diff --git a/bec_widgets/widgets/plots/waveform/utils/alignment_controller.py b/bec_widgets/widgets/plots/waveform/utils/alignment_controller.py
new file mode 100644
index 00000000..ad201efc
--- /dev/null
+++ b/bec_widgets/widgets/plots/waveform/utils/alignment_controller.py
@@ -0,0 +1,342 @@
+from __future__ import annotations
+
+from dataclasses import dataclass
+
+import pyqtgraph as pg
+from qtpy.QtCore import QObject, Qt, Signal
+from qtpy.QtGui import QColor
+
+from bec_widgets.utils.colors import get_accent_colors, get_theme_name
+from bec_widgets.utils.error_popups import SafeSlot
+from bec_widgets.widgets.plots.waveform.utils.alignment_panel import WaveformAlignmentPanel
+
+
+@dataclass(slots=True)
+class AlignmentContext:
+    """Alignment state produced by `Waveform` and consumed by the controller.
+
+    Attributes:
+        visible: Whether alignment mode is currently visible.
+        positioner_name: Name of the resolved x-axis positioner, if available.
+        precision: Decimal precision to use for readback and target labels.
+        limits: Optional positioner limits for the draggable target line.
+        readback: Current cached positioner readback value.
+        has_dap_curves: Whether the waveform currently contains any DAP curves.
+        force_readback: Whether the embedded positioner should refresh its readback immediately.
+    """
+
+    visible: bool
+    positioner_name: str | None
+    precision: int = 3
+    limits: tuple[float, float] | None = None
+    readback: float | None = None
+    has_dap_curves: bool = False
+    force_readback: bool = False
+
+
+class WaveformAlignmentController(QObject):
+    """Own the alignment plot overlays and synchronize them with the alignment panel."""
+
+    move_absolute_requested = Signal(float)
+
+    def __init__(self, plot_item: pg.PlotItem, panel: WaveformAlignmentPanel, parent=None):
+        super().__init__(parent=parent)
+        self._plot_item = plot_item
+        self._panel = panel
+
+        self._visible = False
+        self._positioner_name: str | None = None
+        self._precision = 3
+        self._limits: tuple[float, float] | None = None
+        self._readback: float | None = None
+        self._marker_line: pg.InfiniteLine | None = None
+        self._target_line: pg.InfiniteLine | None = None
+
+        self._panel.position_readback_changed.connect(self.update_position)
+        self._panel.target_toggled.connect(self._on_target_toggled)
+        self._panel.target_move_requested.connect(self._on_target_move_requested)
+        self._panel.fit_selection_changed.connect(self._on_fit_selection_changed)
+        self._panel.fit_center_requested.connect(self._on_fit_center_requested)
+
+    @property
+    def marker_line(self) -> pg.InfiniteLine | None:
+        """Return the current-position indicator line, if it exists."""
+        return self._marker_line
+
+    @property
+    def target_line(self) -> pg.InfiniteLine | None:
+        """Return the draggable target indicator line, if it exists."""
+        return self._target_line
+
+    def update_context(self, context: AlignmentContext):
+        """Apply waveform-owned alignment context to the panel and plot overlays.
+
+        Args:
+            context: Snapshot of the current alignment-relevant waveform/device state.
+        """
+        previous_name = self._positioner_name
+        self._visible = context.visible
+        self._positioner_name = context.positioner_name
+        self._precision = context.precision
+        self._limits = context.limits
+        self._readback = context.readback
+
+        self._panel.set_positioner_device(context.positioner_name)
+        self._panel.set_positioner_enabled(context.visible and context.positioner_name is not None)
+        self._panel.set_status_message(self._status_message_for_context(context))
+
+        if context.positioner_name is None or not context.visible:
+            self.clear()
+            self._refresh_fit_actions()
+            self._refresh_target_controls()
+            return
+
+        if previous_name != context.positioner_name:
+            self._clear_marker()
+            if self._panel.target_active:
+                self._clear_target_line()
+
+        if context.readback is not None:
+            self.update_position(context.readback)
+
+        if self._panel.target_active:
+            if previous_name != context.positioner_name or self._target_line is None:
+                self._show_target_line()
+            else:
+                self._refresh_target_line_metadata()
+                self._on_target_line_changed()
+
+        if context.force_readback or previous_name != context.positioner_name:
+            self._panel.force_positioner_readback()
+
+        self._refresh_fit_actions()
+        self._refresh_target_controls()
+
+    @SafeSlot(float)
+    def update_position(self, position: float):
+        """Update the live position marker from a positioner readback value.
+
+        Args:
+            position: Current absolute position of the active alignment positioner.
+        """
+        self._readback = float(position)
+        if not self._visible or self._positioner_name is None:
+            self._clear_marker()
+            return
+
+        self._ensure_marker()
+        self._marker_line.setValue(self._readback)
+        self._marker_line.label.setText(
+            f"{self._positioner_name}: {self._readback:.{self._precision}f}"
+        )
+
+    @SafeSlot(dict, dict)
+    def update_dap_summary(self, data: dict, metadata: dict):
+        """Forward DAP summary updates into the alignment fit panel.
+
+        Args:
+            data: DAP fit summary payload.
+            metadata: Metadata describing the emitting DAP curve.
+        """
+        self._panel.update_dap_summary(data, metadata)
+        self._refresh_fit_actions()
+
+    @SafeSlot(str)
+    def remove_dap_curve(self, curve_id: str):
+        """Remove a deleted DAP curve from the alignment fit selection state.
+
+        Args:
+            curve_id: Label of the DAP curve that was removed from the waveform.
+        """
+        self._panel.remove_dap_curve(curve_id)
+        self._panel.clear_fit_selection_if_missing()
+        self._refresh_fit_actions()
+
+    def clear(self):
+        """Remove alignment overlay items from the plot and reset target state."""
+        self._clear_marker()
+        self._clear_target_line()
+
+    def cleanup(self):
+        """Disconnect panel signals and remove all controller-owned overlay items."""
+        self.clear()
+        self._disconnect_panel_signals()
+
+    def refresh_theme_colors(self):
+        """Reapply theme-aware styling to any existing alignment overlay items."""
+        self._apply_marker_style()
+        self._apply_target_style()
+
+    def _disconnect_panel_signals(self):
+        signal_pairs = [
+            (self._panel.position_readback_changed, self.update_position),
+            (self._panel.target_toggled, self._on_target_toggled),
+            (self._panel.target_move_requested, self._on_target_move_requested),
+            (self._panel.fit_selection_changed, self._on_fit_selection_changed),
+            (self._panel.fit_center_requested, self._on_fit_center_requested),
+        ]
+        for signal, slot in signal_pairs:
+            try:
+                signal.disconnect(slot)
+            except (RuntimeError, TypeError):
+                continue
+
+    def _selected_fit_has_center(self) -> bool:
+        data = self._panel.selected_fit_summary()
+        params = data.get("params", []) if isinstance(data, dict) else []
+        return any(param[0] == "center" for param in params if param)
+
+    @staticmethod
+    def _status_message_for_context(context: AlignmentContext) -> str | None:
+        if context.positioner_name is None:
+            return "Alignment mode requires a positioner on the x axis."
+        if not context.has_dap_curves:
+            return "Add a DAP curve in Curve Settings to enable alignment fitting."
+        return None
+
+    def _refresh_fit_actions(self):
+        self._panel.set_fit_actions_enabled(
+            self._visible and self._positioner_name is not None and self._selected_fit_has_center()
+        )
+
+    def _refresh_target_controls(self):
+        has_positioner = self._visible and self._positioner_name is not None
+        self._panel.set_target_enabled(has_positioner)
+        self._panel.set_target_move_enabled(has_positioner and self._target_line is not None)
+        if self._target_line is None:
+            self._panel.set_target_value(None)
+
+    def _ensure_marker(self):
+        if self._marker_line is not None:
+            return
+
+        warning = get_accent_colors().warning
+
+        self._marker_line = pg.InfiniteLine(
+            angle=90,
+            movable=False,
+            pen=pg.mkPen(warning, width=4),
+            label="",
+            labelOpts={"position": 0.95, "color": warning},
+        )
+        self._marker_line.skip_auto_range = True
+        self._apply_marker_style()
+        self._plot_item.addItem(self._marker_line)
+
+    def _clear_marker(self):
+        if self._marker_line is None:
+            return
+        self._plot_item.removeItem(self._marker_line)
+        self._marker_line = None
+
+    def _show_target_line(self):
+        if not self._visible or self._positioner_name is None:
+            return
+
+        if self._target_line is None:
+            accent_colors = get_accent_colors()
+            label = f"{self._positioner_name} target={{value:0.{self._precision}f}}"
+            self._target_line = pg.InfiniteLine(
+                movable=True,
+                angle=90,
+                pen=pg.mkPen(accent_colors.default, width=2, style=Qt.PenStyle.DashLine),
+                hoverPen=pg.mkPen(accent_colors.success, width=2),
+                label=label,
+                labelOpts={"movable": True, "color": accent_colors.default},
+            )
+            self._target_line.sigPositionChanged.connect(self._on_target_line_changed)
+            self._apply_target_style()
+            self._plot_item.addItem(self._target_line)
+        self._refresh_target_line_metadata()
+
+        value = 0.0 if self._readback is None else self._readback
+        if self._limits is not None:
+            value = min(max(value, self._limits[0]), self._limits[1])
+        self._target_line.setValue(value)
+        self._on_target_line_changed()
+
+    def _refresh_target_line_metadata(self):
+        if self._target_line is None or self._positioner_name is None:
+            return
+        self._apply_target_style()
+        self._target_line.label.setFormat(
+            f"{self._positioner_name} target={{value:0.{self._precision}f}}"
+        )
+        if self._limits is not None:
+            self._target_line.setBounds(list(self._limits))
+        else:
+            self._target_line.setBounds((None, None))
+        if self._limits is not None:
+            current_value = float(self._target_line.value())
+            clamped_value = min(max(current_value, self._limits[0]), self._limits[1])
+            if clamped_value != current_value:
+                self._target_line.setValue(clamped_value)
+
+    def _clear_target_line(self):
+        if self._target_line is not None:
+            try:
+                self._target_line.sigPositionChanged.disconnect(self._on_target_line_changed)
+            except (RuntimeError, TypeError):
+                pass
+            self._plot_item.removeItem(self._target_line)
+            self._target_line = None
+        self._panel.set_target_value(None)
+
+    def _apply_marker_style(self):
+        if self._marker_line is None:
+            return
+
+        accent_colors = get_accent_colors()
+        warning = accent_colors.warning
+
+        self._marker_line.setPen(pg.mkPen(warning, width=4))
+        self._marker_line.label.setColor(warning)
+        self._marker_line.label.fill = pg.mkBrush(self._label_fill_color())
+
+    def _apply_target_style(self):
+        if self._target_line is None:
+            return
+
+        accent_colors = get_accent_colors()
+        default = accent_colors.default
+        success = accent_colors.success
+
+        self._target_line.setPen(pg.mkPen(default, width=2, style=Qt.PenStyle.DashLine))
+        self._target_line.setHoverPen(pg.mkPen(success, width=2))
+        self._target_line.label.setColor(default)
+        self._target_line.label.fill = pg.mkBrush(self._label_fill_color())
+
+    @staticmethod
+    def _label_fill_color() -> QColor:
+        if get_theme_name() == "light":
+            return QColor(244, 244, 244, 228)
+        return QColor(48, 48, 48, 210)
+
+    @SafeSlot(bool)
+    def _on_target_toggled(self, checked: bool):
+        if checked:
+            self._show_target_line()
+        else:
+            self._clear_target_line()
+        self._refresh_target_controls()
+
+    @SafeSlot(object)
+    def _on_target_line_changed(self, _line=None):
+        if self._target_line is None:
+            return
+        self._panel.set_target_value(float(self._target_line.value()), precision=self._precision)
+        self._refresh_target_controls()
+
+    @SafeSlot()
+    def _on_target_move_requested(self):
+        if self._visible and self._positioner_name is not None and self._target_line is not None:
+            self.move_absolute_requested.emit(float(self._target_line.value()))
+
+    @SafeSlot(str)
+    def _on_fit_selection_changed(self, _curve_id: str):
+        self._refresh_fit_actions()
+
+    @SafeSlot(float)
+    def _on_fit_center_requested(self, value: float):
+        if self._visible and self._positioner_name is not None:
+            self.move_absolute_requested.emit(float(value))
diff --git a/bec_widgets/widgets/plots/waveform/utils/alignment_panel.py b/bec_widgets/widgets/plots/waveform/utils/alignment_panel.py
new file mode 100644
index 00000000..02ada7b8
--- /dev/null
+++ b/bec_widgets/widgets/plots/waveform/utils/alignment_panel.py
@@ -0,0 +1,285 @@
+from __future__ import annotations
+
+from qtpy.QtCore import Qt, Signal
+from qtpy.QtGui import QColor
+from qtpy.QtWidgets import (
+    QCheckBox,
+    QGridLayout,
+    QGroupBox,
+    QHBoxLayout,
+    QLabel,
+    QPushButton,
+    QSizePolicy,
+    QWidget,
+)
+
+from bec_widgets.utils.colors import get_accent_colors, get_theme_name
+from bec_widgets.widgets.control.device_control.positioner_box.positioner_control_line.positioner_control_line import (
+    PositionerControlLine,
+)
+from bec_widgets.widgets.dap.lmfit_dialog.lmfit_dialog import LMFitDialog
+
+
+class WaveformAlignmentPanel(QWidget):
+    """Compact bottom panel used by Waveform alignment mode."""
+
+    position_readback_changed = Signal(float)
+    target_toggled = Signal(bool)
+    target_move_requested = Signal()
+    fit_selection_changed = Signal(str)
+    fit_center_requested = Signal(float)
+
+    def __init__(self, parent=None, client=None, gui_id: str | None = None, **kwargs):
+        super().__init__(parent=parent, **kwargs)
+        self.setProperty("skip_settings", True)
+
+        self.positioner = PositionerControlLine(parent=self, client=client, gui_id=gui_id)
+        self.positioner.hide_device_selection = True
+
+        self.fit_dialog = LMFitDialog(
+            parent=self, client=client, gui_id=gui_id, ui_file="lmfit_dialog_compact.ui"
+        )
+        self.fit_dialog.active_action_list = ["center"]
+        self.fit_dialog.enable_actions = False
+
+        self.target_toggle = QCheckBox("Target: --", parent=self)
+        self.move_to_target_button = QPushButton("Move To Target", parent=self)
+        self.move_to_target_button.setEnabled(False)
+        self.target_group = QGroupBox("Target Position", parent=self)
+
+        self.status_label = QLabel(parent=self)
+        self.status_label.setWordWrap(False)
+        self.status_label.setAlignment(
+            Qt.AlignmentFlag.AlignHCenter | Qt.AlignmentFlag.AlignVCenter
+        )
+        self.status_label.setSizePolicy(QSizePolicy.Policy.Maximum, QSizePolicy.Policy.Fixed)
+        self.status_label.setMaximumHeight(28)
+        self.status_label.setVisible(False)
+
+        self._init_ui()
+        self.fit_dialog.setMinimumHeight(0)
+        self.target_group.setSizePolicy(QSizePolicy.Policy.Fixed, QSizePolicy.Policy.Fixed)
+        self._sync_target_group_size()
+        self.refresh_theme_colors()
+        self._connect_signals()
+
+    def _connect_signals(self):
+        self.positioner.position_update.connect(self.position_readback_changed)
+        self.target_toggle.toggled.connect(self.target_toggled)
+        self.move_to_target_button.clicked.connect(self.target_move_requested)
+        self.fit_dialog.selected_fit.connect(self.fit_selection_changed)
+        self.fit_dialog.move_action.connect(self._forward_fit_move_action)
+
+    def _init_ui(self):
+        self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Preferred)
+        self.setMinimumHeight(260)
+
+        root = QGridLayout(self)
+        root.setContentsMargins(8, 8, 8, 8)
+        root.setSpacing(8)
+
+        self.fit_dialog.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Preferred)
+        root.addWidget(
+            self.status_label,
+            0,
+            0,
+            1,
+            2,
+            alignment=Qt.AlignmentFlag.AlignHCenter | Qt.AlignmentFlag.AlignVCenter,
+        )
+        root.addWidget(self.fit_dialog, 1, 0, 1, 2)
+
+        target_layout = QHBoxLayout(self.target_group)
+        target_layout.addWidget(self.target_toggle)
+        target_layout.addWidget(self.move_to_target_button)
+
+        root.addWidget(self.positioner, 2, 0, alignment=Qt.AlignmentFlag.AlignTop)
+        root.addWidget(self.target_group, 2, 1, alignment=Qt.AlignmentFlag.AlignTop)
+        root.setColumnStretch(0, 1)
+        root.setColumnStretch(1, 0)
+        root.setRowStretch(1, 1)
+
+    def _sync_target_group_size(self):
+        representative_text = "Target: -99999.999"
+        label_width = max(
+            self.target_toggle.sizeHint().width(),
+            self.target_toggle.fontMetrics().horizontalAdvance(representative_text) + 24,
+        )
+        self.target_toggle.setMinimumWidth(label_width)
+
+        # To make those two box the same height
+        target_height = max(
+            self.positioner.height(),
+            self.positioner.ui.device_box.minimumSizeHint().height(),
+            self.positioner.ui.device_box.sizeHint().height(),
+        )
+        self.target_group.setFixedHeight(target_height)
+        self.target_group.setFixedWidth(self.target_group.sizeHint().width() + 16)
+
+    def showEvent(self, event):
+        super().showEvent(event)
+        self._sync_target_group_size()
+
+    def resizeEvent(self, event):
+        super().resizeEvent(event)
+        self._sync_target_group_size()
+
+    def set_status_message(self, text: str | None):
+        """Show or hide the alignment status pill.
+
+        Args:
+            text: Message to display. Pass `None` or an empty string to hide the pill.
+        """
+
+        text = text or ""
+        self.status_label.setText(text)
+        self.status_label.setVisible(bool(text))
+
+    @staticmethod
+    def _qcolor_to_rgba(color: QColor, alpha: int | None = None) -> str:
+        if alpha is not None:
+            color = QColor(color)
+            color.setAlpha(alpha)
+        return f"rgba({color.red()}, {color.green()}, {color.blue()}, {color.alpha()})"
+
+    def refresh_theme_colors(self):
+        """Apply theme-aware accent styling to the status pill."""
+        warning = get_accent_colors().warning
+        is_light = get_theme_name() == "light"
+        text_color = "#202124" if is_light else warning.name()
+        fill_alpha = 72 if is_light else 48
+        border_alpha = 220 if is_light else 160
+
+        self.status_label.setStyleSheet(f"""
+            QLabel {{
+                background-color: {self._qcolor_to_rgba(warning, fill_alpha)};
+                border: 1px solid {self._qcolor_to_rgba(warning, border_alpha)};
+                border-radius: 12px;
+                padding: 4px 10px;
+                color: {text_color};
+            }}
+        """)
+
+    def set_positioner_device(self, device: str | None):
+        """Bind the embedded positioner control to a fixed device.
+
+        Args:
+            device: Name of the positioner device to display, or `None` to clear it.
+        """
+        if device is None:
+            self.positioner.ui.device_box.setTitle("No positioner selected")
+            return
+        if self.positioner.device != device:
+            self.positioner.set_positioner(device)
+        self.positioner.hide_device_selection = True
+
+    def set_positioner_enabled(self, enabled: bool):
+        """Enable or disable the embedded positioner widget.
+
+        Args:
+            enabled: Whether the positioner widget should accept interaction.
+        """
+        self.positioner.setEnabled(enabled)
+
+    def force_positioner_readback(self):
+        """Trigger an immediate readback refresh on the embedded positioner widget."""
+        self.positioner.force_update_readback()
+
+    def set_target_enabled(self, enabled: bool):
+        """Enable or disable the target-line toggle.
+
+        Args:
+            enabled: Whether the target toggle should accept interaction.
+        """
+        self.target_toggle.setEnabled(enabled)
+
+    def set_target_move_enabled(self, enabled: bool):
+        """Enable or disable the move-to-target button.
+
+        Args:
+            enabled: Whether the move button should accept interaction.
+        """
+        self.move_to_target_button.setEnabled(enabled)
+
+    def set_target_active(self, active: bool):
+        """Programmatically toggle the draggable target-line state.
+
+        Args:
+            active: Whether the target line should be considered active.
+        """
+        blocker = self.target_toggle.blockSignals(True)
+        self.target_toggle.setChecked(active)
+        self.target_toggle.blockSignals(blocker)
+        if not active:
+            self.set_target_value(None)
+
+    def set_target_value(self, value: float | None, precision: int = 3) -> None:
+        """
+        Update the target checkbox label for the draggable target line.
+
+        Args:
+            value(float | None): The target value to display. If None, the label will show "--".
+            precision(int): The number of decimal places to display for the target value.
+        """
+        if value is None or not self.target_toggle.isChecked():
+            self.target_toggle.setText("Target: --")
+            return
+        self.target_toggle.setText(f"Target: {value:.{precision}f}")
+
+    def set_fit_actions_enabled(self, enabled: bool):
+        """Enable or disable LMFit action buttons in the embedded fit dialog.
+
+        Args:
+            enabled: Whether fit action buttons should be enabled.
+        """
+        self.fit_dialog.enable_actions = enabled
+
+    def update_dap_summary(self, data: dict, metadata: dict):
+        """Forward a DAP summary update into the embedded fit dialog.
+
+        Args:
+            data: DAP fit summary payload.
+            metadata: Metadata describing the emitting DAP curve.
+        """
+        self.fit_dialog.update_summary_tree(data, metadata)
+
+    def remove_dap_curve(self, curve_id: str):
+        """Remove DAP summary state for a deleted fit curve.
+
+        Args:
+            curve_id: Label of the DAP curve that should be removed.
+        """
+        self.fit_dialog.remove_dap_data(curve_id)
+
+    def clear_fit_selection_if_missing(self):
+        """Select a remaining fit curve if the current selection no longer exists."""
+        fit_curve_id = self.fit_dialog.fit_curve_id
+        if fit_curve_id is not None and fit_curve_id not in self.fit_dialog.summary_data:
+            remaining = list(self.fit_dialog.summary_data)
+            self.fit_dialog.fit_curve_id = remaining[0] if remaining else None
+
+    @property
+    def target_active(self) -> bool:
+        """Whether the target-line checkbox is currently checked."""
+        return self.target_toggle.isChecked()
+
+    @property
+    def selected_fit_curve_id(self) -> str | None:
+        """Return the currently selected fit curve label, if any."""
+        return self.fit_dialog.fit_curve_id
+
+    def selected_fit_summary(self) -> dict | None:
+        """Return the summary payload for the currently selected fit curve.
+
+        Returns:
+            The selected fit summary, or `None` if no fit curve is selected.
+        """
+        fit_curve_id = self.selected_fit_curve_id
+        if fit_curve_id is None:
+            return None
+        return self.fit_dialog.summary_data.get(fit_curve_id)
+
+    def _forward_fit_move_action(self, action: tuple[str, float]):
+        param_name, param_value = action
+        if param_name == "center":
+            self.fit_center_requested.emit(float(param_value))
diff --git a/bec_widgets/widgets/plots/waveform/waveform.py b/bec_widgets/widgets/plots/waveform/waveform.py
index 554e57ee..62f9edce 100644
--- a/bec_widgets/widgets/plots/waveform/waveform.py
+++ b/bec_widgets/widgets/plots/waveform/waveform.py
@@ -6,6 +6,7 @@ from typing import TYPE_CHECKING, Literal
 import numpy as np
 import pyqtgraph as pg
 from bec_lib import bec_logger, messages
+from bec_lib.device import Positioner
 from bec_lib.endpoints import MessageEndpoints
 from bec_lib.lmfit_serializer import serialize_lmfit_params, serialize_param_object
 from bec_lib.scan_data_container import ScanDataContainer
@@ -30,11 +31,18 @@ from bec_widgets.utils.colors import Colors, apply_theme
 from bec_widgets.utils.container_utils import WidgetContainerUtils
 from bec_widgets.utils.error_popups import SafeProperty, SafeSlot
 from bec_widgets.utils.settings_dialog import SettingsDialog
+from bec_widgets.utils.side_panel import SidePanel
+from bec_widgets.utils.toolbars.bundles import ToolbarBundle
 from bec_widgets.utils.toolbars.toolbar import MaterialIconAction
 from bec_widgets.widgets.dap.lmfit_dialog.lmfit_dialog import LMFitDialog
 from bec_widgets.widgets.plots.plot_base import PlotBase
 from bec_widgets.widgets.plots.waveform.curve import Curve, CurveConfig, DeviceSignal
 from bec_widgets.widgets.plots.waveform.settings.curve_settings.curve_setting import CurveSetting
+from bec_widgets.widgets.plots.waveform.utils.alignment_controller import (
+    AlignmentContext,
+    WaveformAlignmentController,
+)
+from bec_widgets.widgets.plots.waveform.utils.alignment_panel import WaveformAlignmentPanel
 from bec_widgets.widgets.plots.waveform.utils.roi_manager import WaveformROIManager
 from bec_widgets.widgets.services.scan_history_browser.scan_history_browser import (
     ScanHistoryBrowser,
@@ -156,6 +164,12 @@ class Waveform(PlotBase):
             "label_suffix": "",
         }
         self._current_x_device: tuple[str, str] | None = None
+        self._alignment_panel_visible = False
+        self._alignment_side_panel: SidePanel | None = None
+        self._alignment_panel_index: int | None = None
+        self._alignment_panel: WaveformAlignmentPanel | None = None
+        self._alignment_controller: WaveformAlignmentController | None = None
+        self._alignment_positioner_name: str | None = None
 
         # Specific GUI elements
         self._init_roi_manager()
@@ -165,6 +179,7 @@ class Waveform(PlotBase):
         self._add_waveform_specific_popup()
         self._enable_roi_toolbar_action(False)  # default state where are no dap curves
         self._init_curve_dialog()
+        self._init_alignment_mode()
         self.curve_settings_dialog = None
 
         # Large‑dataset guard
@@ -195,7 +210,9 @@ class Waveform(PlotBase):
         # To fix the ViewAll action with clipToView activated
         self._connect_viewbox_menu_actions()
 
-        self.toolbar.show_bundles(["plot_export", "mouse_interaction", "roi", "axis_popup"])
+        self.toolbar.show_bundles(
+            ["plot_export", "mouse_interaction", "roi", "alignment_mode", "axis_popup"]
+        )
 
     def _connect_viewbox_menu_actions(self):
         """Connect the viewbox menu action ViewAll to the custom reset_view method."""
@@ -221,6 +238,12 @@ class Waveform(PlotBase):
             theme(str, optional): The theme to be applied.
         """
         self._refresh_colors()
+        alignment_panel = getattr(self, "_alignment_panel", None)
+        alignment_controller = getattr(self, "_alignment_controller", None)
+        if alignment_panel is not None:
+            alignment_panel.refresh_theme_colors()
+        if alignment_controller is not None:
+            alignment_controller.refresh_theme_colors()
         super().apply_theme(theme)
 
     def add_side_menus(self):
@@ -230,6 +253,153 @@ class Waveform(PlotBase):
         super().add_side_menus()
         self._add_dap_summary_side_menu()
 
+    def _init_alignment_mode(self):
+        """
+        Initialize the top alignment panel.
+        """
+        self.toolbar.components.add_safe(
+            "alignment_mode",
+            MaterialIconAction(
+                icon_name="align_horizontal_center",
+                tooltip="Show Alignment Mode",
+                checkable=True,
+                parent=self,
+            ),
+        )
+        bundle = ToolbarBundle("alignment_mode", self.toolbar.components)
+        bundle.add_action("alignment_mode")
+        self.toolbar.add_bundle(bundle)
+        shown_bundles = list(self.toolbar.shown_bundles)
+        if "alignment_mode" not in shown_bundles:
+            shown_bundles.append("alignment_mode")
+            self.toolbar.show_bundles(shown_bundles)
+
+        self._alignment_side_panel = SidePanel(
+            parent=self, orientation="top", panel_max_width=320, show_toolbar=False
+        )
+        self.layout_manager.add_widget_relative(
+            self._alignment_side_panel,
+            self.round_plot_widget,
+            position="top",
+            shift_direction="down",
+        )
+
+        self._alignment_panel = WaveformAlignmentPanel(parent=self, client=self.client)
+        self._alignment_controller = WaveformAlignmentController(
+            self.plot_item, self._alignment_panel, parent=self
+        )
+        self._alignment_panel_index = self._alignment_side_panel.add_menu(
+            widget=self._alignment_panel
+        )
+        self._alignment_controller.move_absolute_requested.connect(self._move_alignment_positioner)
+        self.dap_summary_update.connect(self._alignment_controller.update_dap_summary)
+        self.toolbar.components.get_action("alignment_mode").action.toggled.connect(
+            self.toggle_alignment_mode
+        )
+
+        self._refresh_alignment_state()
+
+    @SafeSlot(bool)
+    def toggle_alignment_mode(self, checked: bool):
+        """
+        Show or hide the alignment panel.
+
+        Args:
+            checked(bool): Whether the panel should be visible.
+        """
+        if self._alignment_side_panel is None or self._alignment_panel_index is None:
+            return
+
+        self._alignment_panel_visible = checked
+        if checked:
+            self._alignment_side_panel.show_panel(self._alignment_panel_index)
+            self._refresh_alignment_state(force_readback=True)
+            self._refresh_dap_signals()
+        else:
+            self._alignment_side_panel.hide_panel()
+            self._refresh_alignment_state()
+
+    def _refresh_alignment_state(self, force_readback: bool = False):
+        """
+        Refresh the alignment panel state after waveform changes.
+
+        Args:
+            force_readback(bool): Force a positioner readback refresh.
+        """
+        if self._alignment_controller is None:
+            return
+
+        context = self._build_alignment_context(force_readback=force_readback)
+        self._alignment_positioner_name = context.positioner_name
+        self._alignment_controller.update_context(context)
+
+    def _resolve_alignment_positioner(self) -> str | None:
+        """
+        Resolve the active x-axis positioner for alignment mode.
+        """
+        if self.x_axis_mode["name"] in {"index", "timestamp"}:
+            return None
+
+        if self.x_axis_mode["name"] == "auto":
+            device_name = self._current_x_device[0] if self._current_x_device is not None else None
+        else:
+            device_name = self.x_axis_mode["name"]
+
+        if not device_name or device_name not in self.dev:
+            return None
+        if not isinstance(self.dev[device_name], Positioner):
+            return None
+        return device_name
+
+    def _build_alignment_context(self, force_readback: bool = False) -> AlignmentContext:
+        """Build controller-facing alignment context from waveform/device state."""
+        positioner_name = self._resolve_alignment_positioner()
+        if positioner_name is None:
+            return AlignmentContext(
+                visible=self._alignment_panel_visible,
+                positioner_name=None,
+                has_dap_curves=bool(self._dap_curves),
+                force_readback=force_readback,
+            )
+
+        precision = getattr(self.dev[positioner_name], "precision", 3)
+        try:
+            precision = int(precision)
+        except (TypeError, ValueError):
+            precision = 3
+
+        limits = getattr(self.dev[positioner_name], "limits", None)
+        parsed_limits: tuple[float, float] | None = None
+        if limits is not None and len(limits) == 2:
+            low, high = float(limits[0]), float(limits[1])
+            if low != 0 or high != 0:
+                if low > high:
+                    low, high = high, low
+                parsed_limits = (low, high)
+
+        data = self.dev[positioner_name].read(cached=True)
+        value = data.get(positioner_name, {}).get("value")
+        readback = None if value is None else float(value)
+
+        return AlignmentContext(
+            visible=self._alignment_panel_visible,
+            positioner_name=positioner_name,
+            precision=precision,
+            limits=parsed_limits,
+            readback=readback,
+            has_dap_curves=bool(self._dap_curves),
+            force_readback=force_readback,
+        )
+
+    @SafeSlot(float)
+    def _move_alignment_positioner(self, value: float):
+        """
+        Move the active alignment positioner to an absolute value requested by the controller.
+        """
+        if self._alignment_positioner_name is None:
+            return
+        self.dev[self._alignment_positioner_name].move(float(value), relative=False)
+
     def _add_waveform_specific_popup(self):
         """
         Add popups to the Waveform widget.
@@ -266,7 +436,7 @@ class Waveform(PlotBase):
         Due to setting clipToView to True on the curves, the autoRange() method
         of the ViewBox does no longer work as expected. This method deactivates the
         setClipToView for all curves, calls autoRange() to circumvent that issue.
-        Afterwards, it re-enables the setClipToView for all curves again.
+        Afterward, it re-enables the setClipToView for all curves again.
 
         It is hooked to the ViewAll action in the right-click menu of the pg.PlotItem ViewBox.
         """
@@ -544,6 +714,7 @@ class Waveform(PlotBase):
         self.sync_signal_update.emit()
         self.plot_item.enableAutoRange(x=True)
         self.round_plot_widget.apply_plot_widget_style()  # To keep the correct theme
+        self._refresh_alignment_state(force_readback=True)
 
     @SafeProperty(str)
     def signal_x(self) -> str | None:
@@ -573,6 +744,7 @@ class Waveform(PlotBase):
         self.sync_signal_update.emit()
         self.plot_item.enableAutoRange(x=True)
         self.round_plot_widget.apply_plot_widget_style()
+        self._refresh_alignment_state(force_readback=True)
 
     @SafeProperty(str)
     def color_palette(self) -> str:
@@ -627,6 +799,8 @@ class Waveform(PlotBase):
                     continue
                 config = CurveConfig(**cfg_dict)
                 self._add_curve(config=config)
+            self._refresh_alignment_state(force_readback=self._alignment_panel_visible)
+            self._refresh_dap_signals()
         except json.JSONDecodeError as e:
             logger.error(f"Failed to decode JSON: {e}")
 
@@ -1002,6 +1176,7 @@ class Waveform(PlotBase):
         QTimer.singleShot(
             150, self.auto_range
         )  # autorange with a delay to ensure the plot is updated
+        self._refresh_alignment_state()
 
         return curve
 
@@ -1257,6 +1432,7 @@ class Waveform(PlotBase):
             self.remove_curve(curve.name())
         if self.crosshair is not None:
             self.crosshair.clear_markers()
+        self._refresh_alignment_state()
 
     def get_curve(self, curve: int | str) -> Curve | None:
         """
@@ -1292,6 +1468,7 @@ class Waveform(PlotBase):
 
         self._refresh_colors()
         self._categorise_device_curves()
+        self._refresh_alignment_state()
 
     def _remove_curve_by_name(self, name: str):
         """
@@ -1342,6 +1519,8 @@ class Waveform(PlotBase):
             and self.enable_side_panel is True
         ):
             self.dap_summary.remove_dap_data(curve.name())
+        if curve.config.source == "dap" and self._alignment_controller is not None:
+            self._alignment_controller.remove_dap_curve(curve.name())
 
         # find a corresponding dap curve and remove it
         for c in self.curves:
@@ -1983,6 +2162,7 @@ class Waveform(PlotBase):
         """
         x_data = None
         new_suffix = None
+        previous_x_device = self._current_x_device
         data, access_key = self._fetch_scan_data_and_access()
 
         # 1 User wants custom signal
@@ -2041,6 +2221,7 @@ class Waveform(PlotBase):
                 if not scan_report_devices:
                     x_data = None
                     new_suffix = " (auto: index)"
+                    self._current_x_device = None
                 else:
                     device_x = scan_report_devices[0]
                     signal_x = self.entry_validator.validate_signal(device_x, None)
@@ -2050,8 +2231,10 @@ class Waveform(PlotBase):
                         entry_obj = data.get(device_x, {}).get(signal_x)
                         x_data = entry_obj.read()["value"] if entry_obj else None
                     new_suffix = f" (auto: {device_x}-{signal_x})"
-                self._current_x_device = (device_x, signal_x)
+                    self._current_x_device = (device_x, signal_x)
         self._update_x_label_suffix(new_suffix)
+        if previous_x_device != self._current_x_device:
+            self._refresh_alignment_state(force_readback=True)
         return x_data
 
     def _update_x_label_suffix(self, new_suffix: str):
@@ -2096,7 +2279,7 @@ class Waveform(PlotBase):
 
     def _categorise_device_curves(self) -> str:
         """
-        Categorise the device curves into sync and async based on the readout priority.
+        Categorize the device curves into sync and async based on the readout priority.
         """
         if self.scan_item is None:
             self.update_with_scan_history(-1)
@@ -2453,6 +2636,8 @@ class Waveform(PlotBase):
         Cleanup the widget by disconnecting signals and closing dialogs.
         """
         self.proxy_dap_request.cleanup()
+        if self._alignment_controller is not None:
+            self._alignment_controller.cleanup()
         self.clear_all()
         if self.curve_settings_dialog is not None:
             self.curve_settings_dialog.reject()
diff --git a/tests/unit_tests/test_alignment_controller.py b/tests/unit_tests/test_alignment_controller.py
new file mode 100644
index 00000000..c46d0f6a
--- /dev/null
+++ b/tests/unit_tests/test_alignment_controller.py
@@ -0,0 +1,142 @@
+from unittest.mock import MagicMock
+
+import numpy as np
+import pyqtgraph as pg
+
+from bec_widgets.widgets.plots.waveform.utils.alignment_controller import (
+    AlignmentContext,
+    WaveformAlignmentController,
+)
+from bec_widgets.widgets.plots.waveform.utils.alignment_panel import WaveformAlignmentPanel
+
+from .client_mocks import mocked_client
+from .conftest import create_widget
+from .test_waveform import make_alignment_fit_summary
+
+
+def create_alignment_controller(qtbot, mocked_client):
+    plot_widget = pg.PlotWidget()
+    qtbot.addWidget(plot_widget)
+    panel = create_widget(qtbot, WaveformAlignmentPanel, client=mocked_client)
+    controller = WaveformAlignmentController(plot_widget.plotItem, panel, parent=plot_widget)
+    return plot_widget, panel, controller
+
+
+def test_alignment_controller_shows_marker_only_when_visible(qtbot, mocked_client):
+    _, panel, controller = create_alignment_controller(qtbot, mocked_client)
+
+    controller.update_context(
+        AlignmentContext(visible=False, positioner_name="samx", precision=3, readback=1.0)
+    )
+    controller.update_position(4.2)
+    assert controller.marker_line is None
+
+    controller.update_context(
+        AlignmentContext(visible=True, positioner_name="samx", precision=3, readback=4.2)
+    )
+
+    assert controller.marker_line is not None
+    assert np.isclose(controller.marker_line.value(), 4.2)
+    assert panel.target_toggle.isEnabled() is True
+
+    controller.update_context(AlignmentContext(visible=False, positioner_name="samx"))
+    assert controller.marker_line is None
+
+
+def test_alignment_controller_target_line_uses_readback_and_limits(qtbot, mocked_client):
+    _, panel, controller = create_alignment_controller(qtbot, mocked_client)
+
+    controller.update_context(
+        AlignmentContext(
+            visible=True, positioner_name="samx", precision=3, limits=(0.0, 2.0), readback=5.0
+        )
+    )
+
+    panel.target_toggle.setChecked(True)
+    assert controller.target_line is not None
+    assert np.isclose(controller.target_line.value(), 2.0)
+
+    panel.target_toggle.setChecked(False)
+    assert controller.target_line is None
+
+    controller.update_context(
+        AlignmentContext(
+            visible=True, positioner_name="samx", precision=3, limits=None, readback=5.0
+        )
+    )
+    panel.target_toggle.setChecked(True)
+    assert controller.target_line is not None
+    assert np.isclose(controller.target_line.value(), 5.0)
+
+
+def test_alignment_controller_preserves_dragged_target_on_context_refresh(qtbot, mocked_client):
+    _, panel, controller = create_alignment_controller(qtbot, mocked_client)
+
+    controller.update_context(
+        AlignmentContext(
+            visible=True, positioner_name="samx", precision=3, limits=(0.0, 5.0), readback=1.0
+        )
+    )
+    panel.target_toggle.setChecked(True)
+    controller.target_line.setValue(3.0)
+
+    controller.update_context(
+        AlignmentContext(
+            visible=True, positioner_name="samx", precision=3, limits=(0.0, 5.0), readback=2.0
+        )
+    )
+
+    assert controller.target_line is not None
+    assert np.isclose(controller.target_line.value(), 3.0)
+
+
+def test_alignment_controller_emits_move_request_for_fit_center(qtbot, mocked_client):
+    _, panel, controller = create_alignment_controller(qtbot, mocked_client)
+
+    move_callback = MagicMock()
+    controller.move_absolute_requested.connect(move_callback)
+
+    controller.update_context(
+        AlignmentContext(visible=True, positioner_name="samx", precision=3, readback=1.0)
+    )
+    controller.update_dap_summary(make_alignment_fit_summary(center=2.5), {"curve_id": "fit"})
+
+    assert panel.fit_dialog.action_buttons["center"].isEnabled() is True
+    panel.fit_dialog.action_buttons["center"].click()
+
+    move_callback.assert_called_once_with(2.5)
+
+
+def test_alignment_controller_emits_move_request_for_target(qtbot, mocked_client):
+    _, panel, controller = create_alignment_controller(qtbot, mocked_client)
+
+    move_callback = MagicMock()
+    controller.move_absolute_requested.connect(move_callback)
+
+    controller.update_context(
+        AlignmentContext(
+            visible=True, positioner_name="samx", precision=3, limits=(0.0, 5.0), readback=1.0
+        )
+    )
+    panel.target_toggle.setChecked(True)
+    controller.target_line.setValue(1.25)
+    panel.move_to_target_button.click()
+
+    move_callback.assert_called_once_with(1.25)
+
+
+def test_alignment_controller_removes_deleted_dap_curve(qtbot, mocked_client):
+    _, panel, controller = create_alignment_controller(qtbot, mocked_client)
+
+    controller.update_context(
+        AlignmentContext(visible=True, positioner_name="samx", precision=3, readback=1.0)
+    )
+    controller.update_dap_summary(make_alignment_fit_summary(center=1.5), {"curve_id": "fit"})
+
+    assert "fit" in panel.fit_dialog.summary_data
+
+    controller.remove_dap_curve("fit")
+
+    assert "fit" not in panel.fit_dialog.summary_data
+    assert panel.fit_dialog.fit_curve_id is None
+    assert panel.fit_dialog.enable_actions is False
diff --git a/tests/unit_tests/test_alignment_panel.py b/tests/unit_tests/test_alignment_panel.py
new file mode 100644
index 00000000..e63d1786
--- /dev/null
+++ b/tests/unit_tests/test_alignment_panel.py
@@ -0,0 +1,40 @@
+from unittest.mock import MagicMock
+
+from bec_widgets.widgets.plots.waveform.utils.alignment_panel import WaveformAlignmentPanel
+
+from .client_mocks import mocked_client
+from .conftest import create_widget
+
+
+def test_alignment_panel_forwards_position_and_target_signals(qtbot, mocked_client):
+    panel = create_widget(qtbot, WaveformAlignmentPanel, client=mocked_client)
+
+    position_callback = MagicMock()
+    target_toggle_callback = MagicMock()
+    target_move_callback = MagicMock()
+
+    panel.position_readback_changed.connect(position_callback)
+    panel.target_toggled.connect(target_toggle_callback)
+    panel.target_move_requested.connect(target_move_callback)
+
+    panel.positioner.position_update.emit(1.25)
+    panel.target_toggle.setChecked(True)
+    panel.move_to_target_button.setEnabled(True)
+    panel.move_to_target_button.click()
+
+    position_callback.assert_called_once_with(1.25)
+    target_toggle_callback.assert_called_once_with(True)
+    target_move_callback.assert_called_once_with()
+
+
+def test_alignment_panel_emits_only_center_fit_actions(qtbot, mocked_client):
+    panel = create_widget(qtbot, WaveformAlignmentPanel, client=mocked_client)
+
+    fit_center_callback = MagicMock()
+    panel.fit_center_requested.connect(fit_center_callback)
+
+    panel.fit_dialog.move_action.emit(("sigma", 0.5))
+    fit_center_callback.assert_not_called()
+
+    panel.fit_dialog.move_action.emit(("center", 2.5))
+    fit_center_callback.assert_called_once_with(2.5)
diff --git a/tests/unit_tests/test_waveform.py b/tests/unit_tests/test_waveform.py
index efab46e0..60a2356a 100644
--- a/tests/unit_tests/test_waveform.py
+++ b/tests/unit_tests/test_waveform.py
@@ -36,6 +36,22 @@ from .conftest import create_widget
 ##################################################
 
 
+def make_alignment_fit_summary(center: float | None = None) -> dict:
+    params = []
+    if center is not None:
+        params.append(["center", center, True, None, -np.inf, np.inf, None, 0.1, {}, 0.0, None])
+    params.append(["sigma", 0.5, True, None, 0.0, np.inf, None, 0.1, {}, 1.0, None])
+    return {
+        "model": "Model(test)",
+        "method": "leastsq",
+        "chisqr": 1.0,
+        "redchi": 1.0,
+        "rsquared": 0.99,
+        "message": "Fit succeeded.",
+        "params": params,
+    }
+
+
 def test_waveform_initialization(qtbot, mocked_client):
     """
     Test that a new Waveform widget initializes with the correct defaults.
@@ -496,6 +512,218 @@ def test_add_dap_curve_custom_source(qtbot, mocked_client_with_dap):
     assert dap_curve.config.signal.dap == "GaussianModel"
 
 
+def test_alignment_mode_toggle_shows_bottom_panel(qtbot, mocked_client):
+    wf = create_widget(qtbot, Waveform, client=mocked_client)
+
+    action = wf.toolbar.components.get_action("alignment_mode").action
+    action.trigger()
+
+    assert wf._alignment_panel_visible is True
+    assert wf._alignment_side_panel.panel_visible is True
+    assert action.isChecked() is True
+
+    action.trigger()
+
+    assert wf._alignment_panel_visible is False
+    assert wf._alignment_side_panel.panel_visible is False
+    assert action.isChecked() is False
+
+
+def test_resolve_alignment_positioner(qtbot, mocked_client):
+    wf = create_widget(qtbot, Waveform, client=mocked_client)
+
+    wf.x_mode = "samx"
+    assert wf._resolve_alignment_positioner() == "samx"
+
+    wf.x_mode = "auto"
+    wf._current_x_device = ("samx", "samx")
+    assert wf._resolve_alignment_positioner() == "samx"
+
+    wf._current_x_device = ("bpm4i", "bpm4i")
+    assert wf._resolve_alignment_positioner() is None
+
+    wf.x_mode = "index"
+    assert wf._resolve_alignment_positioner() is None
+
+    wf.x_mode = "timestamp"
+    assert wf._resolve_alignment_positioner() is None
+
+
+def test_alignment_panel_updates_when_auto_x_motor_changes(
+    qtbot, mocked_client_with_dap, monkeypatch
+):
+    wf = create_widget(qtbot, Waveform, client=mocked_client_with_dap)
+    wf.plot(arg1="bpm4i", dap="GaussianModel")
+    wf.x_mode = "auto"
+    wf.toolbar.components.get_action("alignment_mode").action.trigger()
+
+    wf._current_x_device = ("samx", "samx")
+    wf._alignment_panel.set_positioner_device("samx")
+    wf.scan_item = create_dummy_scan_item()
+    wf.scan_item.metadata["bec"]["scan_report_devices"] = ["samy"]
+
+    data = {
+        "samy": {"samy": {"val": np.array([1.0, 2.0, 3.0])}},
+        "bpm4i": {"bpm4i": {"val": np.array([10.0, 20.0, 30.0])}},
+    }
+    monkeypatch.setattr(wf, "_fetch_scan_data_and_access", lambda: (data, "val"))
+
+    wf._get_x_data("bpm4i", "bpm4i")
+
+    assert wf._current_x_device == ("samy", "samy")
+    assert wf._alignment_positioner_name == "samy"
+    assert wf._alignment_panel.positioner.device == "samy"
+
+
+def test_alignment_panel_disables_without_positioner(qtbot, mocked_client_with_dap):
+    wf = create_widget(qtbot, Waveform, client=mocked_client_with_dap)
+    wf.plot(arg1="bpm4i")
+    wf.x_mode = "index"
+
+    wf.toolbar.components.get_action("alignment_mode").action.trigger()
+
+    assert wf._alignment_panel.positioner.isEnabled() is False
+    assert "positioner on the x axis" in wf._alignment_panel.status_label.text()
+
+
+def test_alignment_marker_updates_from_positioner_readback(qtbot, mocked_client_with_dap):
+    wf = create_widget(qtbot, Waveform, client=mocked_client_with_dap)
+    wf.plot(arg1="bpm4i", dap="GaussianModel")
+    wf.x_mode = "samx"
+
+    wf.toolbar.components.get_action("alignment_mode").action.trigger()
+    wf.dev["samx"].signals["samx"]["value"] = 4.2
+    wf._alignment_panel.positioner.force_update_readback()
+
+    assert wf._alignment_controller is not None
+    assert wf._alignment_controller.marker_line is not None
+    assert np.isclose(wf._alignment_controller.marker_line.value(), 4.2)
+    assert "samx" in wf._alignment_controller.marker_line.label.toPlainText()
+    assert "4.200" in wf._alignment_controller.marker_line.label.toPlainText()
+
+
+def test_alignment_panel_uses_existing_dap_curves_and_moves_positioner(
+    qtbot, mocked_client_with_dap
+):
+    wf = create_widget(qtbot, Waveform, client=mocked_client_with_dap)
+    source_curve = wf.plot(arg1="bpm4i")
+    dap_curve = wf.add_dap_curve(device_label=source_curve.name(), dap_name="GaussianModel")
+    wf.x_mode = "samx"
+
+    wf.toolbar.components.get_action("alignment_mode").action.trigger()
+    fit_summary = make_alignment_fit_summary(center=2.5)
+    wf.dap_summary_update.emit(fit_summary, {"curve_id": dap_curve.name()})
+    wf._alignment_panel.fit_dialog.select_curve(dap_curve.name())
+
+    move_spy = MagicMock()
+    wf.dev["samx"].move = move_spy
+
+    assert wf._alignment_panel.fit_dialog.fit_curve_id == dap_curve.name()
+    assert wf._alignment_panel.fit_dialog.action_buttons["center"].isEnabled() is True
+
+    wf._alignment_panel.fit_dialog.action_buttons["center"].click()
+
+    move_spy.assert_called_once_with(2.5, relative=False)
+
+
+def test_alignment_target_line_toggle_updates_target_value_label(qtbot, mocked_client_with_dap):
+    wf = create_widget(qtbot, Waveform, client=mocked_client_with_dap)
+    wf.plot(arg1="bpm4i", dap="GaussianModel")
+    wf.x_mode = "samx"
+
+    wf.toolbar.components.get_action("alignment_mode").action.trigger()
+    wf._alignment_panel.target_toggle.setChecked(True)
+
+    assert wf._alignment_controller is not None
+    assert wf._alignment_controller.target_line is not None
+    assert wf._alignment_panel.move_to_target_button.isEnabled() is True
+
+    wf._alignment_controller.target_line.setValue(1.5)
+
+    assert "1.500" in wf._alignment_panel.target_toggle.text()
+
+
+def test_alignment_move_to_target_uses_draggable_line_value(qtbot, mocked_client_with_dap):
+    wf = create_widget(qtbot, Waveform, client=mocked_client_with_dap)
+    wf.plot(arg1="bpm4i", dap="GaussianModel")
+    wf.x_mode = "samx"
+
+    wf.toolbar.components.get_action("alignment_mode").action.trigger()
+    wf._alignment_panel.target_toggle.setChecked(True)
+    wf._alignment_controller.target_line.setValue(1.25)
+
+    move_spy = MagicMock()
+    wf.dev["samx"].move = move_spy
+
+    wf._alignment_panel.move_to_target_button.click()
+
+    move_spy.assert_called_once_with(1.25, relative=False)
+
+
+def test_alignment_mode_toggle_off_keeps_user_dap_curve(qtbot, mocked_client_with_dap):
+    wf = create_widget(qtbot, Waveform, client=mocked_client_with_dap)
+    source_curve = wf.plot(arg1="bpm4i")
+    dap_curve = wf.add_dap_curve(device_label=source_curve.name(), dap_name="GaussianModel")
+    wf.x_mode = "samx"
+
+    action = wf.toolbar.components.get_action("alignment_mode").action
+    action.trigger()
+    action.trigger()
+
+    assert wf.get_curve(dap_curve.name()) is not None
+
+
+def test_alignment_mode_toggle_off_clears_controller_overlays(qtbot, mocked_client_with_dap):
+    wf = create_widget(qtbot, Waveform, client=mocked_client_with_dap)
+    wf.plot(arg1="bpm4i", dap="GaussianModel")
+    wf.x_mode = "samx"
+
+    action = wf.toolbar.components.get_action("alignment_mode").action
+    action.trigger()
+    wf._alignment_panel.target_toggle.setChecked(True)
+    wf.dev["samx"].signals["samx"]["value"] = 2.0
+    wf._alignment_panel.positioner.force_update_readback()
+
+    assert wf._alignment_controller.marker_line is not None
+    assert wf._alignment_controller.target_line is not None
+
+    action.trigger()
+
+    assert wf._alignment_controller.marker_line is None
+    assert wf._alignment_controller.target_line is None
+
+
+def test_alignment_panel_removes_deleted_dap_curve_from_fit_list(qtbot, mocked_client_with_dap):
+    wf = create_widget(qtbot, Waveform, client=mocked_client_with_dap)
+    source_curve = wf.plot(arg1="bpm4i")
+    dap_curve = wf.add_dap_curve(device_label=source_curve.name(), dap_name="GaussianModel")
+
+    wf.toolbar.components.get_action("alignment_mode").action.trigger()
+    wf.dap_summary_update.emit(
+        make_alignment_fit_summary(center=1.5), {"curve_id": dap_curve.name()}
+    )
+
+    assert dap_curve.name() in wf._alignment_panel.fit_dialog.summary_data
+
+    wf.remove_curve(dap_curve.name())
+
+    assert dap_curve.name() not in wf._alignment_panel.fit_dialog.summary_data
+
+
+def test_alignment_controller_move_request_moves_positioner(qtbot, mocked_client_with_dap):
+    wf = create_widget(qtbot, Waveform, client=mocked_client_with_dap)
+    wf.plot(arg1="bpm4i", dap="GaussianModel")
+    wf.x_mode = "samx"
+
+    move_spy = MagicMock()
+    wf.dev["samx"].move = move_spy
+
+    wf.toolbar.components.get_action("alignment_mode").action.trigger()
+    wf._alignment_controller.move_absolute_requested.emit(3.5)
+
+    move_spy.assert_called_once_with(3.5, relative=False)
+
+
 def test_curve_set_data_emits_dap_update(qtbot, mocked_client):
     wf = create_widget(qtbot, Waveform, client=mocked_client)
     c = wf.plot(x=[1, 2, 3], y=[4, 5, 6], label="test_curve")