-        "Annotate": initiate_annotation_app_root,
-        "Make Masks": initiate_mask_app_root,
-        "Classify": 'classify',
-        "Sequencing": 'sequencing',
-        "Umap": 'umap'
+        "Main": (lambda frame: initiate_root(frame, None), "Main GUI window."),
+        "Mask": (lambda frame: initiate_root(frame, 'mask'), "Generate cellpose masks for cells, nuclei and pathogen images."),
+        "Measure": (lambda frame: initiate_root(frame, 'measure'), "Measure single object intensity and morphological feature. Crop and save single object image"),
+        "Annotate": (lambda frame: initiate_root(frame, 'annotate'), "Annotation single object images on a grid. Annotations are saved to database."),
+        "Make Masks": (lambda frame: initiate_root(frame, 'make_masks'), "Adjust pre-existing Cellpose models to your specific dataset for improved performance"),
+        "Classify": (lambda frame: initiate_root(frame, 'classify'), "Train Torch Convolutional Neural Networks (CNNs) or Transformers to classify single object images."),
+        "Sequencing": (lambda frame: initiate_root(frame, 'sequencing'), "Analyze sequencing data."),
+        "Umap": (lambda frame: initiate_root(frame, 'umap'), "Generate UMAP embeddings with datapoints represented as images.")
     }
 
     def load_app_wrapper(app_name, app_func):
@@ -285,7 +1452,8 @@ def create_menu_bar(root):
     app_menu = tk.Menu(menu_bar, tearoff=0, bg="#008080", fg="white")
     menu_bar.add_cascade(label="SpaCr Applications", menu=app_menu)
     # Add options to the "SpaCr Applications" menu
-    for app_name, app_func in gui_apps.items():
+    for app_name, app_data in gui_apps.items():
+        app_func, app_desc = app_data
         app_menu.add_command(label=app_name, command=lambda app_name=app_name, app_func=app_func: load_app_wrapper(app_name, app_func))
     # Add a separator and an exit option
     app_menu.add_separator()
@@ -296,8 +1464,8 @@ def create_menu_bar(root):
 def set_dark_style(style):
     font_style = tkFont.Font(family="Helvetica", size=24)
     style.configure('TEntry', padding='5 5 5 5', borderwidth=1, relief='solid', fieldbackground='black', foreground='#ffffff', font=font_style)
-    style.configure('TCombobox', fieldbackground='black', background='black', foreground='#ffffff', font=font_style)
-    style.map('TCombobox', fieldbackground=[('readonly', 'black')], foreground=[('readonly', '#ffffff')])
+    style.configure('TCombobox', fieldbackground='black', background='black', foreground='#ffffff', selectbackground='black', selectforeground='#ffffff', font=font_style)
+    style.map('TCombobox', fieldbackground=[('readonly', 'black')], foreground=[('readonly', '#ffffff')], selectbackground=[('readonly', 'black')], selectforeground=[('readonly', '#ffffff')])
     style.configure('Custom.TButton', background='black', foreground='white', bordercolor='white', focusthickness=3, focuscolor='white', font=('Helvetica', 12))
     style.map('Custom.TButton', background=[('active', 'teal'), ('!active', 'black')], foreground=[('active', 'white'), ('!active', 'white')], bordercolor=[('active', 'white'), ('!active', 'white')])
     style.configure('Custom.TLabel', padding='5 5 5 5', borderwidth=1, relief='flat', background='black', foreground='#ffffff', font=font_style)