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

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the focus down to visualize the tip in the Video panel. As focus changes, the user may adjust illumination
intensity in the video panel (Fig 9b); using the mouse, left click on the “I” slider at the bottom of the
video panel and drag to the left or right. Also, the user may zoom in/out of the view using the slider on
the lower left-hand corner of the Video panel.
In the Video panel (Fig 9b), use the mouse pointer to indicate a location on the tip. At this location, right
click to “spot on” the laser location. This is the detector laser. This laser spot should be close to the tip,
without spilling over the edges of the cantilever. Adjusting the light intensity will help to view this. To
make very fine adjustments to the laser location, use the buttons in the crosshair on the top left-hand
corner of this panel; holding the Shift key+clicking a button moves the laser in the smallest possible
increment. When the laser location is satisfactory, zero the detector by clicking the red dot in the center
of the crosshair on the left-hand side of the Engage Panel. You should see the Deflection value in the
Sum and Deflection panel decrease to 0-0.10 (Fig 10)
In the Video panel (Fig 9b), use the mouse pointer to indicate a location very close to the base of the
cantilever, and right click in this location to “spot on” the BlueDrive laser. This laser is not blue; it is red
and appears larger than the detector laser. Small adjustments to the BlueDrive laser location can be
made with the crosshair on the top right-hand corner of the Video panel.
In the Video panel (Fig 9b), use the mouse pointer to indicate a location very, very close to the tip and
right click to select “tip position”.This action marks the location of the tip in the Video panel with a
green crosshair. The green crosshair remains in the video panel to indicate to the user where the tip will
land on a sample surface. In the Engage panel, find the “Focus on Tip” button and click the “SET” button
to the immediate right. This completes all the steps for locating and marking tip locations.

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Figure 9. Images of the (a) Engage panel and (b) the Video panel that are useful for locating the tip and
the sample surface. In the Video panel (b), the crosshair for moving the red detector laser are circled in
red; the crosshair for moving the BlueDrive laser are circled in blue; the arrow keys for moving the
sample stage are indicated by green boxes; the light intensity slider “I” is indicated with an orange
arrow; and the image zoom in/out slider is indicated with a purple arrow.
Figure 10. An image of the Sum and Deflection Meter panel. The Deflection value is circled in green.
When the detector laser is in the correct location, this can be “zeroed” and a deflection of 0-0.10 can be
obtained.

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Focus on sample surface. For some samples, this may be as easy as bringing the focus down beyond the
tip using the same down arrows in the Engage panel that were used to locate the tip. In the Engage
panel (Fig 9a), there are 2 values called “Focus Position” and “Tip Position.” The user can bring the focus
position down below the tip position by about 1 mm. If the user notices that the focus is not able to
lower, this indicates that the user has approached the 1 mm difference. Now, the user must move the
AFM head. In the Engage panel, click on “Move Tip”, and use the arrow buttons to slowly lower the AFM
head until the sample surface comes into view and then into focus. At this location, the user may move
the stage in small increments in the x- and y-directions to locate a place to scan on the sample surface.
Using the joystick for this is not recommended. There are a few ways of making small movements using
the Video panel that are helpful at this step. In the Video panel, the user may right click on a location in
the image of the sample surface, and click on “Move Here.” The tool will jog the stage to the indicated
location. If the user wishes to manually move the stage, there are arrow buttons on the top, bottom, left
and right edges of the video feed (Fig 9b). Again, the shift+click command on these buttons will move
the stage in the smallest possible increment in the x- and y-directions. The green crosshair used to mark
the tip location indicates to the user where the AFM tip will land during the scan. When the user is
satisfied with the location, click on the “SET” button to the right of the “Focus on Sample” button in the
Engage panel.
The user should click on “Focus on Tip” to toggle back to the tip view, and check that the tip is still in
focus. Then, the user should click “Focus on Surface” to toggle back to the surface view, and verify that
the surface is in focus at the correct location. The user should verify they are in tip view before
proceeding to the next steps.
In the Engage panel, toggle to the tip view and click on “Move to Pre-Engage.”
Tune the cantilever. Note: the user cannot tune if the camera is not in tip view. Click on Tune on the
right-hand side of the Master panel. This opens a Cantilever tune window. Verify that the “target
amplitude” field has 1.00 V (Fig 11). In this window, click on “Get Real.” This opens a menu of commonly
used probes. The user will select the type of probe that is loaded in the tool, then click on Get Real
Calibrate. This opens a new window of Thermal Fit Data (Fig 12). As the computer calibrates, this
particular window will fill in with a Gaussian peak. The user will right click on the apex of the peak, and
select “Fit Thermal Data” from the drop-down menu that opens. Switching back to the Cantilever tune
window, the user will click on “Auto Tune” (Fig 13). The computer calculates a resonance frequency
based on parameters from the selected probe and the thermal data. The tuning is complete when a
black trace (frequency) and teal trace (phase) appear in the window.

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Figure 11. The cantilever tune window has no data when initially opened. Verify the Target Amplitude,
indicated by the red circle is set to 1.00 V. The GetReal button indicated by the green square opens a
menu of commonly used AFM probes.
Figure 12. The thermal tune window, with a Gaussian curve. Right click on the apex of the curve, as
indicated with the red arrow, and select “Fit Thermal Data”

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Figure 13. The Cantilever tune window after clicking Auto Tune, indicated by the red arrow. The
computer calculates the resonance frequency of the cantilever (black trace)
Figure 14. An image of the Master Panel

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In the Engage panel, click on “Start Tip Approach.” The user will now fill in some values in the Master
panel before collecting data (Fig 14)
The Master panel is divided into a few grey sections with parameters that will be adjusted and set by the
user before the scan starts. The top-most section has fields for scan size, points and lines, and a scan
rate. These factors determine the amount of time a scan will take, which is calculated and displayed in
this panel. The maximum scan size is 100 µm. Scan sizes that are smaller than the tip dimensions are
nonsense; for an AC160 tip, this limit is on the order of 7 nm. Most users will find 256 points and lines
to be acceptable. The maximum scan rate for traditional tapping AFM is 1 Hz. With a fast scan tip,
rates up to 4 Hz are accessible.
In the “Imaging Mode” tab of the Master panel, modify the setpoint to a value that is 80% of what was
indicated in the tuning voltage. For a tuning voltage of 1 V, the setpoint should be set to 800 mV. This
is a good starting point for this value. It will be adjusted when data collection begins.
In the “Save Options” tab of the Master Panel, the user inputs an image name and designates a file
path. There is a field for the user to input notes, but this information is not a part of the file name. Note
that the software will append a number to the end of the file name, starting with 000. As the tip rasters
and the tool collects frames of data, every new frame will be sequentially numbered (the next frame will
be 001, then 002, etc.). This continues until the user stops the tip raster. Note that the computer is
connected to the MSE Datashare1 drive ( “the z: drive”) for remote data storage and retrieval. The
cleanroom does not permit using external media (USB sticks or flash drives) to retrieve data from the
computer (C: drive) to minimize the risk of transferring viruses.
When the user is satisfied with the initial changes to the Master panel, begin the tip raster and data
collection by clicking “Frame Up” or “Frame Down” in the Master panel.
As data fills in in the data windows on the right-hand side of the screen, the user will modify image
parameters in order to visualize and optimize the data. First, lower the setpoint in order to bring the tip
closer to the surface to a point where the tip is physically interacting with the surface. In the Master
panel, click on the radio button to the right of the “Setpoint” field. Slowly decrease the setpoint by
turning the inner ring of the hamster wheel counter clockwise (NOTE: increasing the setpoint above
the initial tuning voltage does not make any sense here). Decrease the setpoint until topographic data
begins to fill in in the data windows; specifically, pay attention to the blue and red trace/re-trace and
image that fills in the Height Retrace window.
The user will further optimize the image by modulating the “Gain”. Turn the outer ring of the hamster
wheel to toggle from “Setpoint” to “Gain”. Once in the “Gain” field, turn the inner ring of the hamster
wheel clockwise to slowly increase the gain. As the gain increases the blue trace and retrace lines in the
Height retrace data windows will approach and eventually overlap with minimal noise. If “ringing” in
data occurs, adjust the gain back down.
Now that the image is optimized, the user may make note of the new number that is appended on the
data when a new frame is started. The user may wait for the tool to complete the raster and start a new
frame, or force a new one to start with “Frame Up” or “Frame Down”, or the user may give the file a
new name. It is up to the user to develop a file naming convention that will help them determine which
files will contain the most useful optimized images.

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When a frame is complete and the user is satisfied with data collection, click on “Stop” in the Master
panel. This ends data collection and tip raster.
In the Engage panel, on “Change Sample”. This raises the AFM head far above the sample stage, and
moves the sample stage out of the tool toward the user. The user will remove their sample from the
stage. Turn off the pump. If screws were removed to expand the stage vacuum clamp, please replace
them.
If desired, the user may unload the tip and reclaim it.
Fill out the log book.
Log out of Windows.
Turn off the pump if it was in use; replace screws in sample stage

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Saving data as an image, and image processing
Data is saved in an .ibw (Igor binary wave) file extension. This data formate is not an image or surface
measurement file. The user will use some software, either the Asylum program on the tool or image
processing software such as Gwiddeon, to manipulate the .ibw file to obtain useful data. Here, the user
will find some useful information on how to export data as a 2D image in a JPEG or TIFF format, how to
generate a 3D rendering of data, and how to obtain surface roughness measurements from an image.
Close all other windows, or drag them out of the way. The user will be opening other windows to locate
data and perform image processing.
Open the Data from the Widows file explorer. Locate the desired .ibw file. Left click on the file name
and drag it from the File Explorer into the Asylum software.
A widow with the user’s collected image appears. The user can toggle between the height data,
amplitude data, phase data, and the Z sensor data by toggling between the “HtR,” “AmR,” “PhR,” and
“ZSr”, respectively, tabs in this window.
The user may be curious about the difference between height and z sensor data. The shortest
explanation is that for data in the micron range down to 100 nm, the z sensor data tends to be the best
image with less noise. For images with height data that is less than 100 nm, the height channel is the
best. The other data channels are not useless. Users may also find that they can generate impressive
images with phase data, provided they can tune the scan parameters to optimize phase contrast. At this
point, that is an exercise left up to the user.
At any rate, the data that appears in the window is not truly raw data. The software automatically saves
the data with a 1st order flattening algorithm; the algorithm corrects for distortions in the image that
arise from the nature of the tapping mode raster. To view the raw data, click on the M button in the
data window. This opens a Modify panel that is open to a “Flatten” tab (Fig 16a). Click the “ultra-
restore” option to restore the data to its raw form. There are additional forms of data filtering and
correction that are available, but not yet discussed here.

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Figure 15. An image of the Save Graphics File window that allows the user to export data as an image
Figure 16. An image of the Modify panel (a), in which the user may “ultra restore” data back to the raw
format. An image of the Analyze panel (b) is also included, where the user may obtain useful
information about the surface roughness of a sample.

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To save data as an image (flattened or not), the user will open the main File menu in the software,
and click on “Save Graphics”. This opens a Save Graphics File window (Fig 15), where the user can
define the size of the image, choose the file extension from a drop down menu (including JPEG and
TIFF), and indicate a file name and path. Click “Do It” to execute. Alternatively, from the data window,
clicking on “Command” opens a drop down menu with an option to export the file as a TIFF. This drop
down menu also has the option to toggle between a “classic” and “new” appearance, which may be
helpful to meet the formatting demands of a technical journal or a PI.
To analyze the sample surface, click on the A button in the data window. This opens the Analyze panel
to the “Roughness” tab (Fig 16b).The fields are automatically populated with surface roughness data
related to the full image. The user can define a box-shaped mask to calculate roughness of a box-shaped
subsection of the image. The “Section” tab of this window allows the user to draw a line on the data
image, and the software will calculate the length of the line, or cursors may be dropped on the line in
order to measure a subsegment of the line. The line is a minimum of one pixel thick, but the user may
make the line thicker in order to average more data points on the line.
To see a 3D plot of the data, click the 3D button on the data window. This opens a new window with a
3-dimensional rendering of the data with scales on the x-, y-, and z-axes (Fig 17). The user may click on
the image and drag to rotate and view the rendering from other angles. This image can be saved and
exported to a JPEG or TIFF as previously discussed.
Figure 17. An image of a 3D rendering of data