diff --git a/src/navigate/controller/configurator.py b/src/navigate/controller/configurator.py
index 8231510e1..10385c96c 100644
--- a/src/navigate/controller/configurator.py
+++ b/src/navigate/controller/configurator.py
@@ -33,6 +33,7 @@
 import tkinter as tk
 from time import sleep
 from tkinter import filedialog, messagebox
+from typing import Optional
 
 # Third Party Imports
 
@@ -87,22 +88,17 @@ def __init__(self, root: tk.Tk, splash_screen):
         self.microscope_id = 0
         self.create_config_window(0)
 
-        print(
-            "WARNING: The Configuration Assistant is not fully implemented. "
-            "Users are still required to manually configure their system."
-        )
-
-    def on_cancel(self):
+    def on_cancel(self) -> None:
         """Closes the window and exits the program"""
         self.root.destroy()
         exit()
 
-    def add_microscope(self):
+    def add_microscope(self) -> None:
         """Add a new microscope tab"""
         self.microscope_id += 1
         self.create_config_window(self.microscope_id)
 
-    def delete_microscopes(self):
+    def delete_microscopes(self) -> None:
         """Delete all microscopes"""
         # delete microscopes
         for tab_id in self.view.microscope_window.tabs():
@@ -110,12 +106,12 @@ def delete_microscopes(self):
         self.view.microscope_window.tab_list = []
         self.microscope_id = 0
 
-    def new_configuration(self):
+    def new_configuration(self) -> None:
         """Create new configurations"""
         self.delete_microscopes()
         self.create_config_window(self.microscope_id)
 
-    def save(self):
+    def save(self) -> None:
         """Save configuration file"""
 
         def set_value(temp_dict, key_list, value):
@@ -225,7 +221,7 @@ def set_value(temp_dict, key_list, value):
                 f". Please double check!",
             )
 
-    def write_to_yaml(self, config, filename):
+    def write_to_yaml(self, config: dict, filename: str) -> None:
         """write yaml file
 
         Parameters
@@ -256,8 +252,14 @@ def write_func(prefix, config_dict, f):
             f.write("microscopes:\n")
             write_func("  ", config, f)
 
-    def create_config_window(self, id):
-        """Creates the configuration window tabs."""
+    def create_config_window(self, id: int) -> None:
+        """Creates the configuration window tabs.
+
+        Parameters
+        ----------
+        id : int
+            The id of the microscope
+        """
 
         tab_name = "Microscope-" + str(id)
         microscope_tab = MicroscopeTab(
@@ -285,11 +287,26 @@ def create_config_window(self, id):
             sticky=tk.NSEW,
         )
 
-    def load_configuration(self):
+    def load_configuration(self) -> None:
         """Load configuration"""
 
-        def get_widget_value(name, value_dict):
-            """Get the value from a dict"""
+        def get_widget_value(name, value_dict) -> Optional[str]:
+            """Get the value from a dict
+
+            Parameters
+            ----------
+            name: str
+                key name
+            value_dict: dict
+                value dictionary
+
+            Returns
+            -------
+            value : Optional[str]
+
+                - The value of the key if it exists
+                - None if the key does not exist
+            """
             value = value_dict
             for key in name.split("/"):
                 if key.strip() == "":
@@ -300,7 +317,7 @@ def get_widget_value(name, value_dict):
             return value
 
         def get_widgets_value(widgets, value_dict):
-            """Get all key-value from valude_dict, keys are from widgets"""
+            """Get all key-value from value_dict, keys are from widgets"""
             temp = {}
             for key in widgets:
                 if key == "frame_config":
@@ -327,7 +344,7 @@ def get_widgets_value(widgets, value_dict):
             return temp
 
         def build_widgets_value(widgets, value_dict):
-            """According to valude_dict build values for widgets"""
+            """According to value_dict build values for widgets"""
             if widgets is None or value_dict is None:
                 return [None]
             result = []
diff --git a/src/navigate/controller/controller.py b/src/navigate/controller/controller.py
index b90a200ea..49fa80efb 100644
--- a/src/navigate/controller/controller.py
+++ b/src/navigate/controller/controller.py
@@ -604,8 +604,8 @@ def set_mode_of_sub(self, mode):
 
         Parameters
         __________
-        mode : string
-            string = 'live', 'stop'
+        mode : str
+            The string = 'live', 'stop'
         """
         self.channels_tab_controller.set_mode(mode)
         self.camera_view_controller.set_mode(mode)
@@ -634,8 +634,9 @@ def execute(self, command, *args):
         Parameters
         __________
         command : string
-            string = 'stage', 'stop_stage', 'move_stage_and_update_info',
-        args* : function-specific passes.
+            The string includes 'stage', 'stop_stage', 'move_stage_and_update_info',
+        args* : Iterable.
+            Function-specific passes
         """
 
         if command == "joystick_toggle":
@@ -1163,10 +1164,10 @@ def display_images(
             camera_view_controller : CameraViewController
                 Camera View Controller object.
             show_img_pipe : multiprocessing.Pipe
-                Pipe for showing images.
+                The pipe for showing images.
             data_buffer : SharedNDArray
                 Pre-allocated shared memory array.
-                Size dictated by x_pixels, y_pixels, an number_of_frames in
+                Size dictated by x_pixels, y_pixels, and number_of_frames in
                 configuration file.
             """
             camera_view_controller.initialize_non_live_display(
@@ -1379,8 +1380,8 @@ def register_event_listener(self, event_name, event_handler):
         ----------
         event_name : string
             Name of the event.
-        event_handler : function
-            Function to handle the event.
+        event_handler : callable
+            The function to handle the event.
         """
         self.event_listeners[event_name] = event_handler
 
diff --git a/src/navigate/controller/sub_controllers/camera_view.py b/src/navigate/controller/sub_controllers/camera_view.py
index 8f48d40e0..425f2a269 100644
--- a/src/navigate/controller/sub_controllers/camera_view.py
+++ b/src/navigate/controller/sub_controllers/camera_view.py
@@ -33,20 +33,21 @@
 # Standard Library Imports
 import platform
 import tkinter as tk
+from tkinter import messagebox
 import logging
 import threading
-from typing import Dict
+from typing import Dict, Optional
 import tempfile
 import os
 import time
+import abc
+import copy
 
 # Third Party Imports
 import cv2
 from PIL import Image, ImageTk
 import matplotlib.pyplot as plt
 import numpy as np
-import copy
-import abc
 
 # Local Imports
 from navigate.controller.sub_controllers.gui import GUIController
@@ -117,6 +118,9 @@ def __init__(self, view, parent_controller=None):
         #: numpy.ndarray: The variance map.
         self._variance = None
 
+        #: str: The imaging mode.
+        self.image_mode = None
+
         #: bool: The flag for the display of the cross-hair.
         self.apply_cross_hair = True
 
@@ -520,17 +524,10 @@ def initialize_non_live_display(self, microscope_state, camera_parameters):
         self.is_displaying_image.value = False
         self.image_count = 0  # was image_counter
         self.slice_index = 0
-
         self.image_mode = microscope_state["image_mode"]
         self.stack_cycling_mode = microscope_state["stack_cycling_mode"]
         self.number_of_channels = int(microscope_state["selected_channels"])
-
-        self.selected_channels = []
-        for channel_name, channel_data in microscope_state["channels"].items():
-            if channel_data["is_selected"]:
-                channel_idx = channel_name.split("_")[-1]
-                self.selected_channels.append(f"CH{channel_idx}")
-
+        self.get_selected_channels(microscope_state)
         self.number_of_slices = int(microscope_state["number_z_steps"])
         self.total_images_per_volume = self.number_of_channels * self.number_of_slices
         self.original_image_width = int(camera_parameters["img_x_pixels"])
@@ -552,6 +549,25 @@ def initialize_non_live_display(self, microscope_state, camera_parameters):
         self.update_canvas_size()
         self.reset_display(False, False)
 
+    def get_selected_channels(self, microscope_state: Optional[dict] = None) -> None:
+        """Get the selected microscope channels from the MicroscopeState.
+
+        Parameters
+        ----------
+        microscope_state : Optional[dict]
+            The microscope state dictionary object.
+        """
+        if microscope_state is None:
+            microscope_state = self.parent_controller.configuration["experiment"][
+                "MicroscopeState"
+            ]
+
+        self.selected_channels = []
+        for channel_name, channel_data in microscope_state["channels"].items():
+            if channel_data["is_selected"]:
+                channel_idx = channel_name.split("_")[-1]
+                self.selected_channels.append(f"CH{channel_idx}")
+
     def reset_display(self, display_flag=True, reset_crosshair=True):
         """Set the display back to the original digital zoom.
 
@@ -685,7 +701,7 @@ def move_stage(self):
                 command = "move_stage_and_update_info"
             self.parent_controller.execute(command, stage_position)
         else:
-            tk.messagebox.showerror(
+            messagebox.showerror(
                 title="Warning", message="Can't move to there! Invalid stage position!"
             )
 
@@ -716,7 +732,7 @@ def digital_zoom(self):
 
         Returns
         -------
-        image : np.array
+        image : np.ndarray
             Image after digital zoom applied
         """
         self.zoom_rect = self.zoom_rect - self.zoom_offset
@@ -916,14 +932,8 @@ def process_image(self):
         image = self.apply_lut(image)
         self.populate_image(image)
 
-    def left_click(self, *args):
-        """Toggles cross-hair on image upon left click event.
-
-        Parameters
-        ----------
-        args : tuple
-            Arguments.
-        """
+    def left_click(self, *_):
+        """Toggles cross-hair on image upon left click event."""
         if self.image is not None:
             self.apply_cross_hair = not self.apply_cross_hair
             self.process_image()
@@ -1135,6 +1145,7 @@ def initialize_non_live_display(self, microscope_state, camera_parameters):
         super().initialize_non_live_display(microscope_state, camera_parameters)
         self.update_display_state()
         self.view.live_frame.channel["values"] = self.selected_channels
+        self.view.live_frame.channel.set(self.selected_channels[0])
         self.spooled_images = SpooledImageLoader(
             channels=self.number_of_channels,
             size_y=self.original_image_height,
@@ -1150,14 +1161,8 @@ def update_snr(self):
             self._offset, self._variance = copy.deepcopy(off), copy.deepcopy(var)
             self.image_palette["SNR"].grid(row=3, column=0, sticky=tk.NSEW, pady=3)
 
-    def slider_update(self, *args):
-        """Updates the image when the slider is moved.
-
-        Parameters
-        ----------
-        args : tuple
-            Arguments.
-        """
+    def slider_update(self, *_):
+        """Updates the image when the slider is moved."""
 
         slider_index = self.view.slider.get()
         channel_index = self.view.live_frame.channel.get()
@@ -1177,16 +1182,11 @@ def slider_update(self, *args):
         with self.is_displaying_image as is_displaying_image:
             is_displaying_image.value = False
 
-    def update_display_state(self, *args):
+    def update_display_state(self, *_):
         """Image Display Combobox Called.
 
         Sets self.display_state to desired display format. Toggles state of slider
         widget. Sets number of positions.
-
-        Parameters
-        ----------
-        args : tuple
-            Arguments.
         """
         if self.number_of_slices == 0:
             return
@@ -1205,11 +1205,12 @@ def update_display_state(self, *args):
             )
             self.view.slider.configure(state="normal")
             self.view.slider.grid()
-            self.view.live_frame.channel.configure(state="normal")
+            self.view.live_frame.channel.state(["!disabled", "readonly"])
+            # was normal
             if self.view.live_frame.channel.get() not in self.selected_channels:
                 self.view.live_frame.channel.set(self.selected_channels[0])
 
-    def initialize(self, name, data):
+    def initialize(self, name: str, data: list):
         """Sets widgets based on data given from main controller/config.
 
         Parameters
@@ -1345,13 +1346,13 @@ def display_image(self, image):
             is_displaying_image.value = False
         logger.info(f"Displaying image took {time.time() - start_time:.4f} seconds")
 
-    def set_mask_color_table(self, colors):
+    def set_mask_color_table(self, colors: list):
         """Set up segmentation mask color table
 
         Parameters
         ----------
         colors : list
-            List of colors to use for the segmentation mask
+            The list of colors to use for the segmentation mask
         """
         self.mask_color_table = np.zeros((256, 1, 3), dtype=np.uint8)
         self.mask_color_table[0] = [0, 0, 0]
@@ -1370,8 +1371,8 @@ def display_mask(self, mask):
 
         Parameters
         ----------
-        mask : np.array
-            Segmentation mask to display)
+        mask : np.ndarray
+            Segmentation mask to display
         """
         self.ilastik_seg_mask = cv2.applyColorMap(mask, self.mask_color_table)
         self.ilastik_mask_ready_lock.release()
@@ -1400,6 +1401,15 @@ def __init__(self, view, parent_controller=None):
         #: tkinter.Canvas: The tkinter canvas that displays the image.
         self.view = view
 
+        #: int: The image height.
+        self.XY_image_height = None
+
+        #: int: The image width.
+        self.XY_image_width = None
+
+        #: int: Scaling factor for ratio of lateral and axial dimensions.
+        self.Z_image_value = None
+
         #: np.ndarray: The image data.
         self.image = None
 
@@ -1427,7 +1437,7 @@ def __init__(self, view, parent_controller=None):
         self.menu.entryconfig("Move Here", state="disabled")
         self.menu.entryconfig("Mark Position", state="disabled")
 
-    def initialize(self, name, data):
+    def initialize(self, name: str, data: list):
         """Initialize the MIP view.
 
         Sets the min and max intensity values for the image.Disables the min and max
@@ -1452,9 +1462,12 @@ def initialize(self, name, data):
         self.image_palette["Gray"].widget.invoke()
         self.image_palette["Autoscale"].widget.invoke()
         self.image_palette["SNR"].grid_remove()
+
         self.render_widgets["perspective"].widget["values"] = ("XY", "ZY", "ZX")
         self.render_widgets["perspective"].set("XY")
-        self.render_widgets["channel"].set("CH1")
+
+        self.get_selected_channels()
+        self.render_widgets["channel"].set(self.selected_channels[0])
 
         # event binding
         self.render_widgets["perspective"].get_variable().trace_add(
@@ -1514,17 +1527,23 @@ def get_mip_image(self):
         image : numpy.ndarray
             Image data
         """
-        if self.xy_mip is None:
+        views = [self.xy_mip, self.zy_mip, self.zx_mip]
+        if any(view is None for view in views):
             return None
 
         display_mode = self.render_widgets["perspective"].get()
-        channel_idx = int(self.render_widgets["channel"].get()[2:]) - 1
+        channel = self.render_widgets["channel"].get()
+        if channel in self.selected_channels:
+            channel_idx = self.selected_channels.index(channel)
+        else:
+            return
+
         if display_mode == "XY":
             image = self.xy_mip[channel_idx]
         elif display_mode == "ZY":
-            image = self.zy_mip[channel_idx].T
-        elif display_mode == "ZX":
-            image = self.zx_mip[channel_idx]
+            image = self.zy_mip[channel_idx, :].T
+        else:
+            image = self.zx_mip[channel_idx, :]
 
         image = self.flip_image(image)
         # map the image to canvas size()
@@ -1542,11 +1561,12 @@ def initialize_non_live_display(self, microscope_state, camera_parameters):
             Camera parameters.
         """
         super().initialize_non_live_display(microscope_state, camera_parameters)
+        self.render_widgets["channel"].set(self.selected_channels[0])
         self.perspective = self.render_widgets["perspective"].get()
         self.XY_image_width = self.original_image_width
         self.XY_image_height = self.original_image_height
-        # in microns
         z_range = microscope_state["abs_z_end"] - microscope_state["abs_z_start"]
+
         # TODO: may stretch by the value of binning.
         self.Z_image_value = int(
             self.XY_image_width * camera_parameters["fov_x"] / z_range
@@ -1594,14 +1614,9 @@ def display_image(self, image):
         with self.is_displaying_image as is_displaying_image:
             is_displaying_image.value = False
 
-    def display_mip_image(self, *args):
-        """Display MIP image in non-live view.
+    def display_mip_image(self, *_):
+        """Display MIP image in non-live view."""
 
-        Parameters
-        ----------
-        args : tuple
-            Arguments.
-        """
         if self.perspective != self.render_widgets["perspective"].get():
             self.update_perspective()
         if self.mode != "stop":
@@ -1610,16 +1625,19 @@ def display_mip_image(self, *args):
         if self.image is not None:
             self.process_image()
 
-    def update_perspective(self, *args, display=False):
-        """Update the perspective of the image.
+    def update_perspective(self):
+        """Update the perspective of the image."""
+        attribute_list = [
+            "XY_image_width",
+            "XY_image_height",
+            "Z_image_value",
+        ]
+        if any(
+            not hasattr(self, attr) or getattr(self, attr) is None
+            for attr in attribute_list
+        ):
+            return
 
-        Parameters
-        ----------
-        args : tuple
-            Arguments.
-        display : bool
-            Flag to display the image.
-        """
         display_mode = self.render_widgets["perspective"].get()
         self.perspective = display_mode
         if display_mode == "XY":
diff --git a/src/navigate/view/configurator_application_window.py b/src/navigate/view/configurator_application_window.py
index ca95800de..b70dea90d 100644
--- a/src/navigate/view/configurator_application_window.py
+++ b/src/navigate/view/configurator_application_window.py
@@ -33,6 +33,7 @@
 from tkinter import ttk, simpledialog
 import logging
 from pathlib import Path
+from typing import Optional, Callable
 
 # Third Party Imports
 
@@ -396,6 +397,8 @@ def create_hardware_widgets(self, hardware_widgets, frame, direction="vertical")
                     self.values_dict[k] = v[3]
                     temp = list(v[3].keys())
                     widget.config(values=temp)
+                    widget.state(["!disabled", "readonly"])
+
                     if v[2] == "bool":
                         widget.set(str(temp[-1]))
                     else:
@@ -443,7 +446,7 @@ def build_widgets(self, widgets, *args, parent=None, widgets_value=None, **kwarg
         parent : frame
             parent frame to put widgets
         widgets_value : dict
-            valude dict of widgets
+            value_dict of widgets
         *args
             Variable length argument list.
         **kwargs
@@ -465,9 +468,9 @@ def build_widgets(self, widgets, *args, parent=None, widgets_value=None, **kwarg
             temp_ref = widgets["frame_config"].get("ref", None)
             direction = widgets["frame_config"].get("direction", "vertical")
         if collapsible:
-            self.foldAllFrames()
+            self.fold_all_frames()
             frame = CollapsibleFrame(parent=parent, title=title)
-            # only display one callapsible frame at a time
+            # only display one collapsible frame at a time
             frame.label.bind("<Button-1>", self.create_toggle_function(frame))
         else:
             frame = ttk.Frame(parent)
@@ -493,12 +496,12 @@ def build_widgets(self, widgets, *args, parent=None, widgets_value=None, **kwarg
                 except tk._tkinter.TclError:
                     pass
 
-    def foldAllFrames(self, except_frame=None):
+    def fold_all_frames(self, except_frame: Optional[tk.Frame] = None) -> None:
         """Fold all collapsible frames except one frame
 
         Parameters
         ----------
-        except_frame : tk.Frame
+        except_frame : Optional[tk.Frame]
             the unfold frame
         """
         for child in self.hardware_frame.winfo_children():
@@ -508,7 +511,7 @@ def foldAllFrames(self, except_frame=None):
             if isinstance(child, CollapsibleFrame) and child is not except_frame:
                 child.fold()
 
-    def create_toggle_function(self, frame):
+    def create_toggle_function(self, frame: tk.Frame) -> Callable[..., None]:
         """Toggle collapsible frame
 
         Parameters
@@ -518,12 +521,14 @@ def create_toggle_function(self, frame):
         """
 
         def func(event):
-            self.foldAllFrames(frame)
+            self.fold_all_frames(frame)
             frame.toggle_visibility()
 
         return func
 
-    def build_event_handler(self, hardware_widgets, key, frame, frame_id):
+    def build_event_handler(
+        self, hardware_widgets: dict, key: str, frame: tk.Frame, frame_id: int
+    ) -> Callable[..., None]:
         """Build button event handler
 
         Parameters
@@ -536,6 +541,11 @@ def build_event_handler(self, hardware_widgets, key, frame, frame_id):
             the frame to put/delete widgets
         frame_id : int
             index of the frame
+
+        Returns
+        -------
+        func : Callable
+            event handler function
         """
 
         def func(*args, **kwargs):
@@ -559,7 +569,7 @@ def func(*args, **kwargs):
                     ref=v[2].get("ref", None),
                     direction=v[2].get("direction", "vertical"),
                 )
-                # collaps other frame
+                # collapse other frame
             elif v[2].get("delete", False):
                 frame.grid_remove()
                 self.variables_list[frame_id - self.row_offset] = None
diff --git a/src/navigate/view/main_window_content/display_notebook.py b/src/navigate/view/main_window_content/display_notebook.py
index c62a3d177..ead381506 100644
--- a/src/navigate/view/main_window_content/display_notebook.py
+++ b/src/navigate/view/main_window_content/display_notebook.py
@@ -313,22 +313,18 @@ def __init__(
         self.live_var = tk.StringVar()
 
         #: ttk.Combobox: The combobox that holds the live display functionality.
-        self.live = ttk.Combobox(
-            self, textvariable=self.live_var, state="readonly", width=6
-        )
+        self.live = ttk.Combobox(self, textvariable=self.live_var, width=6)
         self.live["values"] = ("Live", "Slice")
         self.live.set("Live")
         self.live.grid(row=0, column=0)
-        self.live.state = "readonly"
+        self.live.state(["!disabled", "readonly"])
 
         self.channel_var = tk.StringVar()
-        self.channel = ttk.Combobox(
-            self, textvariable=self.channel_var, state="readonly", width=6
-        )
+        self.channel = ttk.Combobox(self, textvariable=self.channel_var, width=6)
         self.channel["values"] = "CH1"
         self.channel.set("CH1")
         self.channel.grid(row=1, column=0)
-        self.channel.state = "readonly"
+        self.channel.state(["disabled", "readonly"])
 
 
 class MipRenderFrame(ttk.Labelframe, CommonMethods):
@@ -377,7 +373,8 @@ def __init__(
                 input_args={"width": 5},
             ),
         }
-
+        self.inputs["perspective"].widget.state(["!disabled", "readonly"])
+        self.inputs["channel"].widget.state(["!disabled", "readonly"])
         self.inputs["perspective"].grid(row=0, column=0, sticky=tk.EW, padx=3, pady=3)
         self.inputs["channel"].grid(row=1, column=0, sticky=tk.EW, padx=3, pady=3)
         self.columnconfigure(0, weight=1)
diff --git a/src/navigate/view/popups/acquire_popup.py b/src/navigate/view/popups/acquire_popup.py
index e5f7dbd12..294fbe1a2 100644
--- a/src/navigate/view/popups/acquire_popup.py
+++ b/src/navigate/view/popups/acquire_popup.py
@@ -142,6 +142,7 @@ def __init__(self, root, *args, **kwargs):
                     input_var=tk.StringVar(),
                     label_args={"padding": [0, 0, 30, 0]},
                 )
+                self.inputs[entry_names[i]].widget.state(["!disabled", "readonly"])
                 self.inputs[entry_names[i]].set_values(tuple(FILE_TYPES))
                 self.inputs[entry_names[i]].set("TIFF")
 
@@ -153,6 +154,7 @@ def __init__(self, root, *args, **kwargs):
                     input_var=tk.StringVar(),
                     label_args={"padding": [0, 0, 36, 0]},
                 )
+                self.inputs[entry_names[i]].widget.state(["!disabled", "readonly"])
                 self.inputs[entry_names[i]].set_values(
                     ("BABB", "Water", "CUBIC", "CLARITY", "uDISCO", "eFLASH")
                 )