diff --git a/docs/source/contributing/feature_container.rst b/docs/source/contributing/feature_container.rst
index 667bdd870..ea25be7fe 100644
--- a/docs/source/contributing/feature_container.rst
+++ b/docs/source/contributing/feature_container.rst
@@ -253,7 +253,7 @@ To create a customized feature list, follow these steps:
                 {"name": PrepareNextChannel},
                 {
                     "name": LoopByCount,
-                    "args": ("experiment.MicroscopeState.selected_channels",),
+                    "args": ("channels",),
                 },
             )
         ]
diff --git a/docs/source/user_guide/acquiring_guide.rst b/docs/source/user_guide/acquiring_guide.rst
index 163cd53fb..73dddcc71 100644
--- a/docs/source/user_guide/acquiring_guide.rst
+++ b/docs/source/user_guide/acquiring_guide.rst
@@ -42,7 +42,7 @@ a :doc:`feature list <features>`, shown in its
         {"name": PrepareNextChannel},
         {
             "name": LoopByCount,
-            "args": ("experiment.MicroscopeState.selected_channels",),
+            "args": ("channels",),
         },
       )
     ]
diff --git a/docs/source/user_guide/features/example_feature_lists.rst b/docs/source/user_guide/features/example_feature_lists.rst
index ec6bc4302..39152cd2e 100644
--- a/docs/source/user_guide/features/example_feature_lists.rst
+++ b/docs/source/user_guide/features/example_feature_lists.rst
@@ -30,7 +30,7 @@ prior to moving to the next position in the multi-position table.
             {"name": CalculateFocusRange,},
             {"name": ZStackAcquisition,"args": (True,True,"z-stack",),},
             {"name": WaitToContinue,},
-            {"name": LoopByCount,"args": ("experiment.MicroscopeState.multiposition_count",),},
+            {"name": LoopByCount,"args": ("positions",),},
         ),
     ]
 
diff --git a/src/navigate/config/config.py b/src/navigate/config/config.py
index e71c8494b..bbd7bb30e 100644
--- a/src/navigate/config/config.py
+++ b/src/navigate/config/config.py
@@ -108,6 +108,7 @@ def get_configuration_paths():
         "rest_api_config.yml",
         "waveform_templates.yml",
         "gui_configuration.yml",
+        "multi_positions.yml"
     ]
 
     base_directory = Path(__file__).resolve().parent
@@ -520,8 +521,6 @@ def verify_experiment_config(manager, configuration):
         "timepoint_interval": 0,
         "experiment_duration": 1.03,
         "is_multiposition": False,
-        "multiposition_count": 1,
-        "selected_channels": 0,
         "stack_z_origin": 0,
         "stack_focus_origin": 0,
         "start_focus": 0.0,
@@ -654,31 +653,6 @@ def verify_experiment_config(manager, configuration):
             if channel_value[k] < 0:
                 channel_value[k] = temp[k]
 
-    microscope_setting_dict["selected_channels"] = selected_channel_num
-
-    # MultiPositions
-    if (
-        "MultiPositions" not in configuration["experiment"]
-        or type(configuration["experiment"]["MultiPositions"]) is not ListProxy
-    ):
-        update_config_dict(manager, configuration["experiment"], "MultiPositions", [])
-    position_ids = []
-    multipositions = configuration["experiment"]["MultiPositions"]
-    for i, position in enumerate(multipositions):
-        try:
-            for j in range(5):
-                float(position[j])
-        except (ValueError, KeyError):
-            position_ids.append(i)
-
-    for idx in position_ids[::-1]:
-        del multipositions[idx]
-    if len(multipositions) < 1:
-        multipositions.append([10.0, 10.0, 10.0, 10.0, 10.0])
-
-    microscope_setting_dict["multiposition_count"] = len(multipositions)
-
-
 def verify_waveform_constants(manager, configuration):
     """Verifies and updates the waveform constants in the configuration dictionary.
 
@@ -1119,3 +1093,18 @@ def verify_configuration(manager, configuration):
         "gui",
         {"channels": {"count": channel_count}},
     )
+
+def verify_positions_config(positions):
+    if positions is None or type(positions) not in (list, ListProxy):
+        return []
+    # MultiPositions
+    position_num = len(positions)
+    for i in range(position_num-1, -1, -1):
+        position = positions[i]
+        try:
+            for j in range(5):
+                float(position[j])
+        except (ValueError, KeyError, IndexError):
+            del positions[i]
+
+    return positions
diff --git a/src/navigate/config/experiment.yml b/src/navigate/config/experiment.yml
index 03dd4f84e..92ff0accd 100644
--- a/src/navigate/config/experiment.yml
+++ b/src/navigate/config/experiment.yml
@@ -54,8 +54,6 @@ MicroscopeState:
   timepoint_interval: 0
   experiment_duration: 600.0899999999995
   is_multiposition: False
-  multiposition_count: 2
-  selected_channels: 3
   channels: {'channel_1': {'is_selected': True, 'laser': '488nm', 'laser_index': 0, 'filter': 'GFP - FF01-515/30-32', 'filter_position': 1, 'camera_exposure_time': 200.0, 'laser_power': '20', 'interval_time': '1', 'defocus': 100.0}, 'channel_2': {'is_selected': True, 'laser': '562nm', 'laser_index': 1, 'filter': 'RFP - FF01-595/31-32', 'filter_position': 2, 'camera_exposure_time': 200.0, 'laser_power': '20', 'interval_time': '1', 'defocus': 200.0}, 'channel_3': {'is_selected': True, 'laser': '642nm', 'laser_index': 2, 'filter': 'Far-Red - BLP01-647R/31-32', 'filter_position': 3, 'camera_exposure_time': 200.0, 'laser_power': '20', 'interval_time': '1', 'defocus': 0.0}}
   stack_z_origin: 0.0
   stack_focus_origin: 0.0
diff --git a/src/navigate/config/multi_positions.yml b/src/navigate/config/multi_positions.yml
new file mode 100644
index 000000000..59f58d0ff
--- /dev/null
+++ b/src/navigate/config/multi_positions.yml
@@ -0,0 +1 @@
+[[0, 0, 0, 0, 0]]
\ No newline at end of file
diff --git a/src/navigate/controller/controller.py b/src/navigate/controller/controller.py
index f540605d7..1137ff76c 100644
--- a/src/navigate/controller/controller.py
+++ b/src/navigate/controller/controller.py
@@ -80,10 +80,16 @@
     update_config_dict,
     verify_experiment_config,
     verify_waveform_constants,
+    verify_positions_config,
     verify_configuration,
     get_navigate_path,
 )
-from navigate.tools.file_functions import create_save_path, save_yaml_file, get_ram_info
+from navigate.tools.file_functions import (
+    create_save_path,
+    load_yaml_file,
+    save_yaml_file,
+    get_ram_info,
+)
 from navigate.tools.common_dict_tools import update_stage_dict
 from navigate.tools.multipos_table_tools import update_table
 from navigate.tools.common_functions import combine_funcs
@@ -108,6 +114,7 @@ def __init__(
         rest_api_path,
         waveform_templates_path,
         gui_configuration_path,
+        multi_positions_path,
         args,
     ):
         """Initialize the Navigate Controller.
@@ -198,6 +205,10 @@ def __init__(
         verify_experiment_config(self.manager, self.configuration)
         verify_waveform_constants(self.manager, self.configuration)
 
+        positions = load_yaml_file(multi_positions_path)
+        positions = verify_positions_config(positions)
+        self.configuration["multi_positions"] = positions
+
         total_ram, available_ram = get_ram_info()
         logger.info(
             f"Total RAM: {total_ram / 1024**3:.2f} GB. "
@@ -460,7 +471,7 @@ def populate_experiment_setting(self, file_name=None, in_initialize=False):
         self.acquire_bar_controller.populate_experiment_values()
         # self.stage_controller.populate_experiment_values()
         self.multiposition_tab_controller.set_positions(
-            self.configuration["experiment"]["MultiPositions"]
+            self.configuration["multi_positions"]
         )
         self.channels_tab_controller.populate_experiment_values()
         self.camera_setting_controller.populate_experiment_values()
@@ -510,10 +521,7 @@ def update_experiment_setting(self):
 
         # update multi-positions
         positions = self.multiposition_tab_controller.get_positions()
-        self.configuration["experiment"]["MultiPositions"] = positions
-        self.configuration["experiment"]["MicroscopeState"][
-            "multiposition_count"
-        ] = len(positions)
+        self.configuration["multi_positions"] = positions
 
         if (
             self.configuration["experiment"]["MicroscopeState"]["is_multiposition"]
@@ -848,6 +856,13 @@ def execute(self, command, *args):
                 filename="waveform_constants.yml",
             )
 
+            # Save multi_positions.yml file
+            save_yaml_file(
+                file_directory=file_directory,
+                content_dict=self.configuration["multi_positions"],
+                filename="multi_positions.yml",
+            )
+
             self.camera_setting_controller.solvent = self.configuration["experiment"][
                 "Saving"
             ]["solvent"]
@@ -952,6 +967,12 @@ def execute(self, command, *args):
                 content_dict=self.configuration["experiment"],
                 filename="experiment.yml",
             )
+            save_yaml_file(
+                file_directory=file_directory,
+                content_dict=self.configuration["multi_positions"],
+                filename="multi_positions.yml",
+            )
+
             if hasattr(self, "waveform_popup_controller"):
                 self.waveform_popup_controller.save_waveform_constants()
 
diff --git a/src/navigate/controller/sub_controllers/acquire_bar.py b/src/navigate/controller/sub_controllers/acquire_bar.py
index d8b6bf568..e9425ecf7 100644
--- a/src/navigate/controller/sub_controllers/acquire_bar.py
+++ b/src/navigate/controller/sub_controllers/acquire_bar.py
@@ -147,7 +147,7 @@ def progress_bar(
             number_of_positions = 1
         else:
             number_of_positions = len(
-                self.parent_controller.configuration["experiment"]["MultiPositions"]
+                self.parent_controller.configuration["multi_positions"]
             )
 
         if mode == "single":
diff --git a/src/navigate/controller/sub_controllers/camera_view.py b/src/navigate/controller/sub_controllers/camera_view.py
index 7ae074b58..4afa9a764 100644
--- a/src/navigate/controller/sub_controllers/camera_view.py
+++ b/src/navigate/controller/sub_controllers/camera_view.py
@@ -526,8 +526,8 @@ def initialize_non_live_display(self, microscope_state, camera_parameters):
         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.get_selected_channels(microscope_state)
+        self.number_of_channels = len(self.selected_channels)
         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"])
@@ -1169,8 +1169,7 @@ def slider_update(self, *_):
 
         slider_index = self.view.slider.get()
         channel_index = self.view.live_frame.channel.get()
-        channel_index = channel_index[-1]
-        channel_index = int(channel_index) - 1
+        channel_index = self.selected_channels.index(channel_index)
         image = self.spooled_images.load_image(
             channel=channel_index, slice_index=slider_index
         )
diff --git a/src/navigate/controller/sub_controllers/channels_tab.py b/src/navigate/controller/sub_controllers/channels_tab.py
index 30b7ac962..c24daf907 100644
--- a/src/navigate/controller/sub_controllers/channels_tab.py
+++ b/src/navigate/controller/sub_controllers/channels_tab.py
@@ -32,7 +32,6 @@
 
 # Standard Library Imports
 import logging
-from functools import reduce
 import datetime
 
 # Third Party Imports
@@ -773,12 +772,6 @@ def execute(self, command, *args):
             Returns parent_controller.execute(command) if command = 'get_stage_position'
         """
         if command == "recalculate_timepoint":
-            # update selected channels num
-            self.microscope_state_dict["selected_channels"] = reduce(
-                lambda count, channel: count + (channel["is_selected"] is True),
-                self.microscope_state_dict["channels"].values(),
-                0,
-            )
             self.update_timepoint_setting()
             # update framerate info in camera setting tab
             exposure_time = max(
diff --git a/src/navigate/controller/sub_controllers/multiposition.py b/src/navigate/controller/sub_controllers/multiposition.py
index 1671425c2..016cf2dd8 100644
--- a/src/navigate/controller/sub_controllers/multiposition.py
+++ b/src/navigate/controller/sub_controllers/multiposition.py
@@ -100,7 +100,12 @@ def set_positions(self, positions):
         """
         axis_dict = {"x": "X", "y": "Y", "z": "Z", "theta": "R", "f": "F"}
         data = {}
-
+        if len(positions) == 0:
+            # add current stage position to the table
+            stage_position = self.parent_controller.configuration["experiment"][
+                "StageParameters"
+            ]
+            positions = [[stage_position[axis] for axis in axis_dict.keys()]]
         for i, name in enumerate(axis_dict.keys()):
             data[axis_dict[name]] = list(pos[i] for pos in positions)
         self.table.model.df = pd.DataFrame(data)
diff --git a/src/navigate/main.py b/src/navigate/main.py
index 5d933308e..73aa8b0dc 100644
--- a/src/navigate/main.py
+++ b/src/navigate/main.py
@@ -103,6 +103,7 @@ def main():
         logging_path,
         configurator,
         gui_configuration_path,
+        multi_positions_path,
     ) = evaluate_parser_input_arguments(args)
 
     log_setup("logging.yml", logging_path)
@@ -119,6 +120,7 @@ def main():
             rest_api_path,
             waveform_templates_path,
             gui_configuration_path,
+            multi_positions_path,
             args,
         )
 
diff --git a/src/navigate/model/features/common_features.py b/src/navigate/model/features/common_features.py
index b35a2381a..d8b638ac9 100644
--- a/src/navigate/model/features/common_features.py
+++ b/src/navigate/model/features/common_features.py
@@ -36,6 +36,7 @@
 from functools import reduce
 from threading import Lock
 import logging
+from multiprocessing.managers import ListProxy
 
 # Third party imports
 
@@ -183,7 +184,16 @@ def __init__(self, model, saving_flag=False):
         self.saving_flag = saving_flag
 
         #: dict: A dictionary defining the configuration for the data capture process.
-        self.config_table = {"data": {"main": self.data_func}}
+        self.config_table = {
+            "signal": {"main": self.signal_func},
+            "data": {"main": self.data_func},
+        }
+
+    def signal_func(self) -> bool:
+        """Mark saving flags in the signal function"""
+        if self.saving_flag:
+            self.model.mark_saving_flags([self.model.frame_id])
+        return True
 
     def data_func(self, frame_ids: list) -> bool:
         """Capture data frames and log camera information.
@@ -201,8 +211,6 @@ def data_func(self, frame_ids: list) -> bool:
         bool
             A boolean value indicating the success of the data capture process.
         """
-        if self.saving_flag:
-            self.model.mark_saving_flags(frame_ids)
         logger.info(f"the camera is:{self.model.active_microscope_name}, {frame_ids}")
         return True
 
@@ -211,7 +219,7 @@ class WaitForExternalTrigger:
     """WaitForExternalTrigger class to time features using external input.
 
     This class waits for either an external trigger (or the timeout) before continuing
-    on to the next feature block in the list. Useful when combined with LoopByCounts
+    on to the next feature block in the list. Useful when combined with LoopByCount
     when each iteration may depend on some external event happening.
 
     Notes:
@@ -451,31 +459,50 @@ def __init__(self, model, steps=1):
         self.model = model
 
         #: bool: A boolean value indicating whether to step by frame or by step.
-        self.step_by_frame = True
+        self.step_by_frame = False if type(steps) is str else True
 
         #: int: The remaining number of steps or frames.
         self.steps = steps
-        if type(steps) is str:
-            self.step_by_frame = False
-            try:
-                parameters = steps.split(".")
-                config_ref = reduce((lambda pre, n: f"{pre}['{n}']"), parameters, "")
-                exec(f"self.steps = int(self.model.configuration{config_ref})")
-            except:  # noqa
-                self.steps = 1
 
         #: int: The remaining number of steps.
-        self.signals = self.steps
+        self.signals = 1
 
         #: int: The remaining number of frames.
-        self.data_frames = self.steps
+        self.data_frames = 1
+
+        #: bool: Initialization flag
+        self.initialized = VariableWithLock(bool)
+        self.initialized.value = False
 
         #: dict: A dictionary defining the configuration for the loop control process.
         self.config_table = {
-            "signal": {"main": self.signal_func},
-            "data": {"main": self.data_func},
+            "signal": {
+                "init": self.pre_func,
+                "main": self.signal_func,
+            },
+            "data": {
+                "init": self.pre_func,
+                "main": self.data_func
+            },
         }
 
+    def pre_func(self):
+        """Initialize loop parameters"""
+        if self.initialized.value:
+            return
+        
+        with self.initialized as initialized:
+            if initialized.value:
+                return
+
+            self.get_steps()
+
+            self.signals = self.steps
+            self.data_frames = self.steps
+            initialized.value = True
+
+            logger.debug(f"LoopByCount-initialize: {self.signals}, {self.data_frames}")
+
     def signal_func(self):
         """Control the signal acquisition loop and update the remaining steps.
 
@@ -520,6 +547,34 @@ def data_func(self, frame_ids):
             return False
         return True
 
+    def get_steps(self):
+        """Get number of steps
+
+        Returns:
+        --------
+        int
+            Number of steps.
+        """
+        if type(self.steps) is int:
+            return self.steps
+        if self.steps == "channels":
+            self.steps = len(self.model.active_microscope.available_channels)
+        elif self.steps == "positions":
+            self.steps = len(self.model.configuration["multi_positions"])
+        else:
+            try:
+                parameters = self.steps.split(".")
+                config_ref = reduce((lambda pre, n: f"{pre}['{n}']"), parameters, "")
+                exec(f"self.steps = self.model.configuration{config_ref}")
+            except:  # noqa
+                self.steps = 1
+
+            if type(self.steps) in [list, ListProxy]:
+                self.steps = len(self.steps)
+            else:
+                self.steps = int(self.steps)
+        return self.steps
+
 
 class PrepareNextChannel:
     """PrepareNextChannel class for preparing microscopes for the next imaging channel.
@@ -635,14 +690,10 @@ def __init__(self, model, resolution_value=None, zoom_value=None, offset=None):
         self.current_idx = 0
 
         #: dict: A dictionary defining the configuration for the position control
-        self.multiposition_table = self.model.configuration["experiment"][
-            "MultiPositions"
-        ]
+        self.multiposition_table = []
 
         #: int: The total number of positions in the multi-position table.
-        self.position_count = self.model.configuration["experiment"]["MicroscopeState"][
-            "multiposition_count"
-        ]
+        self.position_count = 0
 
         #: int: The stage distance threshold for pausing the data thread.
         self.stage_distance_threshold = 1000
@@ -661,6 +712,8 @@ def pre_signal_func(self):
         if self.initialized:
             return
         self.initialized = True
+        self.multiposition_table = self.model.configuration["multi_positions"]
+        self.position_count = len(self.multiposition_table)
         if type(self.offset) is str:
             try:
                 self.offset = ast.literal_eval(self.offset)
@@ -1011,7 +1064,14 @@ def pre_signal_func(self):
         self.stack_cycling_mode = microscope_state["stack_cycling_mode"]
 
         # get available channels
-        self.channels = microscope_state["selected_channels"]
+        self.channels = len(
+            list(
+                filter(
+                    lambda channel: channel["is_selected"],
+                    microscope_state["channels"].values(),
+                )
+            )
+        )
         #: int: The current channel being acquired in the z-stack
         self.current_channel_in_list = 0
 
@@ -1041,7 +1101,7 @@ def pre_signal_func(self):
 
         # position: x, y, z, theta, f
         if bool(microscope_state["is_multiposition"]):
-            self.positions = self.model.configuration["experiment"]["MultiPositions"]
+            self.positions = self.model.configuration["multi_positions"]
         else:
             self.positions = [
                 [
diff --git a/src/navigate/model/metadata_sources/metadata.py b/src/navigate/model/metadata_sources/metadata.py
index aa7d4e1d7..d47280a01 100644
--- a/src/navigate/model/metadata_sources/metadata.py
+++ b/src/navigate/model/metadata_sources/metadata.py
@@ -195,7 +195,7 @@ def set_shape_from_configuration_experiment(self) -> None:
         self._multiposition = state["is_multiposition"]
 
         if bool(self._multiposition):
-            self.positions = len(self.configuration["experiment"]["MultiPositions"])
+            self.positions = len(self.configuration["multi_positions"])
         else:
             self.positions = 1
 
@@ -205,7 +205,7 @@ def set_shape_from_configuration_experiment(self) -> None:
         # let the data sources have the ability to save more frames
         # self._multiposition = True
         # self.positions = len(
-        #     self.configuration["experiment"]["MultiPositions"]
+        #     self.configuration["multi_positions"]
         # )
 
         # Allow additional axes (e.g. f) to couple onto existing axes (e.g. z)
diff --git a/src/navigate/model/model.py b/src/navigate/model/model.py
index 6cdbcc4f0..6ba16c469 100644
--- a/src/navigate/model/model.py
+++ b/src/navigate/model/model.py
@@ -309,7 +309,7 @@ def __init__(
                         {"name": PrepareNextChannel},
                         {
                             "name": LoopByCount,
-                            "args": ("experiment.MicroscopeState.selected_channels",),
+                            "args": ("channels",),
                         },
                     ),
                     {
@@ -338,7 +338,7 @@ def __init__(
                     {"name": WaitToContinue},
                     {
                         "name": LoopByCount,
-                        "args": ("experiment.MicroscopeState.multiposition_count",),
+                        "args": ("positions",),
                     },
                 ),
             ]
@@ -361,7 +361,7 @@ def __init__(
                     },
                     {
                         "name": LoopByCount,
-                        "args": ("experiment.MicroscopeState.multiposition_count",),
+                        "args": ("positions",),
                     },
                 ),
                 {"name": RemoveEmptyPositions, "args": (records,)},
@@ -374,7 +374,7 @@ def __init__(
                     {"name": PrepareNextChannel},
                     {
                         "name": LoopByCount,
-                        "args": ("experiment.MicroscopeState.selected_channels",),
+                        "args": ("channels",),
                     },
                 )
             ],
@@ -383,7 +383,7 @@ def __init__(
                     {"name": PrepareNextChannel},
                     {
                         "name": LoopByCount,
-                        "args": ("experiment.MicroscopeState.selected_channels",),
+                        "args": ("channels",),
                     },
                 )
             ],
@@ -552,6 +552,10 @@ def run_command(
             self.is_save = self.configuration["experiment"]["MicroscopeState"][
                 "is_save"
             ]
+            if len(self.configuration["multi_positions"]) == 0:
+                self.configuration["experiment"]["MicroscopeState"][
+                    "is_multiposition"
+                ] = False
 
             # Calculate waveforms, turn on lasers, etc.
             self.prepare_acquisition()
@@ -1187,7 +1191,7 @@ def reset_feature_list(self) -> None:
                         {"name": PrepareNextChannel},
                         {
                             "name": LoopByCount,
-                            "args": ("experiment.MicroscopeState.selected_channels",),
+                            "args": ("channels",),
                         },
                     )
                 ],
diff --git a/src/navigate/tools/main_functions.py b/src/navigate/tools/main_functions.py
index 393043e48..701503ebf 100644
--- a/src/navigate/tools/main_functions.py
+++ b/src/navigate/tools/main_functions.py
@@ -72,6 +72,8 @@ def evaluate_parser_input_arguments(args):
         True if configurator is enabled
     gui_configuration_path
         Path to gui_configuration file
+    multi_positions_path
+        Path to multi_positions file
     """
     # Retrieve the Default Configuration paths
     (
@@ -81,6 +83,7 @@ def evaluate_parser_input_arguments(args):
         rest_api_path,
         waveform_templates_path,
         gui_configuration_path,
+        multi_positions_path,
     ) = get_configuration_paths()
 
     # Evaluate Input Arguments
@@ -125,7 +128,13 @@ def evaluate_parser_input_arguments(args):
         assert (
             args.gui_config_file.exists()
         ), "gui_configuration Path {} not valid".format(args.gui_config_file)
-        gui_configuration_path = args.gui_config
+        gui_configuration_path = args.gui_config_file
+
+    if args.multi_positions_file:
+        assert (
+            args.multi_positions_file.exists()
+        ), "multi_positions Path {} not valid".format(args.multi_positions_file)
+        multi_positions_path = args.multi_positions_file
 
     # Creating Loggers etc., they exist globally so no need to pass
     if args.logging_config:
@@ -145,6 +154,7 @@ def evaluate_parser_input_arguments(args):
         logging_path,
         configurator,
         gui_configuration_path,
+        multi_positions_path,
     )
 
 
@@ -257,4 +267,13 @@ def create_parser():
         "This file specifies how the logging will be performed.",
     )
 
+    input_args.add_argument(
+        "--multi-positions-file",
+        type=Path,
+        required=False,
+        default=None,
+        help="Non-default path to the multi_positions.yml file.  \n"
+        "This file contains a list of stage positions.",
+    )
+
     return parser
diff --git a/test/config/test_config.py b/test/config/test_config.py
index 851aeba74..02219c97d 100644
--- a/test/config/test_config.py
+++ b/test/config/test_config.py
@@ -77,6 +77,7 @@ def test_config_methods():
         "update_config_dict",
         "verify_experiment_config",
         "verify_waveform_constants",
+        "verify_positions_config",
         "verify_configuration",
         "yaml",
         "logging",
@@ -122,7 +123,7 @@ def test_get_configuration_paths():
     paths = config.get_configuration_paths()
     for path in paths:
         assert isinstance(path, pathlib.Path)
-    assert len(paths) == 6
+    assert len(paths) == 7
 
 
 def test_get_configuration_paths_create_dir(monkeypatch):
@@ -348,8 +349,6 @@ def setUp(self):
             "timepoint_interval": 0,
             "experiment_duration": 1.03,
             "is_multiposition": False,
-            "multiposition_count": 1,
-            "selected_channels": 0,
             "stack_z_origin": 0,
             "stack_focus_origin": 0,
             "start_focus": 0.0,
@@ -366,7 +365,6 @@ def setUp(self):
             "CameraParameters": camera_parameters_dict_sample,
             "StageParameters": stage_parameters_dict_sample,
             "MicroscopeState": microscope_parameters_dict_sample,
-            "MultiPositions": multipositions_sample,
         }
 
     def tearDown(self):
@@ -420,9 +418,9 @@ def test_load_empty_experiment_file(self):
             experiement_config["MicroscopeState"],
         )
 
-        # MultiPositions
-        for i, position in enumerate(self.experiment_sample["MultiPositions"]):
-            assert position == experiement_config["MultiPositions"][i]
+        # # MultiPositions
+        # for i, position in enumerate(self.experiment_sample["MultiPositions"]):
+        #     assert position == experiement_config["MultiPositions"][i]
 
     def test_load_experiment_file_with_missing_parameters(self):
         experiment = load_yaml_file(os.path.join(self.config_path, "experiment.yml"))
@@ -784,12 +782,6 @@ def test_load_experiment_file_with_wrong_parameter_values(self):
                 == expected_value[k]
             )
 
-        # selected_channels
-        assert experiment["MicroscopeState"]["selected_channels"] == 0
-        experiment["MicroscopeState"]["channels"]["channel_2"]["is_selected"] = True
-        config.verify_experiment_config(self.manager, configuration)
-        assert experiment["MicroscopeState"]["selected_channels"] == 1
-
     def select_random_entries_from_list(self, parameter_list):
         n = random.randint(1, len(parameter_list))
         return random.choices(parameter_list, k=n)
@@ -801,3 +793,31 @@ def delete_random_entries_from_dict(self, parameter_list, parameter_dict):
             if k in parameter_dict.keys():
                 del parameter_dict[k]
         return deleted_parameters
+
+    def test_load_empty_multi_positions(self):
+        positions_file_path = os.path.join(self.test_root, "multi_positions.yml")
+        with open(positions_file_path, "w") as f:
+            f.write("")
+        positions = load_yaml_file(positions_file_path)
+        new_positions = config.verify_positions_config(positions)
+        assert isinstance(new_positions, list)
+        assert len(new_positions) == 0
+
+    def test_load_multi_positions_with_corrupted_values(self):
+        positions = [[1, 2, 3], ['a', 'b', 'c', 1, 2], [10, 'a', 30, 40,]]
+        new_positions = config.verify_positions_config(positions)
+        assert isinstance(new_positions, list)
+        assert len(new_positions) == 0
+
+
+        positions = [[1, 2, 3], ['a', 'b', 'c', 1, 2], [1, 2, 3, 4, 5], [10, 'a', 30, 40,]]
+        new_positions = config.verify_positions_config(positions)
+        assert isinstance(new_positions, list)
+        assert len(new_positions) == 1
+
+        positions = [[1, 2, 3], ['a', 'b', 'c', 1, 2], [1, 2, 3, 4, 5], [10, 'a', 30, 40,],
+                     [1, 2, 3, 4, 5, 6]]
+        new_positions = config.verify_positions_config(positions)
+        assert isinstance(new_positions, list)
+        assert len(new_positions) == 2
+
diff --git a/test/config/test_experiment.py b/test/config/test_experiment.py
index fbb02be32..04dfc6f47 100644
--- a/test/config/test_experiment.py
+++ b/test/config/test_experiment.py
@@ -164,8 +164,6 @@ def test_microscope_state(self):
             "timepoint_interval": int,
             "experiment_duration": float,
             "is_multiposition": bool,
-            "multiposition_count": int,
-            "selected_channels": int,
             "channels": dict,
             "stack_z_origin": float,
             "stack_focus_origin": float,
@@ -203,12 +201,3 @@ def test_microscope_state(self):
                     expected_values[key_key],
                 ), f"{key_key} is not of type {expected_values[key_key]}"
 
-    def test_multiposition(self):
-        expected_values = [float, float, float, float, float]
-        positions = self.data["MultiPositions"]
-        print("*** positions:", positions)
-        for position in positions:
-            for i in range(len(expected_values)):
-                assert isinstance(
-                    position[i], expected_values[i]
-                ), f"{i} is not of type {expected_values[i]}"
diff --git a/test/controller/sub_controllers/test_camera_view.py b/test/controller/sub_controllers/test_camera_view.py
index dce8bc4b1..37bfc7c39 100644
--- a/test/controller/sub_controllers/test_camera_view.py
+++ b/test/controller/sub_controllers/test_camera_view.py
@@ -92,7 +92,6 @@ def setup_class(self, dummy_controller):
             },
             "number_z_steps": np.random.randint(10, 100),
             "stack_cycling_mode": "per_stack",
-            "selected_channels": 3,
             "image_mode": "z-stack",
         }
 
diff --git a/test/controller/test_controller.py b/test/controller/test_controller.py
index a4b154567..e9245bb43 100644
--- a/test/controller/test_controller.py
+++ b/test/controller/test_controller.py
@@ -31,6 +31,9 @@ def controller(tk_root):
     gui_configuration_path = Path.joinpath(
         configuration_directory, "gui_configuration.yml"
     )
+    multi_positions_path = Path.joinpath(
+        configuration_directory, "multi_positions.yml"
+    )
     args = SimpleNamespace(synthetic_hardware=True)
 
     controller = Controller(
@@ -42,6 +45,7 @@ def controller(tk_root):
         rest_api_path,
         waveform_templates_path,
         gui_configuration_path,
+        multi_positions_path,
         args,
     )
     # To make sure the testcases won't hang on because of the model.event_queue
diff --git a/test/model/devices/galvo/test_galvo_base.py b/test/model/devices/galvo/test_galvo_base.py
index 1a9e3bd12..574dd4539 100644
--- a/test/model/devices/galvo/test_galvo_base.py
+++ b/test/model/devices/galvo/test_galvo_base.py
@@ -55,6 +55,7 @@ def setUp(self) -> None:
             rest_api_path,
             waveform_templates_path,
             gui_configuration_path,
+            multi_positions_path,
         ) = get_configuration_paths()
 
         self.configuration = load_configs(
diff --git a/test/model/devices/galvo/test_galvo_ni.py b/test/model/devices/galvo/test_galvo_ni.py
index f1c263b30..4d43cebf6 100644
--- a/test/model/devices/galvo/test_galvo_ni.py
+++ b/test/model/devices/galvo/test_galvo_ni.py
@@ -56,6 +56,7 @@ def setUp(self) -> None:
             rest_api_path,
             waveform_templates_path,
             gui_configuration_path,
+            multi_positions_path,
         ) = get_configuration_paths()
 
         self.configuration = load_configs(
diff --git a/test/model/devices/galvo/test_galvo_synthetic.py b/test/model/devices/galvo/test_galvo_synthetic.py
index 08eac5a25..5e9fde1f6 100644
--- a/test/model/devices/galvo/test_galvo_synthetic.py
+++ b/test/model/devices/galvo/test_galvo_synthetic.py
@@ -53,6 +53,7 @@ def setUp(self) -> None:
             rest_api_path,
             waveform_templates_path,
             gui_configuration_path,
+            multi_positions_path,
         ) = get_configuration_paths()
 
         self.configuration = load_configs(
diff --git a/test/model/devices/lasers/test_laser_ni.py b/test/model/devices/lasers/test_laser_ni.py
index 22406c4ef..a420f2708 100644
--- a/test/model/devices/lasers/test_laser_ni.py
+++ b/test/model/devices/lasers/test_laser_ni.py
@@ -24,6 +24,7 @@ def setUp(self) -> None:
             rest_api_path,
             waveform_templates_path,
             gui_configuration_path,
+            multi_positions_path,
         ) = get_configuration_paths()
 
         self.configuration = load_configs(
diff --git a/test/model/dummy.py b/test/model/dummy.py
index 032c7edb3..8fe8d5146 100644
--- a/test/model/dummy.py
+++ b/test/model/dummy.py
@@ -45,6 +45,7 @@
     verify_experiment_config,
     verify_waveform_constants,
     verify_configuration,
+    verify_positions_config,
 )
 from navigate.model.devices.camera.synthetic import (
     SyntheticCamera,
@@ -53,6 +54,7 @@
 from navigate.model.features.feature_container import (
     load_features,
 )
+from navigate.tools.file_functions import load_yaml_file
 
 
 class DummyController:
@@ -189,6 +191,9 @@ def __init__(self):
         gui_configuration_path = Path.joinpath(
             configuration_directory, "gui_configuration.yml"
         )
+        multi_positions_path = Path.joinpath(
+            configuration_directory, "multi_positions.yml"
+        )
 
         #: Manager: The manager.
         self.manager = Manager()
@@ -205,6 +210,10 @@ def __init__(self):
         verify_experiment_config(self.manager, self.configuration)
         verify_waveform_constants(self.manager, self.configuration)
 
+        positions = load_yaml_file(multi_positions_path)
+        positions = verify_positions_config(positions)
+        self.configuration["multi_positions"] = positions
+
         #: DummyDevice: The device.
         self.device = DummyDevice()
         #: Pipe: The pipe for sending signals.
diff --git a/test/model/features/test_common_features.py b/test/model/features/test_common_features.py
index 3b5ae2097..7f1371e49 100644
--- a/test/model/features/test_common_features.py
+++ b/test/model/features/test_common_features.py
@@ -52,7 +52,7 @@ def _prepare_test(self, dummy_model_to_test_features):
             self.config["end_position"] - self.config["start_position"]
         ) / self.config["number_z_steps"]
 
-        position_list = self.model.configuration["experiment"]["MultiPositions"]
+        position_list = self.model.configuration["multi_positions"]
         if len(position_list) < 5:
             for i in range(5):
                 pos = [0] * 5
@@ -94,7 +94,7 @@ def z_stack_verification(self):
         mode = self.config["stack_cycling_mode"]  # per_z/pre_stack
         is_multiposition = self.config["is_multiposition"]
         if is_multiposition:
-            positions = self.model.configuration["experiment"]["MultiPositions"]
+            positions = self.model.configuration["multi_positions"]
         else:
             pos_dict = self.model.configuration["experiment"]["StageParameters"]
             positions = [
@@ -281,7 +281,6 @@ def test_single_position_one_channel_per_z(self, has_ni_galvo_stage):
 
         # 1 channel per_z
         self.config["stack_cycling_mode"] = "per_z"
-        self.config["selected_channels"] = 1
         self.config["channels"]["channel_1"]["is_selected"] = True
         self.config["channels"]["channel_2"]["is_selected"] = False
         self.config["channels"]["channel_3"]["is_selected"] = False
@@ -299,7 +298,6 @@ def test_single_position_one_channel_per_stack(self, has_ni_galvo_stage):
 
         # 1 channel per_stack
         self.config["stack_cycling_mode"] = "per_stack"
-        self.config["selected_channels"] = 1
         self.config["channels"]["channel_1"]["is_selected"] = True
         self.config["channels"]["channel_2"]["is_selected"] = False
         self.config["channels"]["channel_3"]["is_selected"] = False
@@ -316,7 +314,6 @@ def test_single_position_two_channels_per_z(self, has_ni_galvo_stage):
 
         # 2 channels per_z
         self.config["stack_cycling_mode"] = "per_z"
-        self.config["selected_channels"] = 2
         for i in range(3):
             for j in range(3):
                 self.config["channels"]["channel_" + str(j + 1)]["is_selected"] = True
@@ -334,7 +331,6 @@ def test_single_position_two_channels_per_stack(self, has_ni_galvo_stage):
 
         # 2 channels per_stack
         self.config["stack_cycling_mode"] = "per_stack"
-        self.config["selected_channels"] = 2
         for i in range(3):
             for j in range(3):
                 self.config["channels"]["channel_" + str(j + 1)]["is_selected"] = True
@@ -351,7 +347,6 @@ def test_single_position_three_channels_per_stack(self, has_ni_galvo_stage):
         ]["stage"]["has_ni_galvo_stage"] = has_ni_galvo_stage
 
         # 3 channels per_stack
-        self.config["selected_channels"] = 3
         self.config["channels"]["channel_1"]["is_selected"] = True
         self.config["channels"]["channel_2"]["is_selected"] = True
         self.config["channels"]["channel_3"]["is_selected"] = True
@@ -368,7 +363,6 @@ def test_single_position_three_channels_per_z(self, has_ni_galvo_stage):
         ]["stage"]["has_ni_galvo_stage"] = has_ni_galvo_stage
 
         # 3 channels per_z
-        self.config["selected_channels"] = 3
         self.config["channels"]["channel_1"]["is_selected"] = True
         self.config["channels"]["channel_2"]["is_selected"] = True
         self.config["channels"]["channel_3"]["is_selected"] = True
@@ -386,7 +380,6 @@ def test_multi_position_one_channel_per_z(self, has_ni_galvo_stage):
 
         # 1 channel per_z
         self.config["stack_cycling_mode"] = "per_z"
-        self.config["selected_channels"] = 1
         self.config["channels"]["channel_1"]["is_selected"] = True
         self.config["channels"]["channel_2"]["is_selected"] = False
         self.config["channels"]["channel_3"]["is_selected"] = False
@@ -404,7 +397,6 @@ def test_multi_position_one_channel_per_stack(self, has_ni_galvo_stage):
 
         # 1 channel per_stack
         self.config["stack_cycling_mode"] = "per_stack"
-        self.config["selected_channels"] = 1
         self.config["channels"]["channel_1"]["is_selected"] = True
         self.config["channels"]["channel_2"]["is_selected"] = False
         self.config["channels"]["channel_3"]["is_selected"] = False
@@ -422,7 +414,6 @@ def test_multi_position_two_channels_per_z(self, has_ni_galvo_stage):
 
         # 2 channels per_z
         self.config["stack_cycling_mode"] = "per_z"
-        self.config["selected_channels"] = 2
         for i in range(3):
             for j in range(3):
                 self.config["channels"]["channel_" + str(j + 1)]["is_selected"] = True
@@ -441,7 +432,6 @@ def test_multi_position_two_channels_per_stack(self, has_ni_galvo_stage):
 
         # 2 channels per_stack
         self.config["stack_cycling_mode"] = "per_stack"
-        self.config["selected_channels"] = 2
         for i in range(3):
             for j in range(3):
                 self.config["channels"]["channel_" + str(j + 1)]["is_selected"] = True
@@ -459,7 +449,6 @@ def test_multi_position_three_channels_per_stack(self, has_ni_galvo_stage):
         ]["stage"]["has_ni_galvo_stage"] = has_ni_galvo_stage
 
         # 3 channels per_stack
-        self.config["selected_channels"] = 3
         self.config["channels"]["channel_1"]["is_selected"] = True
         self.config["channels"]["channel_2"]["is_selected"] = True
         self.config["channels"]["channel_3"]["is_selected"] = True
@@ -477,7 +466,6 @@ def test_multi_position_three_channels_per_z(self, has_ni_galvo_stage):
         ]["stage"]["has_ni_galvo_stage"] = has_ni_galvo_stage
 
         # 3 channels per_z
-        self.config["selected_channels"] = 3
         self.config["channels"]["channel_1"]["is_selected"] = True
         self.config["channels"]["channel_2"]["is_selected"] = True
         self.config["channels"]["channel_3"]["is_selected"] = True
diff --git a/test/model/test_model.py b/test/model/test_model.py
index 4c133a13d..39f9af948 100644
--- a/test/model/test_model.py
+++ b/test/model/test_model.py
@@ -54,7 +54,9 @@ def model():
         verify_experiment_config,
         verify_waveform_constants,
         verify_configuration,
+        verify_positions_config,
     )
+    from navigate.tools.file_functions import load_yaml_file
 
     with Manager() as manager:
 
@@ -70,6 +72,7 @@ def model():
             configuration_directory, "waveform_constants.yml"
         )
         rest_api_path = Path.joinpath(configuration_directory, "rest_api_config.yml")
+        multi_positions_path = Path.joinpath(configuration_directory, "multi_positions.yml")
 
         event_queue = MagicMock()
 
@@ -84,6 +87,10 @@ def model():
         verify_experiment_config(manager, configuration)
         verify_waveform_constants(manager, configuration)
 
+        positions = load_yaml_file(multi_positions_path)
+        positions = verify_positions_config(positions)
+        configuration["multi_positions"] = positions
+
         model = Model(
             args=SimpleNamespace(synthetic_hardware=True),
             configuration=configuration,
@@ -104,7 +111,7 @@ def test_single_acquisition(model):
     state["image_mode"] = "single"
     state["is_save"] = False
 
-    n_frames = state["selected_channels"]
+    n_frames = len(list(filter(lambda channel: channel["is_selected"], state["channels"].values())))
 
     show_img_pipe = model.create_pipe("show_img_pipe")
 
@@ -219,8 +226,8 @@ def test_multiposition_acquisition(model):
     model.configuration["experiment"]["MicroscopeState"]["is_multiposition"] = True
     update_config_dict(
         model.__test_manager,  # noqa
-        model.configuration["experiment"],
-        "MultiPositions",
+        model.configuration,
+        "multi_positions",
         [[10.0, 10.0, 10.0, 10.0, 10.0]],
     )
     model.configuration["experiment"]["MicroscopeState"]["image_mode"] = "z-stack"
@@ -245,8 +252,8 @@ def test_multiposition_acquisition(model):
     # Multiposition is selected but not actually  True
     update_config_dict(
         model.__test_manager,
-        model.configuration["experiment"],
-        "MultiPositions",
+        model.configuration,
+        "multi_positions",
         [],  # noqa
     )
 
diff --git a/test/view/popups/test_feature_list_popup.py b/test/view/popups/test_feature_list_popup.py
index 315e62e3e..5707a79f6 100644
--- a/test/view/popups/test_feature_list_popup.py
+++ b/test/view/popups/test_feature_list_popup.py
@@ -67,7 +67,7 @@ def test_feature_icon(tk_root):
         ),
         ("ChangeResolution", ["resolution_mode", "zoom_value"], ["high", "N/A"]),
         ("LoopByCount", ["steps"], [1]),
-        ("LoopByCount", ["steps"], ["experiment.MicroscopeState.selected_channels"]),
+        ("LoopByCount", ["steps"], ["channels"]),
     ],
 )
 def test_feature_config_popup(feature_name, args_name, args_value, tk_root):