.. |ImAFM (TM)| unicode:: ImAFM U+2122 .. |MLA (TM)| unicode:: MLA U+2122 .. index:: Scanning .. _scanning-label: Scanning ======== .. image:: ../Icons/scanning.png :width: 20mm :align: left Before scanning the host AFM must be configured for |ImAFM (TM)| 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 (TM)| to the host AFM. The host AFM can then preform scanning feedback on this signal (see :ref:`connection-AFM-label`). 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 :ref:`quant-analysis-label`. Here we describe how to setup and execute the first scan. .. index:: scanner panel, Setup .. _scanner-label: Setup and Scan ++++++++++++++ Three controls in the ``Scanner`` panel specify the parameters for ``Setup``. There must be a :ref:`current-calibration-label` in order for the setup to function. .. index:: oscillation range * ``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``. .. comment out next point, removed index:: modulation range * ``Mod. range`` is the range over which you want to modulate the amplitude. The amplitude will be modulated from the minimum value ( ``Osc. range`` - ``Mod. range`` ) to a maximum value ``Osc. range``. The tip-surface forces will be measured over this range. Typically you want to measure from zero deflection, up to the peak value of the cantilever deflection. In this case you set the modulation range to one half of the oscillation range. * ``Pixel rate (df)`` is the spacing :math:`\Delta f` between tones in the frequency comb (see :ref:`intermodulation-measurement-label`). 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 :ref:`out-of-range-label` message you may need to adjust the oscillation range or attenuate the input signal (see :ref:`advanced-setup-label`). This automatic setup is designed for basic |ImAFM (TM)| with two drive tones close to resonance. Much more complicated measurements and modulation schemes can be setup with the :ref:`drive-constructor-label`. 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 :ref:`status-bar-label`). 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: .. index:: Measure lift .. _measure-lift-label: 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 :ref:`background-comp-label`. 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 :ref:`background-comp-label`. .. index:: Set-point .. _set-point-label: Set-point +++++++++ ``Amplitude set-point`` is the set-point for the AFM scanning feedback. |ImAFM (TM)| 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 :ref:`feedback-setup-label`). 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. .. index:: Scan rate .. _scan-rate-label: 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 (TM)| 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. .. comment out You can also change to new values of ``Osc. range`` during a scan. Input the new values ad press ``Setup``. The cantilever will lift and perform a new setup routine, adjusting to the new parameters. However, you can not change the value of ``Pixel rate (df)`` without first stopping the scan and lifting away from the surface. .. index:: Image Settings, Amplitude image, Phase image, IMP Control, Line direction, Trace, Retrace, Swap, Flip up-dpwn, Flip right-left .. _image-settings-label: 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 :ref:`session-overview-label`. * ``Flip right-left`` and ``Flip up-down`` do not exchange trace and retrace data. This action can also be done later in the :ref:`session-overview-label`. * ``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 :ref:`associate-files-label`). .. index:: Color Bar .. _color-bar-label: Color Bar --------- The color bars have functionality for adjusting the images: .. image:: figures/color_bar.png :width: 75% :align: center * **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. .. index:: image toolbar, Home tool, Forward tool, Back tool, Pan-Zoom tool, Zoom tool, Save image tool .. _image-toolbar-label: Image Toolbar ------------- All plots and images have a toolbar with the following functions: .. |home_icon| image:: ../Icons/home.png :width: 5mm |home_icon| **Home** returns to the initial plot or the full image. .. index: zoom, pan .. |pan_zoom_icon| image:: ../Icons/move.png :width: 5mm |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| image:: ../Icons/zoom_to_rect.png :width: 5mm |zoom_icon| **Zoom** when selected, a right-click-and-drag over the plot will zoom to the selected rectangle upon release. .. index:: saving images .. |save_icon| image:: ../Icons/filesave.png :width: 5mm |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. .. index:: subplots .. |subplots_icon| image:: ../Icons/subplots.png :width: 5mm |subplots_icon| **Configure subplots** opens up a dialog box to adjust the placement of the plot axes within the plot frame. .. index:: Mouse wheel zooming .. _mouse-wheel-zooming-label: 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. .. index:: Pixel Inspector, Line Inspector 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-inspector-label: |pixel_icon| Pixel inspector tool --------------------------------- .. |pixel_icon| image:: ../Icons/icon128cross.png :width: 5mm 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 :ref:`signal-inspector-label` panel. If you have the :ref:`quant-analysis-label` tools installed in your software, the :ref:`force-inspector-label` 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 :ref:`data-tree-label`. The :ref:`quant-analysis-label` tools allow you to analyze the spectral data in many different ways to reveal tip-surface interaction. The :ref:`data-tree-label` allows you to compare different pixels form the same scan, or different scans, in the same plot. .. index:: Area inspector .. _area-inspector-label: |area_icon| Area inspector tool -------------------------------- .. |area_icon| image:: ../Icons/icon_lasso.png :width: 5mm 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 :ref:`quant-analysis-label` 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-inspector-label: |line_icon| Line inspector tool ------------------------------- .. |line_icon| image:: ../Icons/icon128line.png :width: 5mm 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 :ref:`quant-analysis-label` tools installed in your software, the line inspector will allow :ref:`analyze-line-label` and plot parameters of the tip-surface interaction along the selected transect. .. _clear-pixels-label: |clear_icon| Clear pixels tool ------------------------------ .. |clear_icon| image:: ../Icons/icon24cross_red.png :width: 5mm Removes all selected pixels from the image. .. _level-image-label: |level_icon| Level image tool ----------------------------- .. |level_icon| image:: ../Icons/data_level.png :width: 5mm Performs a plane fit to the amplitude and phase image data and subtracts off the plane, thereby flattening the data. .. index:: Status Bar .. _status-bar-label: 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. .. image:: figures/status_bar.png :width: 100% :align: center