spacr 0.0.36__py3-none-any.whl → 0.0.61__py3-none-any.whl

spacr/gui.py

@@ -1,5 +1,6 @@
 import tkinter as tk
 from tkinter import ttk
+from tkinter import font as tkFont
 from PIL import Image, ImageTk
 import os
 import requests
@@ -17,7 +18,7 @@ class MainApp(tk.Tk):
     def __init__(self):
         super().__init__()
         self.title("SpaCr GUI Collection")
-        self.geometry("1200x350")
+        self.geometry("1100x1500")
         self.configure(bg="black")
         #self.attributes('-fullscreen', True)
 
@@ -58,24 +59,24 @@ class MainApp(tk.Tk):
 
         # Load the logo image
         if not self.load_logo(logo_frame):
-            tk.Label(logo_frame, text="Logo not found", bg="black", fg="white", font=('Open Sans', 24)).pack(padx=20, pady=20)
+            tk.Label(logo_frame, text="Logo not found", bg="black", fg="white", font=('Arial', 24, tkFont.NORMAL)).pack(padx=10, pady=10)
 
         # Add SpaCr text below the logo with padding for sharper text
-        tk.Label(logo_frame, text="SpaCr", bg="black", fg="#008080", font=('Open Sans', 24)).pack(padx=20, pady=20)
+        tk.Label(logo_frame, text="SpaCr", bg="black", fg="#008080", font=('Arial', 24, tkFont.NORMAL)).pack(padx=10, pady=10)
 
         # Create a frame for the buttons and descriptions
         buttons_frame = tk.Frame(self.content_frame, bg="black")
-        buttons_frame.pack(pady=20, expand=True, padx=20)
+        buttons_frame.pack(pady=10, expand=True, padx=10)
 
         for i, (app_name, app_data) in enumerate(self.gui_apps.items()):
             app_func, app_desc = app_data
 
             # Create custom button with text
             button = CustomButton(buttons_frame, text=app_name, command=lambda app_name=app_name: self.load_app(app_name))
-            button.grid(row=i, column=0, pady=20, padx=20, sticky="w")
+            button.grid(row=i, column=0, pady=10, padx=10, sticky="w")
 
-            description_label = tk.Label(buttons_frame, text=app_desc, bg="black", fg="white", wraplength=800, justify="left", font=('Open Sans', 12))
-            description_label.grid(row=i, column=1, pady=20, padx=20, sticky="w")
+            description_label = tk.Label(buttons_frame, text=app_desc, bg="black", fg="white", wraplength=800, justify="left", font=('Arial', 10, tkFont.NORMAL))
+            description_label.grid(row=i, column=1, pady=10, padx=10, sticky="w")
 
         # Ensure buttons have a fixed width
         buttons_frame.grid_columnconfigure(0, minsize=150)
@@ -141,4 +142,4 @@ def gui_app():
     app.mainloop()
 
 if __name__ == "__main__":
-    gui_app()
+    gui_app()

spacr/gui_2.py

@@ -0,0 +1,90 @@
+import customtkinter as ctk
+from PIL import Image, ImageTk
+import os
+import requests
+
+class MainApp(ctk.CTk):
+    def __init__(self):
+        super().__init__()
+        self.title("SpaCr GUI Collection")
+        self.geometry("1200x800")
+        ctk.set_appearance_mode("dark")  # Modes: "System" (standard), "Dark", "Light"
+        ctk.set_default_color_theme("dark-blue")  # Themes: "blue" (standard), "green", "dark-blue")
+        
+        # Set scaling factor for high DPI displays; use a floating-point value.
+        self.tk.call('tk', 'scaling', 1.5)
+        
+        self.create_widgets()
+
+    def create_widgets(self):
+        self.content_frame = ctk.CTkFrame(self)
+        self.content_frame.pack(fill="both", expand=True, padx=20, pady=20)
+
+        logo_frame = ctk.CTkFrame(self.content_frame)
+        logo_frame.pack(pady=20, expand=True)
+
+        if not self.load_logo(logo_frame):
+            ctk.CTkLabel(logo_frame, text="Logo not found", text_color="white", font=('Helvetica', 24)).pack(padx=10, pady=10)
+
+        ctk.CTkLabel(logo_frame, text="SpaCr", text_color="#00BFFF", font=('Helvetica', 36, "bold")).pack(padx=10, pady=10)
+
+        button = ctk.CTkButton(
+            self.content_frame,
+            text="Mask",
+            command=self.load_mask_app,
+            width=250,
+            height=60,
+            corner_radius=20,
+            fg_color="#1E90FF",
+            hover_color="#4682B4",
+            text_color="white",
+            font=("Helvetica", 18, "bold")
+        )
+        button.pack(pady=20)
+
+    def load_logo(self, frame):
+        def download_image(url, save_path):
+            try:
+                response = requests.get(url, stream=True)
+                response.raise_for_status()
+                with open(save_path, 'wb') as f:
+                    for chunk in response.iter_content(chunk_size=8192):
+                        f.write(chunk)
+                return True
+            except requests.exceptions.RequestException as e:
+                print(f"Failed to download image from {url}: {e}")
+                return False
+
+        try:
+            img_path = os.path.join(os.path.dirname(__file__), 'logo_spacr.png')
+            logo_image = Image.open(img_path)
+        except (FileNotFoundError, Image.UnidentifiedImageError):
+            if download_image('https://raw.githubusercontent.com/EinarOlafsson/spacr/main/spacr/logo_spacr.png', img_path):
+                try:
+                    logo_image = Image.open(img_path)
+                except Image.UnidentifiedImageError as e:
+                    return False
+            else:
+                return False
+        except Exception as e:
+            return False
+
+        try:
+            logo_image = logo_image.resize((200, 200), Image.Resampling.LANCZOS)
+            logo_photo = ImageTk.PhotoImage(logo_image)
+            logo_label = ctk.CTkLabel(frame, image=logo_photo)
+            logo_label.image = logo_photo  # Keep a reference to avoid garbage collection
+            logo_label.pack()
+            return True
+        except Exception as e:
+            return False
+
+    def load_mask_app(self):
+        print("Mask app loaded.")  # Placeholder for mask app loading function
+
+def gui_app():
+    app = MainApp()
+    app.mainloop()
+
+if __name__ == "__main__":
+    gui_app()

spacr/gui_classify_app.py

@@ -1,7 +1,6 @@
-import sys, ctypes, csv, matplotlib
+import sys, ctypes, matplotlib
 import tkinter as tk
 from tkinter import ttk, scrolledtext
-from ttkthemes import ThemedTk
 from matplotlib.figure import Figure
 from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
 from matplotlib.figure import Figure
@@ -70,13 +69,13 @@ def import_settings(scrollable_frame):
     vars_dict = generate_fields(new_settings, scrollable_frame)
 
 #@log_function_call
-def initiate_classify_root(parent_frame, width, height):
+def initiate_classify_root(parent_frame):#, width, height):
     global vars_dict, q, canvas, fig_queue, canvas_widget, thread_control
     
     style = ttk.Style(parent_frame)
     set_dark_style(style)
     style_text_boxes(style)
-    set_default_font(parent_frame, font_name="Open Sans", size=8)
+    set_default_font(parent_frame, font_name="Arial", size=8)
 
     parent_frame.configure(bg='#333333')
     parent_frame.grid_rowconfigure(0, weight=1)

spacr/gui_mask_app.py

@@ -1,7 +1,8 @@
+#import customtkinter as ctk
+
 import sys, ctypes, matplotlib
 import tkinter as tk
 from tkinter import ttk, scrolledtext
-from ttkthemes import ThemedTk
 from matplotlib.figure import Figure
 from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
 matplotlib.use('Agg')
@@ -15,7 +16,7 @@ except AttributeError:
     pass
 
 from .logger import log_function_call
-from .gui_utils import ScrollableFrame, StdoutRedirector, ToggleSwitch, CustomButton
+from .gui_utils import ScrollableFrame, StdoutRedirector, ToggleSwitch, CustomButton, ToolTip
 from .gui_utils import clear_canvas, main_thread_update_function, set_dark_style, generate_fields, process_stdout_stderr, set_default_font, style_text_boxes
 from .gui_utils import mask_variables, check_mask_gui_settings, preprocess_generate_masks_wrapper, read_settings_from_csv, update_settings_from_csv, create_menu_bar
 
@@ -102,7 +103,7 @@ def initiate_mask_root(parent_frame, width, height):
     style = ttk.Style(parent_frame)
     set_dark_style(style)
     style_text_boxes(style)
-    set_default_font(parent_frame, font_name="Open Sans", size=8)
+    set_default_font(parent_frame, font_name="Arial", size=8)
     parent_frame.configure(bg='black')
     parent_frame.grid_rowconfigure(0, weight=1)
     parent_frame.grid_columnconfigure(0, weight=1)
@@ -165,12 +166,12 @@ def initiate_mask_root(parent_frame, width, height):
     # Button section
     test_mode_button = CustomButton(scrollable_frame.scrollable_frame, text="Test Mode", command=toggle_test_mode)
     test_mode_button.grid(row=47, column=1, pady=10, padx=10)
-    import_btn = CustomButton(scrollable_frame.scrollable_frame, text="Import Settings", command=lambda: import_settings(scrollable_frame))
-    import_btn.grid(row=47, column=0, pady=20, padx=20)
+    import_btn = CustomButton(scrollable_frame.scrollable_frame, text="Import", command=lambda: import_settings(scrollable_frame))
+    import_btn.grid(row=47, column=0, pady=10, padx=10)
     run_button = CustomButton(scrollable_frame.scrollable_frame, text="Run", command=lambda: start_process(q, fig_queue))
-    run_button.grid(row=45, column=0, pady=20, padx=20)
+    run_button.grid(row=45, column=0, pady=10, padx=10)
     abort_button = CustomButton(scrollable_frame.scrollable_frame, text="Abort", command=initiate_abort)
-    abort_button.grid(row=45, column=1, pady=20, padx=20)
+    abort_button.grid(row=45, column=1, pady=10, padx=10)
     progress_label = ttk.Label(scrollable_frame.scrollable_frame, text="Processing: 0%", background="black", foreground="white") # Create progress field
     progress_label.grid(row=50, column=0, columnspan=2, sticky="ew", pady=(5, 0), padx=10)
 
@@ -218,5 +219,4 @@ def gui_mask():
     root.mainloop()
 
 if __name__ == "__main__":
-    gui_mask()
-
+    gui_mask()

spacr/gui_measure_app.py

@@ -3,10 +3,8 @@ import tkinter as tk
 from tkinter import ttk, scrolledtext
 from matplotlib.figure import Figure
 from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
-import matplotlib.pyplot as plt
 matplotlib.use('Agg')  # Use the non-GUI Agg backend
 from multiprocessing import Process, Queue, Value
-from ttkthemes import ThemedTk
 from tkinter import filedialog
 
 try:
@@ -15,7 +13,7 @@ except AttributeError:
     pass
 
 from .logger import log_function_call
-from .gui_utils import ScrollableFrame, StdoutRedirector, CustomButton, ToggleSwitch
+from .gui_utils import ScrollableFrame, StdoutRedirector, CustomButton, ToggleSwitch, ToolTip
 from .gui_utils import process_stdout_stderr, set_dark_style, set_default_font, generate_fields, main_thread_update_function, create_menu_bar
 from .gui_utils import measure_variables, measure_crop_wrapper, clear_canvas, check_measure_gui_settings, read_settings_from_csv, update_settings_from_csv, style_text_boxes
 
@@ -98,13 +96,13 @@ def import_settings(scrollable_frame):
     vars_dict = generate_fields(new_settings, scrollable_frame)
 
 #@log_function_call
-def initiate_measure_root(parent_frame, width, height):
+def initiate_measure_root(parent_frame):#, width, height):
     global vars_dict, q, canvas, fig_queue, canvas_widget, thread_control, variables, advanced_var, scrollable_frame
     
     style = ttk.Style(parent_frame)
     set_dark_style(style)
     style_text_boxes(style)
-    set_default_font(parent_frame, font_name="Open Sans", size=8)
+    set_default_font(parent_frame, font_name="Arial", size=8)
 
     parent_frame.configure(bg='black')
     parent_frame.grid_rowconfigure(0, weight=1)

spacr/gui_utils.py

@@ -6,6 +6,10 @@ import tkinter as tk
 from tkinter import ttk, messagebox
 import tkinter.font as tkFont
 from torchvision import models
+#from ttf_opensans import opensans
+
+from tkinter import font as tkFont
+
 
 from .logger import log_function_call
 
@@ -14,6 +18,29 @@ try:
 except AttributeError:
     pass
 
+class ToolTip:
+    def __init__(self, widget, text):
+        self.widget = widget
+        self.text = text
+        self.tooltip_window = None
+        widget.bind("<Enter>", self.show_tooltip)
+        widget.bind("<Leave>", self.hide_tooltip)
+
+    def show_tooltip(self, event):
+        x = event.x_root + 20
+        y = event.y_root + 10
+        self.tooltip_window = tk.Toplevel(self.widget)
+        self.tooltip_window.wm_overrideredirect(True)
+        self.tooltip_window.wm_geometry(f"+{x}+{y}")
+        label = tk.Label(self.tooltip_window, text=self.text, background="yellow", relief='solid', borderwidth=1)
+        label.pack()
+
+    def hide_tooltip(self, event):
+        if self.tooltip_window:
+            self.tooltip_window.destroy()
+        self.tooltip_window = None
+
+
 def load_app(root, app_name, app_func):
     # Destroy the current window
     root.destroy()
@@ -61,18 +88,14 @@ class CustomButton(tk.Frame):
         self.text = text
         self.command = command
 
-        self.canvas = tk.Canvas(self, width=200, height=50, highlightthickness=0, bg="black")
+        self.canvas = tk.Canvas(self, width=150, height=50, highlightthickness=0, bg="black")
         self.canvas.grid(row=0, column=0)
 
-        self.button_bg = self.create_rounded_rectangle(0, 0, 200, 50, radius=20, fill="#800080")
-
-        # Load the Open Sans font
-        self.font_path = 'fonts/OpenSans-Regular.ttf'
-        if not os.path.exists(self.font_path):
-            self.download_font()
+        self.button_bg = self.create_rounded_rectangle(0, 0, 150, 50, radius=20, fill="#800080")
 
-        self.open_sans = tkFont.Font(family="Open Sans", size=10)
-        self.button_text = self.canvas.create_text(100, 25, text=self.text, fill="white", font=self.open_sans)
+        # Create a Tkinter font object using OpenSans
+        self.font_style = tkFont.Font(family="Arial", size=12, weight=tkFont.NORMAL)
+        self.button_text = self.canvas.create_text(75, 25, text=self.text, fill="white", font=self.font_style)
 
         self.bind("<Enter>", self.on_enter)
         self.bind("<Leave>", self.on_leave)
@@ -114,7 +137,7 @@ class CustomButton(tk.Frame):
                   x1, y1]
 
         return self.canvas.create_polygon(points, **kwargs, smooth=True)
-
+    
 class ToggleSwitch(ttk.Frame):
     def __init__(self, parent, text="", variable=None, command=None, *args, **kwargs):
         super().__init__(parent, *args, **kwargs)
@@ -203,7 +226,7 @@ class ToggleSwitch(ttk.Frame):
 
         return self.canvas.create_polygon(points, **kwargs, smooth=True)
     
-def set_default_font(root, font_name="Helvetica", size=12):
+def set_default_font(root, font_name="Arial", size=12):
     default_font = (font_name, size)
     root.option_add("*Font", default_font)
     root.option_add("*TButton.Font", default_font)
@@ -211,7 +234,7 @@ def set_default_font(root, font_name="Helvetica", size=12):
     root.option_add("*TEntry.Font", default_font)
 
 def check_and_download_font():
-    font_name = "Open Sans"
+    font_name = "Arial"
     font_dir = "fonts"
     font_path = os.path.join(font_dir, "OpenSans-Regular.ttf")
 
@@ -234,36 +257,25 @@ def check_and_download_font():
             tkFont.nametofont("TkTextFont").configure(family=font_name, size=10)
             tkFont.nametofont("TkHeadingFont").configure(family=font_name, size=12)
         except tk.TclError:
-            tkFont.nametofont("TkDefaultFont").configure(family="Open Sans", size=10)
-            tkFont.nametofont("TkTextFont").configure(family="Open Sans", size=10)
-            tkFont.nametofont("TkHeadingFont").configure(family="Open Sans", size=12)
+            tkFont.nametofont("TkDefaultFont").configure(family="Arial", size=10)
+            tkFont.nametofont("TkTextFont").configure(family="Arial", size=10)
+            tkFont.nametofont("TkHeadingFont").configure(family="Arial", size=12)
     else:
         tkFont.nametofont("TkDefaultFont").configure(family=font_name, size=10)
         tkFont.nametofont("TkTextFont").configure(family=font_name, size=10)
         tkFont.nametofont("TkHeadingFont").configure(family=font_name, size=12)
 
-def style_text_boxes_v1(style):
-    style.configure('TEntry', padding='5 5 5 5', borderwidth=1, relief='solid', fieldbackground='#000000', foreground='#ffffff')
-    style.configure('TCombobox', fieldbackground='#000000', background='#000000', foreground='#ffffff')
-    style.configure('Custom.TButton', padding='10 10 10 10', borderwidth=1, relief='solid', background='#008080', foreground='#ffffff', font=('Open Sans', 10, 'bold'))
-    style.map('Custom.TButton',
-              background=[('active', '#66b2b2'), ('disabled', '#004d4d'), ('!disabled', '#008080')],
-              foreground=[('active', '#ffffff'), ('disabled', '#888888')])
-    style.configure('Custom.TLabel', padding='5 5 5 5', borderwidth=1, relief='flat', background='#000000', foreground='#ffffff', font=('Open Sans', 10))
-    style.configure('TCheckbutton', background='#333333', foreground='#ffffff', indicatoron=False, relief='flat')
-    style.map('TCheckbutton', background=[('selected', '#555555'), ('active', '#555555')])
-
 def style_text_boxes(style):
     check_and_download_font()
-    open_sans = tkFont.Font(family="Open Sans", size=10)  # Define the Open Sans font
-    style.configure('TEntry', padding='5 5 5 5', borderwidth=1, relief='solid', fieldbackground='#000000', foreground='#ffffff', font=open_sans)
-    style.configure('TCombobox', fieldbackground='#000000', background='#000000', foreground='#ffffff', font=open_sans)
-    style.configure('Custom.TButton', padding='10 10 10 10', borderwidth=1, relief='solid', background='#008080', foreground='#ffffff', font=open_sans)
+    font_style = tkFont.Font(family="Arial", size=10)  # Define the Arial font
+    style.configure('TEntry', padding='5 5 5 5', borderwidth=1, relief='solid', fieldbackground='#000000', foreground='#ffffff', font=font_style)
+    style.configure('TCombobox', fieldbackground='#000000', background='#000000', foreground='#ffffff', font=font_style)
+    style.configure('Custom.TButton', padding='10 10 10 10', borderwidth=1, relief='solid', background='#008080', foreground='#ffffff', font=font_style)
     style.map('Custom.TButton',
               background=[('active', '#66b2b2'), ('disabled', '#004d4d'), ('!disabled', '#008080')],
               foreground=[('active', '#ffffff'), ('disabled', '#888888')])
-    style.configure('Custom.TLabel', padding='5 5 5 5', borderwidth=1, relief='flat', background='#000000', foreground='#ffffff', font=open_sans)
-    style.configure('TCheckbutton', background='#333333', foreground='#ffffff', indicatoron=False, relief='flat', font=open_sans)
+    style.configure('Custom.TLabel', padding='5 5 5 5', borderwidth=1, relief='flat', background='#000000', foreground='#ffffff', font=font_style)
+    style.configure('TCheckbutton', background='#333333', foreground='#ffffff', indicatoron=False, relief='flat', font=font_style)
     style.map('TCheckbutton', background=[('selected', '#555555'), ('active', '#555555')])
 
 
@@ -701,11 +713,98 @@ def add_mask_gui_defaults(settings):
 def generate_fields(variables, scrollable_frame):
     vars_dict = {}
     row = 0
+    tooltips = {
+        "src": "Path to the folder containing the images.",
+        "metadata_type": "Type of metadata to expect in the images. This will determine how the images are processed. If 'custom' is selected, you can provide a custom regex pattern to extract metadata from the image names",
+        "custom_regex": "Custom regex pattern to extract metadata from the image names. This will only be used if 'custom' is selected for 'metadata_type'.",
+        "experiment": "Name of the experiment. This will be used to name the output files.",
+        "channels": "List of channels to use for the analysis. The first channel is 0, the second is 1, and so on. For example, [0,1,2] will use channels 0, 1, and 2.",
+        "magnification": "At what magnification the images were taken. This will be used to determine the size of the objects in the images.",
+        "nucleus_channel": "The channel to use for the nucleus. If None, the nucleus will not be segmented.",
+        "nucleus_background": "The background intensity for the nucleus channel. This will be used to remove background noise.",
+        "nucleus_Signal_to_noise": "The signal-to-noise ratio for the nucleus channel. This will be used to determine the range of intensities to normalize images to for nucleus segmentation.",
+        "nucleus_CP_prob": "The cellpose probability threshold for the nucleus channel. This will be used to segment the nucleus.",
+        "cell_channel": "The channel to use for the cell. If None, the cell will not be segmented.",
+        "cell_background": "The background intensity for the cell channel. This will be used to remove background noise.",
+        "cell_Signal_to_noise": "The signal-to-noise ratio for the cell channel. This will be used to determine the range of intensities to normalize images to for cell segmentation.",
+        "cell_CP_prob": "The cellpose probability threshold for the cell channel. This will be used to segment the cell.",
+        "pathogen_channel": "The channel to use for the pathogen. If None, the pathogen will not be segmented.",
+        "pathogen_background": "The background intensity for the pathogen channel. This will be used to remove background noise.",
+        "pathogen_Signal_to_noise": "The signal-to-noise ratio for the pathogen channel. This will be used to determine the range of intensities to normalize images to for pathogen segmentation.",
+        "pathogen_CP_prob": "The cellpose probability threshold for the pathogen channel. This will be used to segment the pathogen.",
+        "preprocess": "Whether to preprocess the images before segmentation. This includes background removal and normalization. Set to False only if this step has already been done.",
+        "masks": "Whether to generate masks for the segmented objects. If True, masks will be generated for the nucleus, cell, and pathogen.",
+        "examples_to_plot": "The number of images to plot for each segmented object. This will be used to visually inspect the segmentation results and normalization .",
+        "randomize": "Whether to randomize the order of the images before processing. Recommended to avoid bias in the segmentation.",
+        "batch_size": "The batch size to use for processing the images. This will determine how many images are processed at once. Images are normalized and segmented in batches. Lower if application runs out of RAM or VRAM.",
+        "timelapse": "Whether to process the images as a timelapse.",
+        "timelapse_displacement": "The displacement between frames in the timelapse. This will be used to align the frames before processing.",
+        "timelapse_memory": "The number of frames to in tandem objects must be present in to be considered the same object in the timelapse.",
+        "timelapse_frame_limits": "The frame limits to use for the timelapse. This will determine which frames are processed. For example, [5,20] will process frames 5 to 20.",
+        "timelapse_remove_transient": "Whether to remove transient objects in the timelapse. Transient objects are present in fewer than all frames.",
+        "timelapse_mode": "The mode to use for processing the timelapse. 'trackpy' uses the trackpy library for tracking objects, while 'btrack' uses the btrack library.",
+        "timelapse_objects": "The objects to track in the timelapse (cell, nucleus or pathogen). This will determine which objects are tracked over time. If None, all objects will be tracked.",
+        "fps": "Frames per second of the automatically generated timelapse movies.",
+        "remove_background": "Whether to remove background noise from the images. This will help improve the quality of the segmentation.",
+        "lower_quantile": "The lower quantile to use for normalizing the images. This will be used to determine the range of intensities to normalize images to.",
+        "merge_pathogens": "Whether to merge pathogen objects that share more than 75% of their perimiter.",
+        "normalize_plots": "Whether to normalize the plots.",
+        "all_to_mip": "Whether to convert all images to maximum intensity projections before processing.",
+        "pick_slice": "Whether to pick a single slice from the z-stack images. If False, the maximum intensity projection will be used.",
+        "skip_mode": "The mode to use for skipping images. This will determine how to handle images that cannot be processed.",
+        "save": "Whether to save the results to disk.",
+        "plot": "Whether to plot the results.",
+        "workers": "The number of workers to use for processing the images. This will determine how many images are processed in parallel. Increase to speed up processing.",
+        "verbose": "Whether to print verbose output during processing.",
+        "input_folder": "Path to the folder containing the images.",
+        "cell_mask_dim": "The dimension of the array the cell mask is saved in.",
+        "cell_min_size": "The minimum size of cell objects in pixels2.",
+        "cytoplasm_min_size": "The minimum size of cytoplasm objects in pixels2.",
+        "nucleus_mask_dim": "The dimension of the array the nucleus mask is saved in.",
+        "nucleus_min_size": "The minimum size of nucleus objects in pixels2.",
+        "pathogen_mask_dim": "The dimension of the array the pathogen mask is saved in.",
+        "pathogen_min_size": "The minimum size of pathogen objects in pixels2.",
+        "save_png": "Whether to save the segmented objects as PNG images.",
+        "crop_mode": "The mode to use for cropping the images. This will determine which objects are cropped from the images (cell, nucleus, pathogen, cytoplasm).",
+        "use_bounding_box": "Whether to use the bounding box of the objects for cropping. If False, only the object itself will be cropped.",
+        "png_size": "The size of the PNG images to save. This will determine the size of the saved images.",
+        "normalize": "The percentiles to use for normalizing the images. This will be used to determine the range of intensities to normalize images to., if None, no normalization is done.",
+        "png_dims": "The dimensions of the PNG images to save. This will determine the dimensions of the saved images. Maximum of 3 dimensions e.g. [1,2,3].",
+        "normalize_by": "Whether to normalize the images by field of view (fov) or by PNG image (png).",
+        "save_measurements": "Whether to save the measurements to disk.",
+        "representative_images": "Whether to save representative images of the segmented objects (Not working yet).",
+        "plot": "Whether to plot results.",
+        "plot_filtration": "Whether to plot the filtration steps.",
+        "include_uninfected": "Whether to include uninfected cells in the analysis.",
+        "dialate_pngs": "Whether to dialate the PNG images before saving.",
+        "dialate_png_ratios": "The ratios to use for dialating the PNG images. This will determine the amount of dialation applied to the images before cropping.",
+        "timelapse_objects": "The objects to track in the timelapse (cell, nucleus or pathogen). This will determine which objects are tracked over time. If None, all objects will be tracked.",
+        "max_workers": "The number of workers to use for processing the images. This will determine how many images are processed in parallel. Increase to speed up processing.",
+        "cells: ": "The cell types to include in the analysis.",
+        "cell_loc": "The locations of the cell types in the images.",
+        "pathogens": "The pathogen types to include in the analysis.",
+        "pathogen_loc": "The locations of the pathogen types in the images.",
+        "treatments": "The treatments to include in the analysis.",
+        "treatment_loc": "The locations of the treatments in the images.",
+        "channel_of_interest": "The channel of interest to use for the analysis.",
+        "compartments": "The compartments to measure in the images.",
+        "measurement": "The measurement to use for the analysis.",
+        "nr_imgs": "The number of images to plot.",
+        "um_per_pixel": "The micrometers per pixel for the images.",
+    }
+
     for key, (var_type, options, default_value) in variables.items():
         label, widget, var = create_input_field(scrollable_frame.scrollable_frame, key, row, var_type, options, default_value)
         vars_dict[key] = (label, widget, var)  # Store the label, widget, and variable
+        
+        # Add tooltip to the label if it exists in the tooltips dictionary
+        if key in tooltips:
+            ToolTip(label, tooltips[key])
+        
         row += 1
     return vars_dict
+
+
     
 class TextRedirector(object):
     def __init__(self, widget, queue):
@@ -735,7 +834,7 @@ def create_dark_mode(root, style, console_output):
     style.map('TCombobox', fieldbackground=[('readonly', input_bg)], selectbackground=[('readonly', input_bg)], foreground=[('readonly', dark_text)])
     
     if console_output != None:
-        console_output.config(bg=dark_bg, fg=light_text, insertbackground=light_text) #, font=("Open Sans", 12)
+        console_output.config(bg=dark_bg, fg=light_text, insertbackground=light_text) #, font=("Arial", 12)
     root.configure(bg=dark_bg)
     
 def set_dark_style(style):