JPK Nanowizard 3 Bioscience AFM

Short manual

Use an optical microscope image as backgound map

How to start ImAFM software

How to use phase contrast imaging

This is a short from manual to get started with the JPK Nanowizard Bioscience system. The AFM head is mounted on top of an inverted optical microscope. The microscope has two illumination scources which can be used concurrently with the AFM scanning.

The most sensitive part is the afm tip holder and of course the tip itself. Therefore this instruction start with how to handel the tip holders and how to mount a tip.

 

This is the mounting tool for the tip holder. It has a circular opening for the tip holder, and two locking tabs at the top and bottom (green arrows). The locking tabs can be released or locked by turning the outer white sliders (red arrows) clockwise or anti clockwise.

 

Here the tip holder is inserted into the mounting tool. There are two cutouts in the holder that fits the locking tabs. The tip holder is rotated 90 degrees and the white sliders are moved so the locking tabs fixate the tip holder.

 

Side view of the mounting tool with the tip holder. Please note that the mounting tool is slanted to compensate for the slanted bottom surface of the tip holder.

Rotate the tip holder in the correct direction prior to locking.

In this way the top surface of the tip holder become horisontal, making it possible to mount the tip without it falling off.

 

Top view of tip holder. This is the variant of tip holder that has a piezo shaker at the top. The piezo crystal (light yellow) is mounted on a plastic part which is glued to the glass part of the tip holder.

At the top in th image is the clamp with its fastening screw. The screw should never be overtightened, there is a high risk of deforming the clamp and even break the holder.

The glass part is of high optical quality, the glass surface directly below the piezo in the image must be handled with care, not to be scratched.

Side view of the tip holder in the mounting tool. The clamp with its screw, the piezo shaker is clearly visible. Placing the piezo shaker directly in contact with the cantilever is more efficient than shaking the whole glass body.

Pic of holder with cantilever.

The Microscope X-Y Stage controller has to be powered on before starting the software!

The software

 

Overview of software, left half. There are two screens, this is the left screen.

At the top, below the dropdown menues, are function buttons for different parts of the setup and scanning.
Below are the controls for engaging, scanning and retraction.
In the center are two data viewers showing height and phase in AC-mode (tapping mode).
At the bottom is an "oscilloscope" showing trace and retrace of the height signal.

 

The left screen usually shows this, although screen layout is of course fully configurable.

The CCD camera window showing a live video image of the sample. Here is ordinary transmission illumination (white light). The sample is a microscope object slide with some pen markings. The cantilever is clearly visible, it is quite near the top surface of the glass slide, therefore it is in good focus.
The white oblong dots are the laser spot (and its secondary maxima) that is positioned on the back of the cantilever.

Behind the camera window is the laser alignment window, it will be shown separately below.

To the right is a stack of image data collected. These are kept in memory, and only saved to disk by user interaction. When the software is exited the user is prompted for saving data that is still only in RAM.

WARNING!!!

When the X-Y stage control and Joystick box are used, please note that when the stage control is Enabled, almost everything else is disabled. You cannot change scanning mode, not move leg motors, not engage.
Click once on Engage button to activate, click again to de-activate.
The stage control window is opened with this func. button . The stage control is described in more detail below.

When the cantilever has been mounted on the tip holder and the holder mounted on the scanhead, the scanhead is placed on the microscope table. Each leg of the scan head fits in a separate place of the table, a flat, a groove and a conical hole. This way the scan head is positioned in a reproducible way on the stage.

The scan head must have its legs so much extended so there is now risk of damaging the cantilever. This is usually ensured by the extension from a previous retraction at the end of a scanning session.

Each separate window is opened by a corresponding function button.

 

From left to right:
  • Z Motor control
  • X-Y Microscope Stage control
  • Laser on/Off
  • Laser Alignment
  • Cantilever Stiffness Calibration
  • Tuning cantilever
  • Camera window
  • Save camera image????
  • Save camera image????

It is good to always open the Camera Control window first in order to keep track of where the cantilever is. This is done by clicking

Initially the sample should NOT be mounted.

When setting up the cantilever, adjusting laser spot, etc. it is much easier without any sample slide between the microscope objective and the cantilever.

The microscope should be focused on the cantilever. This will be a great help when aligning the laser spot onto the backside of the cantilever (see further below).

The CCD camera window showing a live video image of the sample. Here is ordinary transmission illumination (white light). The sample is a microscope object slide with some pen markings. The cantilever is clearly visible, it is quite near the top surface of the glass slide, therefore it is in good focus.
The white oblong dots are the laser spot (and its secondary maxima) that is positioned on the back of the cantilever.

 

Laser Alignment is opened by

First the Sum signal should be maximised by aiming the laser spot as well as possible on the back of ther cantilever. The camera image is of great help here, since the laser spot is visible in the camera image.

The illumination intensity may have to be balanced against the laser spot intensity in order to make it visible in the camera image.

After that the Vertical and Lateral deflections are minimised using the knobs on the scan head.

 

The resonance frequency has to be found for the current cantilever mounted, window is opened by clicking

Frequency sweep displayed in oscilloscope-like window. The sweep can be zoomed using the pointer and scroll wheel. When the resonance peak is filling most of the display, the drive frequency and amplitude can be set by pointing and clicking in the graph. Amplitude should usually be around 0.7 V. The range of the sweep can also be set by the fields at the upper right, "Start Freq." and "End Freq.".

 

Now it is time to mount the sample. Lower the microscope objective much downward. The objective has been quite high up, probably above the surface of the microscope stage, this in order to be able to focus on the cantilever.

Motor Control window is opened by clicking

At the right are Up and Down arrows to step all three legs equally to approach or retract form the sample surface. The step size can be set, 100 ‐ 500 µm are common values.
When approaching the surface the optical microscope should be used to check how close to the surface the cantilever is. This to avoid crashing into the surface, breaking the cantilever.
The Zero button is for setting the current position to zero. The three stepper motors can be controlled separately by the center arrows, although this is rarely used.

 

There is a motor controlled microscope stage for movement in the X-Y directions.

The stage motor controller has to be powered on before starting the software

The X-Y stage software control window is opened by clicking

At the top are four function buttons. The "Engage" button has to be clicked in order for the stage to work at all. Please note that this will disable almost ALL other parts of the software! Press "Engage" again to disable and get the other parts of the software to work again.

The "Joystick Mode" has to be clicked in order to activate the joystick on the controller.
At the top of the joystick on the controller there is a push button for high and low speed. This button is a toggle button, one push for high speed, one more push: back to low speed.

 

Scan Control / Feedback Control

This part of the software is always present on the screen, it is located at the top left of the screen. It does not have a function button to open it.

In order to do the approach and engage the cantilever to the sample surface, a slow approach is done. This is started by clicking the blue down arrow.

The approach will happen in a saw-tooth like movement. The Z-piezo for the tip will extend slowly for 15 µm. If the surface is not reached the Z-piezo will retract 15 µm and the three leg motors will lower the scan head 15 µm very fast. Then the process starts over again.

The value for Gain is usually correctly set up. The values for Setpoint, Drive Ampl. and Drive Freq. are taken from the tuning window.

When the engage has been completed, the cantilever tip is resting on, or is extremely near the surface.

In order for the actual scanning of the surface to start you have to click the white left-pointing arrow, center top button.

During the approach (engage), the Z position for the tip is displayed here. It will be a cyclic process, the piezo will slowly extend downwards from zero to 15 µm, then retract at the same time as the leg motors quickly move the scan head down 15 µm.

Here is also shown the Z-range used during scanning of the sample surface.

 

During scanning the sample surface is displayed in a "Data Viewer". This window have several controls for which signal to be displayed, the levelling etc.

The viewable area can be zoomed using the pointer and scroll wheel. A new scan area can be drawn using pointer and drag left button.

Using a drop down menu item under "Accessories????" it is possible to acquire and calibrate an optical image from the microscope as a coarse map to find interesting areas for detailed AFM/SPM scanning. This optical image will be shown underneath the areas scanned with the afm.

 

The size of the scan area can be set here, as well as offsets, rotation (scan angle), size of image, and scan speed (line rate).

During scanning the traces can be displayed in an oscilloscope like window, this is opened by clicking

Here the "Height" signal is displayed, both trace and retrace. To the right are numerous controls for how the signals will be displayed. Up to four channels can be displayed, and here "Levelling" is set to "Linear" to get rid of extra tilt on the sample surface.

Using the shape of the "Height" signal Gain and Setpoint settings can be adjusted for best surface tracking.

 

All scans are collected in system RAM (volatile memory). The are displayed in a stack like manner. In the upper part there are data sets that are only residing in RAM, not yet stored to disk. The little button after the tick mark indicates this by a red dash over a small bent arrow pointing to a disk icon.

In the lower part, "Old Image Data", there are data sets stored to disk, the button shows a green tick mark next to a green bent arrow pointing to the disk icon.

It is recommended to save data regularly, either by clicking for an individual important dataset, or save all datasets to disk by clicking the double green arrow button at the bottom (partly hidden)

Clicking the "Hold" button will transfer data sets to "Old Image Data". Data sets can be deleted from disk (permanently) by clicking the trashcan icon.

Upon exit of the software, the user is prompted to save all unsaved data sets still in volatile memory.

How to start ImAFM software

  1. Start JPK controller
  2. Start JPK Software
  3. Set it to "Contact Mode"
  4. Start ImAFM software (desktop icon)
  5. In JPK software: Advanced ‐ Open Script
  6. Double-click "ImAFMSetup.py", this will add a button "ImAFM" along the other function buttons in the JPK software
  7. Click on "ImAFM" button, opens a small window.
  8. Click "Setup" in this small window, will enable trigger signals necessary for ImAFM software.

Use an optical microscope image as backgound map


Anders Liljeborg Albanova Nanolab, KTH, SU.