Atomic Force Microscopy​ (​Tapping​ ​Mode​)

This manual is expected to make the user familiar in handling the software (Nano Drive) for obtaining
images using tapping mode AFM (Bruker Innova). It is a brief overview of the steps required to do so.
Before proceeding further, make sure that the cartridge with loaded probe is mounted properly inside the
stage and the sample is placed upon the sample holder.

Step 1​ : ​Starting the Software

I. After turning on the PC set-up, switch ​ON​ the controller.

II. Open ​Nano Drive​ software.

Note : The user may encounter a pop up regarding whether the controller is ​ON ​or ​not​. ​If so​, ​make
sure that the controller is on & then proceed.

III. As the system configuration window appears, select ​Tapping & then ​Load Experiment ​(as shown
in Fig 1 : ​1→2→3​)
IV. After this, the main window (Fig 2) will appear for accessing and controlling the system.

​Figure 1 Figure 2

Step 2​ : ​Laser alignment

There are three pair of knobs in the stage (Fig 3)

​a​,​ b​ - ​Laser movement

c​, ​d​ - ​PSPD alignment
e​, ​f​ - ​Stage movement

I. First locate the laser spot with naked eye.

II. Rotate (​a​, ​b)​ to place the laser spot on the probe.
 III. Locate the cantilever and the laser spot in the navigator window. If the laser is not on the cantilever,
then again rotate (​a​, ​b)​ to place it right on the edge of the cantilever (Fig 4).

​Figure 3 Figure 4

Step 3​ : ​PSPD​ ( ​Position Sensitive Photodetector​ ) ​alignment

The ​Workflow Toolbar ​looks like this (Fig 5).

Figure 5

I. Open the ​Laser Alignment Dialog​ . A window appears (Fig 6)

Note ​: The window is divided into ​four quadrants ​which are used to locate the laser spot falling
onto the ​PSPD​, after being deflected from the edge of the cantilever (Fig 7). The two voltage
readouts at the axes indicates the offset of the spot from the center. The ​Sum is the combined value
of the laser power falling onto each of the quadrants.

Figure 6 Figure 7

II. Notice the five light indicators of the stage (Fig 3). Goal is to make the center indicator turn green.
If any of the other indicators is red, rotate (​c, d​) in the opposite direction until the red is turned off.

Note​ : Do not disturb the laser alignment knobs (​a,b​) while doing the PSPD alignment.
 III. If the deflected laser is placed right on the center of the PSPD, only the center indicator will stay
green while the other indicators will remain off. Also observe that the circular spot in the ​Laser
Alignment Window​ will be near the center of the cross and pink in colour.

Note ​: Optimize the alignment by placing the spot exactly at the center of the cross and try to
maximize the ​Sum​ signal. Sometimes it may happen that the ​Alignment Window ​is showing the
Sum to be near zero or negative although the laser is placed right on the edge of the cantilever. ​If
so​, remove the cartridge, mount the probe properly & reinsert the cartridge into the stage. The user
has to repeat the laser alignment & PSPD alignment again in that case.

Step 4​ : ​Approach the Sample

I. Open the ​Motors Control Dialog (Fig 8). Bring the

stage downward.

Note ​: Reduce the speed when the sample and the cantilever
are quite close.

II. Locate the sample and the cantilever in the navigator window &
focus on the sample and then defocus a little.
III. Again lower the stage at slow speed till both the sample and
the cantilever can be found within a small rotation of the
focusing knob.
Figure 8
Note​ : The cantilever should not crash upon the sample. If
somehow the stage is moving downwards automatically, press the stop button immediately.

IV. Cover the stage with the lid.

Step 5​ : ​Cantilever Tuning​ (​Before Engaging​) :

I. Open the ​Tune Cantilever Dialog​ (Fig 9).

II. Set the suitable range (resonant frequency of the probe in
use, is most likely to be found within this range).

Note : ​We are using ​RTESPA 300 ​probe. It has a

resonant frequency near 300 kHz. So the range of 0-1000
kHz is appropriate.
Figure 9
The cantilever can be tuned both manually and automatically. In our case we opt for auto tuning as
it is much easier. As ​Auto Tune ​is selected, an additional parameter - ​Target Tapping Signal​, can
be seen.

The cartridge for ​Tapping Mode AFM​ contains a ​Piezo​ element. As the piezo starts to vibrate near
the cantilevers’ resonant frequency, it induces the cantilever to oscillate (Fig 10).

Drive Amplitude ​- The amplitude of the piezo vibration.

Drive Frequency ​- The frequency of the piezo vibration. If it matches the resonant frequency of the
cantilever then only the cantilever will oscillate with significant resonant deflection.
 Target Tapping Signal ​- It refers to the​ ​amplitude of cantilever oscillation in free air.
Phase ​- It is the phase shift between the piezo vibration & the cantilever oscillation (Fig 11)

Figure 10 Figure 11

III. Click the ​Auto Tune​ and select the ​Target Tapping Signal​.

Note ​: The value of ​Target Tapping Signal​ depends on the choice of cantilever. In our case, ​3-4 V
is recommended but the user may change it at his/her own convenience.

IV. Select the ​Input Gain​.

Note : ​Input gain refers to the gain applied to the cantilever signal. Working at higher gain values
indicate small amplitude oscillation of the cantilever. In our case, x​4​/x​8​/x​10 value is recommended
as ​Input Gain​ but the user may change it at his/her own convenience.

V. Click the start icon to initiate the autotuning procedure.

Note : ​The software adjusts ​Drive Amplitude​ and ​Phase​ by itself & replaces any previous value in
the drive amplitude box. After the tuning is finished, a plot similar to Fig 12 is obtained :

Figure 12

Observe the ​Peak Amplitude ​is at a frequency slightly lower than the ​Resonant Frequency
obtained. ​Peak Amplitude ​corresponds to the ​Target Tapping Signal ​given by the user.

VI. Close the ​Tune Cantilever Dialog​.

Step 6​ : ​Engaging the Tip of the Cantilever​ :

I. Focus the camera over the sample & click on the ​Engage the Tip ​icon from ​Workflow
Toolbar​.

Note : ​In the navigator window, the cantilever can be seen approaching towards the sample and
getting engaged.

II. After successful engage, the ​Scanning Control​ window appears (Fig 13).

Figure 13

Step 7​ ​: ​Taking a Tapping Mode Image​ ​:

I. Click on the ​Channels option from ​Additional Controls​. From the ​Acquire ​window, select the
desired display channels. Selected channels will appear in the ​Image Panel ​of the ​Main Window​.

Note : In our case we will be using ​Height - Forward & ​Backward, Tapping Amplitude - Forward
& ​Backward ​channel. But the user is encouraged to select any other channel he/she wants to. The
Height ​channel is selected to study the ​Surface Topography of the sample, ​Tapping Amplitude
channel is selected to observe how the amplitude of the cantilever oscillation changes as it scans
over the surface.

II. In the ​Image Panel​, select the ​Imaging Options​.

Note : ​For all the ​Image Channels​, selected options should be the same. In our case, we will be
using ​‘1D Bow Removal’ as ​Leveling Type​. Select ‘​ Auto’ for all the channels. Again the user is
encouraged to explore other options.

III. In the ​Scanning Control ​window, set the following parameters :

A. Sample​/​Lines​ - Number of data points acquired while scanning in X-Y direction.

​256 ​or ​512 w
​ ill be sufficient.
B. Scan Rate​ - Number of lines scanned per second in X direction.
Begin with ​1.000​ ​Hz​. Lower scan rate improves image quality.
C. Scan Range​ - Sets the area of scanning. Set as required. Max​ ​- ​5​ ​μm ​x ​5 μm​.
D. Rotation​ - For scanning the sample an angle offset from the usual axis. Keep it ​0.0​o​.
 E. X,Y Offset​ - Offset in X and Y direction from the center of the full XY scan range.
Make both of them zero to avail the maximum scan range.

IV. In the ​Scanning Control ​window, click on the ​Play ​icon .

Note ​: This initiates scanning process. Images will appear in respective channel windows. In
Scanning Control ​window, select ​Profile ​to observe the line being scanned (Switch to the proper
channel from the drop down menu just below). ​Red ​& ​Black ​corresponds to ​Forward ​& ​Backward
scanning respectively. In case of ​proper scanning​, ​profile​ for both type of scanning must be
identical​.

V. Go to ​Feedback Parameter Controls ​in ​Main Window and modify the following parameters to
obtain better quality images :

A. Setpoint - Reduced target amplitude of cantilever oscillation after ​successful Engaging of

tip onto the sample surface. ​Autotuning ​automatically sets it to ​60% ​of the ​Target Tapping
Signal​. User can set it as per his/her own requirement. ​Feedback ​loop keeps the amplitude
of cantilever oscillation (while it scans), close to ​Setpoint ​value.

B. PID Feedback Loop - The ​Proportional (​P​), ​Integral (​I​) and ​Derivative (​D)​ gains are the
scaling factors that specifies how quickly the corrections are applied in the feedback loop.
The user may modify the values to record the scanning with minimal noise.

Note ​: If ​too much dragg (​noise in obtained signal) is observed, try to ​reduce ​the ​Setpoint ​value.
Do not ​change the ​PID values drastically as ​severe oscillation may ​damage the probe or the
sample. If the image obtained is still not good, ​Withdraw ​(in ​Workflow Toolbar​) the tip, ​Tune ​it
again with different parameters, ​Engage ​it & scan again.

Red cross will appear in all the channels in ​Image Panel once scan is finished. Save the image only
if it is ​good​ (​Take someone else’s opinion​ 😅).

To Scan a Particular Region​ ​:

A. In ​Scanning Control window select ‘​Scan Area​’. A black window with a red cross will
appear (Fig 14)

Figure 14

B. Drag any one of the images from the measurement window to that black screen.
 C. Select from ​Image Processing Tools​. Draw a square around the region of interest.
D. Right click at the centre of the selected area.
E. Click on ​Play​ icon again to start the scan.

Step 8​ ​: ​Closing the Software​ ​:

I. After saving the data, cancel the ​Scanning Control Window ​first.

II. Withdraw ​the tip.

III. Open the ​Motors Control Dialog ​(Fig 8) & bring the stage upward.
IV. Close the ​Nanodrive​ application, turn off the PC setup & the Controller.