Oxford Asylum Jupiter XR User manual

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The User’s Guide for the Oxford Asylum Jupiter XR Atomic Force Microscope (AFM) in Tapping Mode
The Shortest Possible Version of this Manual
1. Turn on pump if needed
2. Check in to tool reservation on Lab Resources
3. Log onto Windows
4. Launch Jupiter software
5. Select BlueDrive AC Air Mode from Mode Master panel
6. Load probe
7. Load sample
8. Lower AFM head ~2 mm above sample surface using joystick
9. Focus on tip. Set detector laser. Set BlueDrive Laser. Mark tip location. SET tip focus
10. Focus on sample surface. SET sample focus location
11. Toggle back to tip view, and click “Move to Pre-Engage Height”
12. Tune cantilever for 1V amplitude
13. Click “Start Tip Approach”
14. Set up Master Panel. Input scan size and rate. Set Setpoint to 800 mV. Give file a name and
designate a file path for saving data.
15. Click “Frame Up”/”Frame Down” to start tip raster. Optimize data image.
a. Lower and tune setpoint, until image shows up in Height data window
b. Increase Gain until trace/retrace have good overlap and no ringing
16. To collect an optimized image “Frame Up”/”Frame Down” to start a new frame with optimized
data
17. Done?
a. Click stop
b. Click Remove Sample
c. Open AFM hood and remove sample.
d. Optional: remove and reclaim the tip
e. Turn off pump
f. Log out of Windows.
g. Fill out log book

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Table of Contents
Introduction and Hardware Overview…………………………………………………………………………………………..pg 3
Before You Get Started…………………………………………………………………………………………………………………pg 6
Performing Tapping Mode AFM……………………………………………………………………………………………………pg 6
Saving data as an image, and image processing……………………………………………………………………………pg 18
Changing the AFM Probe……………………………………………………………………………………………………………..pg 21

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Introduction and Hardware Overview
Welcome to the UTD Cleanroom’s newest characterization tool, the Jupiter AFM. You are
probably here because you want to take an image of a sample surface and/or because you want to make
some topographic measurements of a sample surface. This tool will help you achieve that. This guide
was written to instruct users on using the AFM in tapping mode microscopy.
A note for users of the previous tool: There are some ways that this Oxford Asylum Research
tool differs from the previous Veeco Dimension V tool. Notably, the old tool achieved the tapping
frequency by oscillating the tip with piezo electric elements in the AFM tip holder. This tool achieves the
tapping frequency by thermally exciting the tip with a laser. This technology is called BlueDrive, although
in this tool, the laser appears red. Another exciting improvement is the capability of a fast scan mode. A
surface scan that would take 4-5 minutes in traditional tapping mode takes about 1 minute with fast
scan tapping mode. This mode requires a tip especially designed for fast scans, and the tool has some
hardware differences that make fast scan possible.
The Hardware
The large module to the left of the desk is the AFM (Fig 1a). The AFM is housed in a noise-
blocking hood. The hood is opened by turning the black knob on the left-hand side of the tool and
opening the door. The hood has a view port that the user can look through when the hood is closed. The
door opens to the right and swings around the tool, and it should not bump into the computer monitors
on the table (Figs 1b and 1c).
Figure 1. Image of the AFM (a.) with the hood closed; (b.) the hood is unlatched by turning the black
knob on the left-hand side of the tool counter clockwise; and (c.) the hood opens by swinging out and to
the right

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Inside the shielding, the sample stage is housed inside the tool. The stage is mounted on a
granite slab that is supported by an air table in order to reduce noise. The sample stage clamps samples
in place during scans. Samples are clamped in place by a vacuum or by magnets that are embedded in
the stage (Fig 2b). The stage moves in the x- and y-directions by being floated on a column of air in order
to eliminate noise. Above the sample stage, there is a black module, the AFM head, with a silver box
that is labeled "Jupiter XR 12 um AFM Scanner" (Fig 2a). The scanner houses the AFM probe, and can be
moved up and down in the z-direction to engage with a sample. Other components of the AFM head not
viewable to the user: the optical camera that allows the user to view the AFM tip and the sample
surface; the deflection laser; the deflection laser detector; and the BlueDrive laser.
Figure 2. An image of the AFM components viewed with the hood opened. Including (a), an image of the
stage in the foreground and the z-scanner head in the background, indicated by a green box. Also
pictured (b) is an image of the stage from the top-down. The locations of the embedded sample
clamping magnets are indicated by red circles and are labeled with letters that match the labeling in the
Jupiter software
Computer components that are control the tool are outside of the AFM, also a strategy to
minimize/eliminate noise. This includes the "backpack" on the left side of the AFM shielding (Fig 3a), the
black CPU (Fig 3b) on the floor to the right of the AFM, and the two white boxes on the floor under the
monitors (Fig 3c--these boxes are the AFM and the stage controllers). The "backpack," CPU, and AFM
controller operate the tool and perform data processing, while the stage controller moves the stage and
controls the column of air that the stage floats on. Additionally, beneath the desk there is an un-
interruptible power source (UPS) that powers the instrument in case of a power failure, and a
mechanical pump that delivers clamping vacuum force to the sample stage (Figs 3b and 3c).

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Figure 3. Images of external components. This includes (a) the “backpack” on the left-hand side of the
AFM hood, indicated with a red arrow. Image (b) includes, from top to bottom, the stage controller, the
AFM controller, and the black UPS box. Image (c) shows the CPU, indicated by a blue arrow, and the
sample stage pump, indicated by a purple arrow.
On the desk, there are 2 pieces of hardware. One is the joystick (Fig 4a). The other piece of
hardware is a dark blue box with silver wheels, referred to as the "hamster wheel;” it has 2 wheels, inner
and outer, that move independently of each other (Figs 4b and 4c). The hamster wheel is useful in the
software to optimize data scanning parameters.
Figure 4. Images of the desktop hardware, including (a) the joystick. In (b) the user’s finger is
manipulating the outer ring of the “hamster wheel” and in (c) the user’s finger is manipulating the inner
ring. The rings can be moved clockwise or counterclockwise and independently of each other.

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Before you get started
You need an account on the UTD Cleanroom Scheduler, Lab Resources. This system is the
scheduler for time on the tool, and manages billing for tool usage. AFM tips are also available for
purchase through the scheduler as an accessory, although staff need to be notified when they need to
supply the tip. A user may buy their own tips and learn how to install them in the z-scanner as well.
Determine the type of AFM scanning you will perform and select the appropriate probe (“tip”).
Most people will be satisfied with tapping mode AFM using a relatively “stiff” probe. Some people may
be interested in performing a “fast scan”. Performing fast scan microscopy with a tip that is not designed
for the method will break the tip and potentially damage your sample. You may supply your own tips, or
they are available for purchase from our lab.
Determine the sample size and how it will be clamped into place on the sample holder. There
are 2 methods for clamping a sample in place on the tool’s sample holder: vacuum clamping or magnetic
force. The vacuum clamping force is provided by an external pump, and is delivered through circular
channels on the sample stage. The smallest sample that can by clamped by the vacuum is 2 cm x 2 cm.
Additional screws may be removed from the stage to expand the clamping area to accommodate an 8”
wafer. If your sample is too small to be clamped by the vacuum, we recommend mounting the sample to
a magnetic disk with paste. Magnetic disks and paste are available for purchase from various vendors, or
they are available for purchase from our lab.
Performing Tapping Mode AFM
Turn on pump, if vacuum force will be used to clamp sample to tool stage. Otherwise, the user will
mount the sample to a magnetic disk.
Log into Windows
Check into Lab Resources reservation.
Launch Jupiter software (Fig 5a). Wait for tool to initialize and close any windows related to the status
of the software/providing feedback about the software. The bottom of the software window should
read “Ready” with 2 green check marks. The Mode Master panel will launch. Select BlueDrive AC Air
Topography mode, located in the Standard tab (Fig 5b). There may be a pop-up window regarding
“homing the BlueDrive polarizer.” Click the option that will enable this action. Note that the homing
action will not proceed if the AFM hood is open and/or unlocked.

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Figure 5. Launching the Jupiter software (a) from the icon indicated by the orange square. When the
software launches (b), wait for the “Ready” message and check marks, indicated by the green rectangle.
In the Standard tab of the Mode Master panel, select BlueDrive AC Air Topography
Configure screen. Drag the Jupiter software window in the bottom right hand corner to expand the
Jupiter software into both monitors. Left click on any panel and drag it to move it to a new location. A
useful configuration would be to put the Engage Panel, Video Panel, the Sum and Deflection meter, and
the Master Panel on the left, and to put the Height Retrace, Amplitude Retrace, Phase Retrace, Z sensor
retrace, and the Master Channel Panel on the right.

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Figure 6. Images of a dual screen configuration. In (a), an image of the left-hand screen is shown with 4
numbered panels; these panels are the Master panel, the Engage panel, the Sum and Deflection panel,
and the Video panel. In (b), an image of the right-hand screen is shown with 5 numbered panels,
including the Height Retrace, Phase Retrace, Z Sensor Retrace, Amplitude Retrace, and the Master
Channel panel.

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Load probe. On the Engage panel, click on “Change Cantilever” (Fig 7). Wait for this button to turn
green. On the AFM head, the “Ok to Remove” light will come on. At this point, reach into the AFM and
grab the green lever to the right of the z-scanner. Push the lever down to disengage, and push it back. At
the end of the travel path, a magnet locks the lever in place. With a thumb and index finger, use one
hand to carefully grab and pull the AFM head out. Install a new probe. Refer to another section of this
manual for detailed instruction on installation. Replace the z-scanner in the AFM head, carefully lining
up the z-scanner with the dovetail channels on the AFM head. Lock the z-scanner in place with the green
lever.
Figure 7. The “Stage Control” section of the Engage panel that shows the locations of the “Change
Cantilever” and “Move to Position” buttons
Load sample. In the Engage panel, click on “Change Sample.” This moves the sample stage from beneath
the AFM head and toward front of the tool where the user can access it. Open the hood. If the sample is
mounted to a magnetic disk, clamp it to one of the stage-embedded magnets. Or, use the vacuum
clamping force to clamp a sample to the stage. The vacuum pump must be on and the vacuum control
must be activated in the Engage panel. An Allen key can be used to remove additional stage screws to
expand the vacuum clamping force (Fig 8). DO NOT LOSE THESE SCREWS. When the sample is loaded
and clamped, close and lock the AFM hood.

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Figure 8 (a) using the Allen key to remove screw from the sample stage to access the vacuum clamping
force. In (b), please note that there is a sample box in the tool. The Allen key should be kept here, along
with any screws that are temporarily removed for a user’s work.
Drive stage to sample location. If the sample is on a magnetic disk, the stage can be automatically
driven to the locations of the magnetic sample holders in the Engage panel (Fig 7). In this panel, select
the lettered location in the drop-down menu under the “Move to Position” button. When the correct
location is selected, clicking “Move to Position” will move the stage in the x- and y- directions to a
position where the tip is roughly over the center of this lettered location.
If the sample is not mounted to a magnetic disk, use the joystick. Position yourself where you
can see inside the hood view port and hold the joystick. Press “3” on the joystick to engage the stage
float. Use the joystick to move the sample stage in the x- and y-directions. The joystick transduces force
as velocity in movement. Pressing the joystick all the way to its travel path in any direction moves the
stage more quickly than lightly tapping the joystick in any direction. The goal here is to get the AFM
head in a general location relative to the sample. Finding a location for scanning and fine tuning the
location is done later. Press “3” on the joystick when you are satisfied with the location to disengage the
stage floatation.
Lower AFM head to ~2mm above sample surface while looking into the hood viewport. Continually
hold the “4” button to lower the AFM head with the joystick. This is just to get the AFM head close
enough to the surface for the instrument’s optics to be able to locate the surface, finer adjustments to
the height and location on the sample surface are made in later steps
Adjust optical focus to focus on the tip, adjust lasers, and mark tip position. This is accomplished with
the “Approach Controls” in the Engage panel (Fig 9a), and the visual feedback from the Video panel (Fig
9b). In the Engage panel, click on “Move Focus”. To the right of this button the single- and double-arrow
buttons will jog the focus of the optical microscope up and down slowly or quickly. The user will move