SPM/AFM calibration, X-Y

The scanning movement of the sample relative to the tip is performed by piezo-electric crystals. These crystals have a very non-linear relation between applied voltage and movement (elongation, contraction).

Therefore the scanner has to be calibrated so that the software "knows" how much the scanner is moved for a certain applied voltage. This is shortly described in this web-page for software version 6.

You must also refer to the chapter about calibration in the printed manual for the Nanoscope system, Veeco, formerly Digital Instruments.

Here is an overview of the desktop for the version 6 of the SPM controlling software. From left to right:

  1. The workspace parts, you can load and save workspaces. The workspace automatically remembers the scan-method and opened images you used. Items in the list are added as you select other methods of scanning, open new images and do processing on them etc.
  2. A scanning window. Here the image is collected and parameters for scanning is set. Note that this is the scanning method called "Scan - Single".

    This method MUST be used for calibration.

    You will get a prompt to set it if it is not active.
  3. The complete parameter window. Here all settings are available for all types of scanning.
  4. The directory (folder) where images are captured, here it is empty. Images will appear with a small icon as they captured.
  5. The real-time status bar for the Z-piezo.

Overview of desktop in ver. 6.


A calibration sample with a known pattern size is used. With the system is currently two scanners:

Scanner Serial # Max. Scan area Ref. sample
J 5337EJ 100 × 100 µm 10 µm pitch, square grid
E 5346EV 10 × 10 µm 1 µm pitch, square grid

The reference sample is a matrix of squares etched down to 200 nm below surface with a size of roughly half the pitch. Please remember that it is the pitch that is the reference distance, not the size of each square.

The calibration is done in three steps:

  1. The linearity and center compression/expansion are adjusted in a special scanning window, follow the manual, chapter about calibration.
  2. The calibration images are captured, the user must do some adjustments during the four first images.
  3. The calibration images are presented one by one for the user who indicates the real distances in the images. When indicating distances always use a full pitch distance, not just the size of a square. Preferably indicate several multiples of the pitch for higher accuracy in the calibration.


  1. See to it that the correct scanner is selected in the software, and that the scanner is mounted on the Multimode SPM.
  2. It is good practice to make backup copies of the calibration files in the equip-folder. The filename is the scanner serial number with suffix .scn
  3. Set up the scanner for contact mode using a good tip intended for contact mode.
  4. Start the "Scan Single" scanning mode.
  5. Approach the surface, set-point -0.5 V to 0.0 V.
  6. Adjust the proportional gain and integral gain so that you are a couple of clicks below self oscillations. By clicks is meant left-arrow clicks on the corresponding parameter.
  7. Follow the manual, chapter about calibration, there is described which parameters should be adjusted for linearity and center adjustment. The description is for software version 5. Below is described how to use software version 6, it is quite similar. The most important scanning parameters should be set so that: Follow the manual, there are other parameters to change also.
There is a difficulty when using the 1 µm reference sample. The matrix is not resolved by the microscope and there is very little dirt particles on the surface. To set the cantilever close to the surface manually using the microscope image you have to use the mirror image of the cantilever. The surface is midpoint between the focus positions for the real cantilever and the mirror image of it.

To start the adjustment of linearity and center compression/expansion use drop-down menu Tools —> Calibrate —> X-Y... to start a special scanning window used for these adjustments.

Start adjustment window


A new window showing all the parameters for the scanner is popped up.

Scanner calibration parameters.


Click button Image, this will extend the window with a live image scan.

Parameter window extended with live scanning window


To start measure, click and drag in the image window. A rectangle will be displayed and its x-y size is shown in the lower left corner (marked in green). The size-values should be near the reference values unless the initial calibration done at the factory is seriously wrong.

Size the window by clicking and dragging at the borders of the rectangle. Set the size so that it is equal to 2 × the pitch, i.e. covering two periods of the reference pattern.

Compare the size of the scanned pattern at the first third of the scan with the size at the last third of the scan. All this is described in detail in the calibration chapter in the printed manual. Follow the instructions to adjust linearity and center compression/expansion.

Size rectangle to two full periods of the ref. pattern.
Compare sizes of 1:st and last thirds of the scan.


Capture calibration images

Use drop-down menu RealTime —> Capture Calibration to start the capture of calibration images.

Start Capture Calibration


Here is decided which parts of the calibration is to be performed. Usually all variants should be ticked. All images will have a filename according to the prefix with a suffix according to the type of calibration, cxx, cyy etc.

To start click Capture.

Click Capture to start.


During the capture there is a window for adjustments of capture. The four first images are scanned either horizontally or vertically, much like when scanning with Slow Scan Axis = Disabled. Then the user have to adjust so that the scan line is completely across the squares. Here it is a horizontal scan that can be adjusted up or down to scan over the center of a row of reference squares.

The Skip button is to increase the number of image scans that are skipped before the actual capture takes place. The two first images are always skipped in order for the piezos to settle in the scan mode.

Adjust Y offset so that scan is over row of ref. squares.


Here is an image being scanned during adjustment, the new image is being scanned from top to bottom, i.e. it is the upper half that is the current image.

During the scanning the offset buttons were clicked to center the scan-line on a row of reference squares. The irregular scan-lines in the upper third of the image are disturbances from the adjustment.

Image scan during adjustment of capture,
up/down to center scan-line across ref. squares.

Twelve images are captured, one for each type of parameter to be calibrated. This takes about an hour in total. The four first images needs the user adjustment during scanning, as described above. The rest should not need user attention unless temperature drift makes the Z-piezo go to either fully extended or fully retracted.

The calibration capture can be stopped and continued, only tick in the types of images that are missing. See the Capture Calibration start window.


Auto calibration, user measurement

The next step is where all the calibration images are presented for the user one by one, and the user indicates a length in each image and supplies the real length according to the known reference sample.

Drop down menu Tools —> Calibrate —> Auto Calibration.


Select the folder where the calibration images were stored, select the first image, click Open.

Open first calibration image.


The calibration image called calibrat.cxx is displayed.
To the right is a list of parameters to calibrate. In most cases they should all be set to Yes.
Start the calibration by clicking the Calibrate button.

Start by clicking Calibrate.


The image belonging to the first parameter to be calibrated, is displayed. You can only draw a vertical line in the image.

Start drawing a vertical line.


You can only draw vertically, start at a well defined boundary and count a whole number of periods.
Do not start the line at the very edge of the image, start some 10-20 % inside the image.
One period is equal to the pitch of the reference sample.
In this image ten periods are indicated by the vertical line. Please note that the little info-square is showing completely wrong information.

Draw line over an integer number of periods, reference sample pitch.


When the mouse button is released the software "guess" the actual distance, it is displayed in the New Distance-entry.
It should normally be rather close to the real distance given by the known reference sample pitch.

Mouse button released, distance "guessed" by software.


Next the user enters the known distance value as given by the number of periods spanned by the line,
in this case 10 × 1 µm.
The "E"-scanner is used in this example, it requires a reference sample with a pitch of 1 µm.
Click Apply-button, the parameters are recalculated according to the new distance given, and the next calibration image is displayed.

Enter true distance value, clickApply-button.


The next image is displayed, draw vertical line over an integer number of periods, and give the true length value, click Apply.

Next image, draw line over integer number of periods,
give true length value, click Apply.


And so on...

And so on...


Some image require a horizontal line instead.

Horizontal line...


When all images have been measured, the pop-up below appears instead of a new calibration image.
The calibration data has been re-computed and the calibration file is re-written.

Just click OK


In order to use the new calibration parameters you must re-load the workspace.

Reload workspace to use new calibration parameters.

Anders Liljeborg Nanostructure Physics, KTH.