Scanning

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Before scanning the host AFM must be configured for ImAFM™ by simply putting it in contact mode with the feedback set-point set to zero volts. On some AFM’s software scripts or special modes are provided to do this automatically. Other AFM’s require that you set the break-out box switches in the correct position, so that a ‘fake’ deflection signal is fed from the MLA™ to the host AFM. The host AFM can then preform scanning feedback on this signal (see Connection to host AFM). The feedback parameters, integral and proportional gain, are set in the host AFM software.

The default scanner view has three components: The Scanner panel, the Image Settings panel and the main view showing the Amplitude and Phase images. More panels can be added, for example when you want to perform analysis as you scan, making force curves or analyzing transects. These panels will be addressed in the section on Quantitative Analysis. Here we describe how to setup and execute the first scan.

Setup and Scan

Three controls in the Scanner panel specify the parameters for Setup. There must be a Current calibration in order for the setup to function.

  • Osc. range is the desired maximum amplitude of oscillation (peak-to-peak) in nanometers of the cantilever when it is free from the surface. When the surface is engaged, the oscillation range will be somewhat reduced, depending on the Amplitude set point.
  • Pixel rate (df) is the spacing \Delta f between tones in the frequency comb (see Intermodulation Measurement). The pixel rate, together with the number of pixels per line determine the scan rate.
  • Resolution: x y sets the number of pixels to acquire in the fast scan direction (x) and the slow scan direction (y). The x resolution does not depend on the host AFM setting of pixels per scan line. The x resolution together with the pixel rate determines the Scan Rate given by the AFM Suite. The scan rate must be set on the host AFM to the value given by the IMP Suite. The y resolution must also be set to the same value on the host AFM, which determines the number of scan lines at the given rate.

Setup runs a routine to determine the frequency and amplitude of the two drive tones. You must be well above the surface when you perform setup, several cantilever widths or at least 0.1 mm. If you get an Out of Range Error message you may need to adjust the oscillation range or attenuate the input signal (see Advanced Setup). This automatic setup is designed for basic ImAFM™ with two drive tones close to resonance. Much more complicated measurements and modulation schemes can be setup with the Drive Constructor. When the setup is complete, the Scan button will not have gray text, indicating that you are ready to scan.

Scan makes the software ready to acquire measurement data. After pressing Scan:

  • Set the scan rate on the host AFM to the Scan rate given in the scanner panel.
  • Make sure your host AFM is set to contact mode and the set-point is set to zero volts.
  • Use the host AFM software to engage the sample and start the scan.

When the end-of-line (EOL) triggers are detected, the AFM Suite will begin to collect and display the scan data. After the last scan line when an end-of-frame (EOF) trigger is detected, a scan file is stored (see Status Banner). However, the EOL and EOF triggers do not code for the direction of the scan. It may be necessary to sometimes Flip left-right or Flip up-down to make your image match that displayed on the host AFM.

On some AFM’s you can move to the top or bottom of a frame to start a fresh scan without waiting for the current scan to finish. If this action is performed on the host AFM, and if the EOF trigger is sent, the IMP will save a scan file and automatically start collecting a new scan. Some AFM’s (notably Asylum) do not send and EOF trigger when you move to the top or bottom of a frame. When the IMP suite is configured for such an AFM, two buttons appear which allow you to Move to top or Move to bottom to keep the synchronization with the host AFM scan.

During the scan, you can at any time perform the following actions and set the following parameters:

Measure just lifted

Measure just lifted starts a routine to measure the oscillating cantilever at a point where the tip just stops interacting with the surface. The response at this just-lifted position is needed for Background force compensation. Dialog boxes open to explain what the routine is doing. You can choose the Quick option to quickly extend the scanner to its full lift position and measure lift, but for accurate measurement you should stop the scan while maintaining engagement with the surface (e.g. temporarily set the scan size to zero) and choose OK. The feedback set-point is slowly increased until the total Intermodulation Distortion (IMD) at the surface drops below a target value, determined by the measured IMD at the full lift position (where Setup was performed). This full lift IMD is usually just noise as the cantilever response is linear, meaning that there is no IMD far from the surface. When the IMD falls below the target IMD, the response is measured and stored as the lift response. You can Abort if something is not working.

If you did not measure just lifted during the scan, it is possible to perform background force compensation, if your scan file has a parachuting pixel in the image, as described in Background force compensation.

Set-point

Amplitude set-point is the set-point for the AFM scanning feedback. ImAFM™ feedback is based on the response amplitude at one of the two drive frequencies (Drive 1), and the set-point is given as a percent of the free response amplitude at this drive frequency (see Setup Feedback). If you are having trouble engaging the surface, you can lower this set-point. Sometimes background forces cause drop in amplitude by as much as 75% at the surface. This effect can cause a false engage at a position well lifted from the surface. If Measure just lifted is performed, amplitude change is calculated as a percent of the amplitude at the just-lifted position. Setting the set-point to more than 100% will cause the probe to lift from the surface – a useful way to lift away from the surface without stopping the scan, if you want to check or adjust something.

Scan rate

Scan rate is the required rate of scanning, determined by the chosen pixel rate (measurement bandwidth, df) and number of pixels in the scan line (x resolution). You must set the host AFM to scan at the given scan rate, otherwise the images will not be synchronized. Some host AFMs do not allow arbitrary scan rate, but it is not necessary that the scan rates match exactly. A 1% deviation is not noticeable in the images and it is better that the host AFM scan rate be slightly smaller than the ImAFM™ scan rate. You can slow down the scan rate using the same measurement bandwidth and pixel rate, to help track better on a rough surface. normal means scanning at the maximum rate and you can choose half or quarter speed. Making this choice will result in a new calculation of the scan rate which must be set in the host AFM. Slowing down the scan will help to track the surface more closely, making the force measurement more accurate.

Image settings

The panel Image Settings contains the controls for displaying which images are plotted

  • IMP Control lets you select the frequency at which the Amplitude and Phase images are plotted. The frequencies are ordered from lowest to highest, going from left to right. The text below the slider displays which frequency is being plotted
  • Scan direction has two buttons which control whether the Trace or Retrace will be plotted. Data is acquired and stored for both scan directions. Note that both trace and retrace are always stored in every scan. Flipping between trace and retrace can be a good way to see if feedback errors are affecting your image.
  • Swap will exchange the data stored as trace and retrace. The host AFM trigger signals do not distinguish between different scan directions, and sometimes it is necessary to swap so that trace and retrace are the same as that in the host AFM. Do not worry if you do not get this correct during the scan as it can be easily corrected after the scan session using the Session Overview.
  • Flip right-left and Flip up-down do not exchange trace and retrace data. This action can also be done later in the Session Overview.
  • Scan size , when checked, will display axis labels with the image size which must be entered in the x and y data fields. Units should be given in either nanometers or micrometers, using the characters: nm, um or µm (u will be displayed as µ). Scan size values will be stored when the scan is saved, and these values will be overwritten if and when the scan size is imported together with height data from the host AFM (see Import host AFM data).

Color Bar

The color bars have functionality for adjusting the images:

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  • Right click on the color bar to see a histogram of the plotted values. You can adjust the image contrast by left-click-and-drag on the borders to the shaded region. These borders mark the max. and min. values for the color map used. Data outside the shaded region is forced to either min. or max. If the check box is activated, the software will automatically choose the max. and min. excluding the given percent of outlying values. You can also change the color map in the histogram window.
  • Click-and-drag upward or downward on the color bar, to adjust the minimum and maximum values respectively. The color value of the center will remain constant. You can do this action with the histogram open.
  • Double click on the color bar to return to the automatic setting settings.

Image Toolbar

All plots and images have a toolbar with the following functions:

home_icon Home returns to the initial plot or the full image.

pan_zoom_icon Pan-Zoom when selected, left-click-and-drag will cause the plot to zoom, starting from the point of click. Dragging horizontally will zoom only the x-axis, dragging vertically will zoom only the y-axis. Dragging at an angle controls the relative rate of zoom of each axis. Right-click-and-drag will grab the plot at the point of click and slide it in the direction of the drag. Performing these actions while holding down the x, y or ctrl keys will restrict the pan or zoom to occur only in the x-axis, y-axis, or preserving current aspect ratio, respectively.

zoom_icon Zoom when selected, a right-click-and-drag over the plot will zoom to the selected rectangle upon release.

save_icon Save image opens a dialog box for saving the image in several formats (png, eps, pdf and more). Sometimes you would like to change the aspect ratio of the plot, or the relative size of the frame and text in your saved image. Simply rescale the entire suite (click-and-drag on the lower right corner), or re-size a particular frame, before you save. This action will rescale the plot and axes while keeping the text and line size fixed.

subplots_icon Configure subplots opens up a dialog box to adjust the placement of the plot axes within the plot frame.

Mouse wheel zooming

In addition to the zoom tools in the image toolbar, you can use the mouse wheel to rapidly zoom plots and images:

  • Hover over the x or y axis of a plot, just outside the plot frame, and roll the mouse wheel. Only that axis will zoom about the location of the mouse pointer. Click the mouse wheel to auto-scale the axis.
  • Hower over any point in a plot or an image and roll the mouse wheel. The plot or image will zoom about that point with equal zoom in the x and y directions. Click the mouse wheel to auto-scale the image or plot.

Selecting Data in a Scan

Two important tools in the image toolbar are the pixel inspector and line inspector tools. These tools do more than simply controlling the plot. They select data at pixels and analyze the data to generate force and parameter plots.

pixel_icon Pixel inspector tool

A left-click on the icon will activate this tool. When the tool is activated, a left click on either the amplitude or phase image will select the data at the point-of-click, mark it with an X, and open the Signal Inspector panel. If you have the Quantitative Analysis tools installed in your software, the Force Inspector will also open and display a force curve. When the pixel inspector tool is active, left-click on the plot will un-select the X nearest to the point-of-click and remove the data from the Data Tree. The Quantitative Analysis tools allow you to analyze the spectral data in many different ways to reveal tip-surface interaction. The Data Tree allows you to compare different pixels form the same scan, or different scans, in the same plot.

area_icon Area inspector tool

A left-click on the icon will activate this tool. When the tool is activated, a left click and drag to form a loop in either the amplitude or phase image will select the data inside the loop, marking it a transparent color. All intermodulation spectral data will be averaged in the enclosed area. if you have the Quantitative Analysis tools installed in your software, this averaged data will be analyzed as one effective pixel. Averaging over areas with the same response can give much lower noise, and smoother force curves.

line_icon Line inspector tool

A left-click on the icon will activate the tool. When active, a left-click-and-drag on either the amplitude or phase image will select a transect line upon release and a left click will un-select the line nearest to the point-of-click. The Line Inspector panel will open and a plot of the amplitude and phase of the currently viewed image will be shown. All data along this line will be selected and available for analysis. If you have the Quantitative Analysis tools installed in your software, the line inspector will allow Analyzing Linear Transects and plot parameters of the tip-surface interaction along the selected transect.

clear_icon Clear pixels tool

Removes all selected pixels from the image.

level_icon Level image tool

Performs a plane fit to the amplitude and phase image data and subtracts off the plane, thereby flattening the data.

Status Banner

The banner at the very bottom of every view has text describing what task the software is currently performing (sweeping, calibrating, scanning, etc.) and a status bar that graphically shows the time required to finish the task. If Autosave is checked data is continuously saved to file save when the task is finished. The name of the most recent saved file is also given.

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