diff --git a/csaxs_bec/bec_ipython_client/plugins/flomni/x_ray_eye_align.py b/csaxs_bec/bec_ipython_client/plugins/flomni/x_ray_eye_align.py
index 6979c81..55f4722 100644
--- a/csaxs_bec/bec_ipython_client/plugins/flomni/x_ray_eye_align.py
+++ b/csaxs_bec/bec_ipython_client/plugins/flomni/x_ray_eye_align.py
@@ -31,6 +31,11 @@ class XrayEyeAlign:
     test_wo_movements = False
     PIXEL_CALIBRATION = 0.1 / 113  # .2 with binning
 
+    # Sign for the automatic vertical-centering move in the height-centering
+    # branch of _align_impl (search for `_height_centered`).
+
+    HEIGHT_CENTERING_SIGN = -1
+
     def __init__(self, client, flomni: Flomni) -> None:
         self.client = client
         self.flomni = flomni
@@ -58,6 +63,11 @@ class XrayEyeAlign:
     def _reset_init_values(self):
         self.shift_xy = [0, 0]
         self._xray_fov_xy = [0, 0]
+        # Guards the height-centering branch below: True once the automatic
+        # vertical-centering move has been applied for this alignment run,
+        # so a second submission at step==1 is treated as the real angle-0
+        # fit point instead of triggering another height correction.
+        self._height_centered = False
 
     def update_frame(self, keep_shutter_open=False):
         if self.flomni._flomnigui_check_attribute_not_exists("xeyegui"):
@@ -106,7 +116,7 @@ class XrayEyeAlign:
         self.flomni.flomnigui_show_xeyealign()
         self.gui.set_dap_params_forwarding(True)
         self.gui.reset_zoom()
-    
+
         try:
             self._align_impl(keep_shutter_open)
         finally:
@@ -196,6 +206,12 @@ class XrayEyeAlign:
                 print(f"Corrected position {k}: x {self.alignment_values[k]}")
                 # reset submit channel
                 dev.omny_xray_gui.submit.set(0)
+
+                # Controls whether `k` advances to the next step below. Left
+                # True except for the height-centering submission, which
+                # reuses k==1 for a second, real submission afterwards.
+                advance_step = True
+
                 if k == 0:  # received center value of FZP
                     self.send_message("please wait ...")
                     self.movement_buttons_enabled(False, False)
@@ -222,10 +238,49 @@ class XrayEyeAlign:
                     self.gui.set_crosshair_position(fzp_center_x, fzp_center_y)
                     self.gui.show_crosshair()
 
-                    self.send_message("Step 1/5: Adjust sample height and submit center")
+                    self.send_message(
+                                            "Adjust sample height with the arrows if needed, then mark "
+                                            "the sample and submit - height will be centered automatically"
+                                        )
                     self.gui.enable_submit_button(True)
                     self.movement_buttons_enabled(True, True)
 
+                elif k == 1 and not self._height_centered:
+                    # First submission after the FZP center: a ROI mark of
+                    # the sample, used only to auto-center fsamy against the
+                    # FZP-center crosshair (not yet a real fit point - see
+                    # HEIGHT_CENTERING_SIGN above for the open sign question).
+                    self.send_message("please wait ...")
+                    self.gui.enable_submit_button(False)
+                    self.movement_buttons_enabled(False, False)
+
+                    fzp_center_y = dev.omny_xray_gui.yval_y_0.get()
+                    mark_y = dev.omny_xray_gui.yval_y_1.get()
+                    delta_y_mm = (
+                        self.HEIGHT_CENTERING_SIGN
+                        * (fzp_center_y - mark_y)
+                        / 2
+                        * self.PIXEL_CALIBRATION
+                    )
+                    print(
+                        f"Height centering: fzp_center_y={fzp_center_y}, mark_y={mark_y}, "
+                        f"delta_fsamy={delta_y_mm:.5f} mm"
+                    )
+
+                    self.flomni.feedback_disable()
+                    if not self.test_wo_movements and delta_y_mm != 0:
+                        self.flomni.umvr_fsamy_tracked(delta_y_mm)
+                        time.sleep(2)
+                    self.flomni.feedback_enable_with_reset()
+
+                    self._height_centered = True
+                    self.update_frame(keep_shutter_open)
+
+                    self.send_message("Step 1/5: Submit sample center")
+                    self.gui.enable_submit_button(True)
+                    self.movement_buttons_enabled(True, False)
+                    advance_step = False
+
                 elif 1 <= k < 5:  # received sample center value at samroy 0 ... 315
                     self.send_message("please wait ...")
                     self.gui.enable_submit_button(False)
@@ -248,8 +303,9 @@ class XrayEyeAlign:
                     self.gui.hide_crosshair()
                     break
 
-                k += 1
-                dev.omny_xray_gui.step.set(k)
+                if advance_step:
+                    k += 1
+                    dev.omny_xray_gui.step.set(k)
 
             _xrayeyalignmvx = dev.omny_xray_gui.mvx.get()
             if _xrayeyalignmvx != 0: