Focus Stacking

You can capture a series of images with varying focus that can be combined with third-party software to give you a greater depth of field. This is useful for macro where a typical f8 depth may be only 1 mm, but the subject has greater depth. ControlMyNikon can capture the images, but does not combine them. It can automatically export to Zerene Stacker, an excellent focus stacking application, or you can manually import your images to other processing applications.

Focus not moving while capturing a stack?  Check out our troubleshooting articlese for more info.

Creating a Focus Stack using the Lens Focus Motor

  1. Start ControlMyNikon and connect to your camera.
  2. Open live view.
  3. Go to the Workflow menu and select ‘Focus Stacking’.
  4. Position the camera, lighting and subject as desired.
  5. Set the focus on the nearest part of the subject by using the focus adjust buttons on the Stacking tab or contrast autofocus button on the live view screen toolbar.
  6. Enter the number of slices. This is the number of images that will be captured.
  7. Enter the step. This is how far the focus moves between image captures. The higher the number, the farther it moves. The lowest value of 10 barely moves the focus. This does not correspond to distance, but is an internal (unknown) firmware unit that varies per lens and body combination.
  8. Press the Preview button to see if you have adequate steps and slices to ensure you have enough depth of field coverage. If not, adjust the slices and steps and try again.
  9. When the preview looks ok, press the Capture button. If you have put a check-mark beside the ‘Subfolders’ box, a sub folder name ex. ‘Stack_20120808_132218’ will be created and the images inside it will have a counter that starts at zero. If the sub-folders box was unchecked, the images are placed in a ‘Stack’ folder and the filenames will use the normal file-naming settings from the body tab.

Using a StackShot to change the focus

Some Focus Stacking photographers prefer to physically move the camera during stacking, rather than have the focus motor adjust the focus. The leading hardware for this is the StackShot, available from CogniSys. It moves the camera on a rail in very precise increments.  You can use a Stackshot or StackShot 3X. If using the 3X, use Axis X on the Stackshot controller box.  If you have a StackShot, set it up with your camera and test object to shoot.

  1. Plug the StackShot into a USB2.0/3.0 connection.
  2. Position the camera with the Stackshot physcal console.
  3. In the ControlMyNikon Preferences screen Stacking tab, put a checkmark beside ‘Use StackShot’.
  4. Set the step to 1000. For StackShot use, the step represents x/1000 mm. So 1000 would be 1mm. The StackShot will move the camera 1mm per shot. Set this value as needed for your stack.
  5. Use the focus adjust buttons on the Stacking tab to move the camera along the StackShot rail until you arrive at the nearest focus needed for your capture. Press the ‘Zero’ button to mark this as the start point. This will be also done automatically when you start a preview or capture.
  6. Press the ‘Preview’ button. You will see the composition change in the live view screen after each increment. Make sure that you have enough slices of the correct step to get full depth of field coverage as needed.
  7. Keep previewing until it looks good. Then press the ‘Capture’ button to start the capture.
  8. Note: If you accidentally set too many steps resulting in too much rail travel, the StackShot will hit the endstop and make a growling noise. If you need to do an emergency stop, press the Cancel in the stacking tab.


  • If you enable the ‘Capture Live View image during stacking preview’ option in the Preferences screen, stacking tab, the current live view image is saved for each step. You can then stack these streamed jpegs very quickly and get a reasonable idea of whether you have enough depth of field coverage. Then, when you have everything set just right, do the Capture and the full size images will be saved and you can then use these for stack processing.
  • Put a checkmark beside ‘Auto-export to Zerene Stacker’ if you want the stack to be automatically loaded into Zerene Stacker upon capture completion. You’ll need to specify the path to Zerene Stacker in the Preferences window, Focus Stacking tab.
  • If you want a folder name that does not change in subsequent stacks, put a checkmark in the ‘Subfolders’ checkbox. This is required for Zerene Stacker ‘Directory Watch’ functionality so that it can start processing as the images are captured, not when the captured set is complete.
  • Only ‘CPU’ lenses can be controlled by ControlMyNikon. These allow for remote focus motor control Some non-Nikon lenses are CPU controlled, but may not respond to the Nikon body commands to change the focus during stacking.
  • Be sure to read the ‘Preparing Your Camera’ help. This will show how to configure the body for focus stacking.
  • This is only available for cameras that have live view.
  • This is also known as ‘Depth of Field Stacking’ or ‘DOF Stacking’
  • Be sure to calibrate your white balance before capturing. This will save you a lot of post processing.
  • To get started with processing the stack, there is also the free CombineZP that is still around the internet. It is somewhat old and does not do as good as a job as Zerene Stacker, but is good to experiment with.
  • Mirror-up: This doesn’t work while tethered and cause live view to hang. This is a firmware limitation.