diff --git a/PYME/Acquire/SpoolController.py b/PYME/Acquire/SpoolController.py
index ae1dd27c9..666414bbe 100644
--- a/PYME/Acquire/SpoolController.py
+++ b/PYME/Acquire/SpoolController.py
@@ -414,7 +414,8 @@ def StartSpooling(self, fn=None, stack=None, compLevel=None,
         if stack:
             protocol = protocol_z
             protocol.dwellTime = z_dwell
-            #print(protocol)
+            stack_settings = stack if hasattr(stack, 'keys') else None
+            protocol.set_stack_positions(stack_settings)
         else:
             protocol = protocol
 
diff --git a/PYME/Acquire/protocol.py b/PYME/Acquire/protocol.py
index 056d6fc77..6950bd621 100644
--- a/PYME/Acquire/protocol.py
+++ b/PYME/Acquire/protocol.py
@@ -192,11 +192,14 @@ def __init__(self, taskList, startFrame, dwellTime, metadataEntries=[], prefligh
             self.slice_order = slice_order
 
         self.require_camera_restart = require_camera_restart
-
-    def Init(self, spooler):
-        self.zPoss = np.arange(scope.stackSettings.GetStartPos(),
-                               scope.stackSettings.GetEndPos() + .95 * scope.stackSettings.GetStepSize(),
-                               scope.stackSettings.GetStepSize() * scope.stackSettings.GetDirection())
+    
+    def set_stack_positions(self, stack_mdh=None):
+        stack_mdh = dict() if stack_mdh is None else stack_mdh
+        start = stack_mdh.get('StackSettings.StartPos', scope.stackSettings.GetStartPos())
+        stop = stack_mdh.get('StackSettings.EndPos', scope.stackSettings.GetEndPos())
+        direction = 1 if stop > start else -1
+        step = direction * stack_mdh.get('StackSettings.StepSize', scope.stackSettings.GetStepSize())
+        self.zPoss = np.arange(start, stop + .95 * step, step)
 
         if self.slice_order != 'saw':
             if self.slice_order == 'random':
@@ -208,9 +211,10 @@ def Init(self, spooler):
                 else:
                     # even
                     self.zPoss = np.concatenate([self.zPoss[::2], self.zPoss[-1::-2]])
+        
+        self.piezoName = 'Positioning.%s' % stack_mdh.get('StackSettings.ScanPiezo', scope.stackSettings.GetScanChannel())
 
-
-        self.piezoName = 'Positioning.%s' % scope.stackSettings.GetScanChannel()
+    def Init(self, spooler):
         self.startPos = scope.state[self.piezoName + '_target'] #FIXME - _target positions shouldn't be part of scope state
         self.pos = 0