Abbreviated AFM manual

Version 27-5-2014

Contents
1.

Atomic force microscopy ............................................................................................................ 2

2.

Mounting a sample ..................................................................................................................... 3

3.

Initializing the easyScan 2 Controller ......................................................................................... 3

4.

Positioning the sample under the AFM ...................................................................................... 3

5.

Loading parameter values .......................................................................................................... 4

6.

Approaching the sample............................................................................................................. 4

6.1. Manual course approach....................................................................................................... 4
6.2. Manual approach using the motorized approach stage ....................................................... 5
6.3. Automatic final approach ...................................................................................................... 5

7.

Starting a measurement ............................................................................................................. 6

8.

Image quality deteriorates ......................................................................................................... 7

9.

Storing a measurement .............................................................................................................. 7

10. Finishing measurements............................................................................................................. 7

11. Turning off the instrument ......................................................................................................... 7
12. Using the Gwyddion software for visualization and processing of images ................................ 7

1. Atomic force microscopy

The AFM microscopy technique works without optical focusing elements. Instead, a small sharp probing tip is scanned
very closely across the sample surface. The distance between
the tip and the sample surface is so small that atomic-range
forces act between them. In an AFM, a tip is attached to the
end of a cantilever in order to measure these forces (figure 1).
The force acting on the tip can then be determined by detecting the deflection of this cantilever.

Figure 1: Cantilever. 228 m long silicon

cantilever with integrated tip.

The measurement of the cantilever deflection can be used to control the tipsurface distance on an
atomic scale. Thus, enormous resolution can be achieved, so that even the atomic arrangement of
surfaces can be probed. This measurement is a so-called static operating mode, in which the static
deflection of the cantilever is used. Generally, the forces acting on the tip will cause it to snap onto
the sample, which result in an effective, nanometre-range flattening of the tip, and friction and stiction between the tip and the sample.
To circumvent the aforementioned problems, we will use the AFM in so-called dynamic mode. In this
mode, the cantilever vibrates during the operation. Changes in the free resonance frequency and the
damping of the cantilever vibration caused by the forces between the tip and the cantilever are
measured and used to regulate the tipsample distance.
In dynamic mode, the cantilever is excited using a piezo element. This piezo is oscillated with a fixed
amplitude at an operating frequency close to the free resonance frequency of the cantilever. The
repulsive force acting on the tip will increase the resonance frequency of the cantilever. This will
cause the vibration amplitude of the cantilever to decrease. The vibration of the cantilever is also
detected using the cantilever deflection detection system. The measured laser beam deflection or
cantilever vibration amplitude can now be used as an input for a feedback loop that keeps the tip
sample interaction constant by changing the tip height. The output of this feedback loop thus corresponds to the local sample height (figure 2).

Figure 2: SPM system. Cantilever with deflection detection system scanning the sample. The sample is visualized on a computer with installed
scan software, which also directs the scan itself.

An image of the surface is made by scanning over the sample surface in the X and Y direction. The
sample structure image is now obtained by recording the output of the height control loop as a function of the tip position.

2. Mounting a sample
To mount a sample onto the Sample Holder:
1. Put a double-sided adhesive tape on the front side of a
Post-it note, so that it is on the opposite side of the sticky
part.
2. Cut off all parts of the note that do not have adhesive tape
on it.
3. Fix the tape-side of the prepared note to the Sample Holder.
4. Put the sample on the sticky side of the Post-it note, and
press on it lightly.

Figure 3: Sample mounted onto

the Sample Holder

The result should resemble figure 3.

3. Initializing the easyScan 2 Controller

To initialize the easyScan 2 controller:
1. Make sure that the easyScan 2 controller is connected to the mains power, to the scan head
and to the USB port of the control computer.
2. Turn on the power of the easyScan 2 controller.
First all status lights on top of the controller briefly light up. Then the Scan Head lights and
the lights of the detected modules will start blinking, and all other status lights turn off.
3. Start the Nanosurf easyScan 2 Control Software on the control computer.
The main program window appears, and all status lights are turned off. Now a Message
Controller Startup in progress is displayed on the computer screen, and the module lights
are turned on one after the other. When initialization is completed, a Message Starting System is briefly displayed on the computer screen, and the Probe Status light, the Scan Head
status light of the detected scan head, and the Module lights of the detected modules will
light up. If no scan head is detected, both Scan Head Status lights blink

4. Positioning the sample under the AFM

IMPORTANT
Never touch the cantilever! The cantilever and the tip are made of silicon which is extremely brittle.
The slightest touch will break it. Tips are expensive and it might cost half an hour to replace one. Be
extremely careful when you move the sample holder under the tip. Make sure the tip is at least 1.5
mm above the sample when you move the sample holder.
See figure 4.

Place the Sample Holder on the Sample Stage. The Sample Holder is magnetic so it will stick onto
the Sample Stage.

Use the three levelling screws to raise the

Scan head so that the cantilever is at least 5
mm above the sample on the Sample Holder.
Position the sample under the tip of the AFM
by sliding the Sample Holder over the Sample
Stage.

5. Loading parameter values

1. Open the menu item File >> Parameters >>
Figure 4: The easyScan 2 AFM Scan Head on its Sample
Load..., and load the file AFM ST222.par
Stage
from the directory
D:\Nanosurf\Configuration.
2. Open the menu item File >> Chart Arrangement >> Load..., and load the file AFM ST222.chart
from the directory D:\Nanosurf\Configuration.

6. Approaching the sample

To start measuring, the cantilever tip must come within a fraction of a nanometre of the sample
without touching it with too much force. To achieve this, a very careful and sensitive approach of the
cantilever is required. This delicate operation is carried out in three steps: Manual coarse approach,
Manual approach using the motorized approach stage, and the Automatic final approach.
The controls for positioning the cantilever with respect to the sample are located in the Approach
group.
During the approach steps described in the following sections, use the side view lens of the scan
head to judge the distance between tip and sample surface.

6.1. Manual course approach

In this step, the sample surface is brought within the range of the motorized approach stage of the
Scan Head. To perform a manual coarse approach:

Use the three levelling screws to lower the

Scan head so that the cantilever is within 12
mm of the sample. Take care that the Scan
head remains parallel to the sample surface by
approximately turning all screws equally and
using the accompanying level.
The side view should now look as shown in
figure 5. When the sample is reflective, the
mirror image of the cantilever should be visible. When the sample is not reflective, the
shadow of the cantilever may be visible. If neither a mirror image nor a shadow is visible,
change the environment light until it is. You
can use the cantilever as a ruler to judge distances in the views of the integrated optics.

Figure 5: Side view of sample and cantilever after manual

coarse approach.

6.2. Manual approach using the motorized approach stage

In this step, the tip is brought as close to the sample surface as possible, without touching it. The
closer the two are together, the less time the automatic final approach takes.
1. Observe the distance between tip and sample in the side view of the integrated optics.

Figure 6: View of sample and cantilever after manual approach using the motorized approach stage. (Left) side view,
(Right) top view.

2. While observing the tipsample distance, click and hold the Advance button in the Approach group of the Acquisition tab until the tip is close enough to the sample:

The tip should not come closer to the sample than a few times the cantilever width (figure 6,
left).
Now that the sample is in focus, the top view image can be used to find a suitable location to measure on. In top view, the sample is seen from a direction perpendicular to its surface (see figure 9,
right).

Use the top view lens to observe the sample. If necessary, move the Sample Holder to find a
suitable location that is free of dust particles. Note that if the sample touches the tip while repositioning, the tip will be destroyed. Therefore, because a sample is never completely level,
only small corrections of the position are allowed. Before larger corrections, first raise the tip at
least 1.5 mm above the surface of the sample.

6.3. Automatic final approach

In this last step, the tip automatically approaches the sample until a given Setpoint is reached.
Once the automatic final approach is started, the colour of the Status light on the controller shows
the current status of the approach:

Orange/yellow
Normal state during approach: the Z-scanner is fully extended toward the sample.

Red
The approach has gone too far: the tip was driven into the sample, and the Z-scanner is fully
retracted from the sample. In this case, the tip is probably damaged and you will have to install a new cantilever again.
Green
The approach has finished successfully: the Z-scanner is within the measuring range.

1. In the Approach group of the Acquisition tab, click the Approach button:

The cantilever is moved towards the sample via the approach stage, with the Z-Controller
turned on. This movement continues until the Z-Controller error becomes zero. From this
point onward, the distance between sample and tip is maintained automatically by the electronics. The probe status light changes to a constant green, and a message Approach done
appears:

2. Click the OK button.

7. Starting a measurement
Now that the tipsample interaction defined by Setpoint is established between tip and sample,
measurements can start. By default, the instrument is set to automatically start measuring after the
automatic approach. If this is not the case start measurements manually by clicking the Start button in the Imaging group of the Acquisition tab.
Two representations of the on-going measurement are drawn in the Imaging panel. One representation is a colour coded height image (Topography) called a Colour map. The other is a plot of height as
a function of X position called a Line graph. With the current settings, the software automatically
adjusts the contrast of the Colour map, and height range of the Line graph to the data that have been
measured.
To judge the imaging quality, watch the displays until at least one fourth of the measurement has
been completed.

IMPORTANT
Measurements on the micrometre/nanometre scale are very sensitive to environment influences.
Direct light or fast movements causing air flow and temperature variations near the Scan Head
can influence and disturb the measurement.
The parameters of the scan may be changed during scanning. Scanning will automatically restart with
the new parameters.

With the loaded parameters, the time per line is 0.5 s and the number of points is 128. This is
suitable for a fast exploratory scan. For a final scan, adjust these parameters to 1 s per line and
256 points per line.

8. Image quality deteriorates

When a scan line suddenly starts reproducing badly, the tip may have picked up some particles.
To get rid of these particles, follow the procedure below until the image quality improves:
1. Continue measuring for a while (12 images), as the tip may eventually lose these particles
again.
2. In the Approach group of the Acquisition tab, click the Withdraw button to retract the cantilever, and then perform a new approach.
If no improvement occurs after following the steps above, refer to the instructions in the easyScan 2
AFM Operating Instructions manual (Chapter 9: Problems and solutions, page 99).

9. Storing a measurement
By default, each completed measurement is temporarily stored (automatically) in the directory
D:\Nanosurf so that it can be used later. Additionally, you can also take snapshots of measurements
still in progress. To do this click the Capture button in the Chart bar.
Stored measurements will show up in the History page of the Gallery panel. Measurement documents in the temporary History folder should always be moved to a new location (and preferably
renamed) for permanent storage when you are done measuring.

10. Finishing measurements

Once you are done measuring:
1. In the Imaging group of the Acquisition tab, click the Stop button to stop measuring.
2. Retract the cantilever to a safe distance from the sample by clicking the Home button and
waiting for the automatic full withdraw process to finish.
3. Remove the sample holder from the sample stage while taking care that you dont touch the
cantilever.
4. Remove the sample from the sample holder.

11. Turning off the instrument

To turn off the instrument:
1.
2.
3.
4.

Exit the Nanosurf easyScan 2 Control Software.

Turn off the power switch on the controller.
Remove the cable from the Scan head.
Store the Scan head in the Scan head case.

12. Using the Gwyddion software for visualization and processing of images
1. Start the Gwyddion program.
2. Open a measurement file (.nid file extension).
7

3. Display a 3D view of the data by clicking the corresponding icon in the View pane of the main
window.
4. Use the controls in the window of the 3D view to adapt the view: rotation, scaling, colours,
labels etc.
5. Process the data by clicking the function icon in the Data Process pane of the main window.
Two much used functions are:
- Level data by mean plain subtraction
- Correct lines by matching height median.
Use Ctrl+Z and Ctrl+Y to undo or redo applied functions.
6. The 3D image can be saved by clicking the Save icon in the window of the 3D view. The file
extension you enter determines the file format: .png, .gif, .jpg or .bmp.
7. Height differences and distances can be measured in the window of the 2D view by clicking
the corresponding icon in the Tools pane of the main window:
- Read value under mouse cursor
- Measure distances and directions between points.
8. The 2D image can be saved by clicking File >> Save As in the main window. The file extension you enter determines the file format: .png, .jpg or .bmp.