Page 1 of 37

Software Manual

For afm+TM, nanoIRTM , and nanoIR2TM Systems

Part #00-0009-03 Issued March 2014 © 2014 by Anasys Instruments Inc, 325 Chapala St, Santa Barbara, CA 93101

Page 2 of 37

Table of contents Anasys Instruments office, service, trademarks 3 Chapter 1: The Document Window 4 1.1 Overview 4

AFM Map 5 Measurement Toolbar 6

1.2 File Menu 6 Export 6 Document Properties 8

1.3 Edit Menu 9 Under and Redo 10 Insert 10

1.4 Setup Menu 10 Initialize/Deinitialize 10 Initialize Stage 10 Hardware 11 Engage Settings 11 Video Settings 15 Edit Data Channels 15 Control Panels 15

1.5 Tools Menu 16 Thermal Tune 16 Video Capture 16

1.6 Help Menu 16 Chapter 2: Ramp and Spectrum Analysis 18 2.1 Process Functions 18

Arithmetic 18 Average 19 Gain 19 Normalize 19 Offset 20 Smooth 20 FFT 21 Filter 21 Derivative 21 Integral 21 Savitzky-Golay 21

2.2 Analyze Functions 22 Slope 22 Onset Temperature 22 Peak Find 23 Show all peaks 24 Intersect 24 Snap-In 25

Chapter 3: AFM Image Analysis 27 3.1 Process Functions 27

Flatten 27 Plane fit 28 Resolution 29

3.2 Analyze Functions 30 RGB Overlay 30

Histogram 31 Profile Analysis 32 Image Ratio 32 Calculate Drift 34 3D View 36

Page 3 of 37

Anasys Instruments Office

For information on our latest products and more, see our web site at: www.anasysinstruments.com Anasys Instruments Inc. 325 Chapala St. Santa Barbara, CA 93101 Email: support@anasysinstruments.com www.anasysinstruments.com Tel: (805) 730-3310 HELPLINE For assistance with applications or instrument service and repairs, please call the Anasys Instruments Help Desk at: (805) 730-3310 or email us at support@anasysinstruments.com

Anasys Instruments Trademarks ThermaLever™, nanoIR™, nanoIR2™, and afm+™ are trademarks of Anasys Instruments, 325 Chapala St., Santa Barbara, CA 93101

Page 4 of 37

Chapter 1 The Document Window

1.1 Overview The Document Window displays data that has been collected. All the software

menus are along the top of this window and the system status bar runs along the bottom. The status bar displays information such as which IR background file or nanoTA calibration file is loaded.

Figure 1-1: A new file opened in the Document Window (nanoTA™ mode).

As IR spectra or nanoTA ramps are acquired, the data are plotted in the Spectra/Ramp Graph. The name of each spectrum/ramp appears as a folder in the list along the left edge of the window. Spectra/ramps which are checked in the list are displayed in the graph. Individual data channels of a spectrum/ramp can be shown or hid in the graph as desired using the list. There is right-click functionality to select, hide, and show the spectra/ramps or their channels. To delete a spectra or ramp from a document, select it in the list and press Delete on the keyboard or right-click and select delete.

Figure 1-2: The Document Window after data collection (nanoIR™ mode).

Page 5 of 37

In a nanoTA document, the graph is a tabbed view. There is also a Data tab which

displays the selected data in a tabular format.

Figure 1-3: The Graph and Data tabs of a nanoTA document.

PLEASE NOTE: no data – spectra, ramps, or images - are saved until the document

is saved (File/Save). Each document is a tab in the window. Multiple documents can be open

simultaneously. Select File/Open or File/New to open or create a document. A document is closed by clicking the Close (X) button at the right edge of the window below the upper toolbar.

AFM Map The AFM Map on the right of the window does not appear until an image is written to

the document (via the Capture buttons on the Microscope window). The AFM Map displays all the AFM images of a certain data type (i.e. height or IR amplitude) in a spatial map.

Figure 1-4: The AFM Map.

A list of the AFM images is directly above the map. The top image in the list is the “top layer” of the map. For overlapping images, the image higher up in the list is displayed in the map. When a new image is captured, it is added at the top of the list. Click and drag on an image in the list to reorder it.

Global Coords. – By default, the lower left corner of the map is set at (0, 0). When Global Coordinates are used the true x,y scanner positions are displayed.

Page 6 of 37

Measurement Toolbar

Figure 1-5: The Measurement Toolbar on the Document Window. The measurement toolbar in the Document Window is unique to Analysis Studio. The buttons put the cursor into different modes which are used on the Spectra or Ramp Graph and the Image Map.

Pointer – Click and drag a vertical cursor on the Spectra/Ramp graph. In a nanoTA document, click a plot on the graph to select it in the ramp list.

Ruler – Draw a measurement line on the Image Map.

Pan – Click and drag on the Spectra/Ramp Graph or Image Map to move the field of view around. (Or hold the Ctrl key while dragging cursor)

Zoom In – Draw a box on the Spectra/Ramp Graph or Image Map to zoom in on that data. (Or press the Shift key while drawing a box on the graph).

Reset Zoom and Pan – Reset the Spectra/Ramp Graph and Image Map to their full views, clearing any zooms or pans.

Target – Click anywhere in the Image Map to move the probe to that location.

1.2 File Menu The commands in this menu are mostly standard commands used in any Windows program. There are two commands specific to Analysis Studio, Export and Document Properties.

Export Export has three functions: CSV, TSV, and Image. The first two functions export IR

spectra, nanoTA ramps, or an AFM image into a text file where each value is separated by either a comma (CSV) or a tab (TSV). The text file can be used to import the spectra, ramp, or image into other programs such as Excel.

The type of data, AFM or spectrum/ramp, to be exported is determined by which kind of data is currently selected (highlighted within their respective lists). Choose the data before opening the export function. To export AFM data, click the desired channel in the AFM Map Images list. To export spectra or ramp data, click its name in the list. Use shift-click and ctrl-click to highlight multiple spectra/ramps.

Figure 1-6: Selecting data for export. Left shows a spectrum selected; right shows an AFM channel selected.

Page 7 of 37

There are several options to customize a CSV or TSV export for spectrum/ramp data.

The Export Options dialog has a checkbox to include column headers. There are three options to specify which data to include in the export:

- Same as document - exports only the spectra/ramps and data channels currently displayed in the graph.

- All data - exports all the spectra/ramps (with all their data channels) in the document.

- Selection only - exports only the spectra/ramps (with all their data channels) highlighted in the list.

Figure 1-7: The Export Options menu for spectra/ramp CSV and TSV export. Export/Image creates a graphics file of the AFM Map and/or the Spectra/Ramp graph. There are several lay out and sizing options set in the “Export to Image” preview window.

Figure 1-8: The Export to Image preview window.

Page 8 of 37

Document Properties When File/Document Properties is selected, a Properties panel is displayed at the

right of the Document window.

Figure 1-9: Properties panel on the right of the Document window.

When a single spectrum name is highlighted in the Spectra List, the Properties menu displays information about that spectrum.

Figure 1-10: The Properties menu showing information about a spectrum.

When a single data channel of one of the Spectra or Ramps is highlighted in the list, the Properties menu displays information that includes how that data is displayed on the graph. All the graph related properties are editable. Select the property you want to edit and then click on the drop down arrow to see the available options (except for Point Size which is edited directly). ‘Color’ and ‘Style’ set the characteristics of the line drawing of the data. The ‘Point’ properties are the display options for the data points themselves, which are not shown by default (Point style = None).

Page 9 of 37

Figure 1-11: The Properties menu when an individual data channel is highlighted within a spectrum (left) or ramp (right).

The graphing properties of a single data channel can be applied to other data channels in the Spectra or Ramp list. In the list, right-click the data channel with the desired formatting and select “Copy format”. Now select the channels to be formatted. Right-click and select “Paste format”.

When a single data channel of one of the AFM maps is highlighted in the ‘AFM Map

Images’ list, the Properties menu displays information about that AFM image. If the AFM list is not visible, click the + symbol to the left of the “AFM Map Images” label (above the AFM Map display) to expand the list.

Figure 1-12: The Properties menu showing information about an AFM image.

1.3 Edit Menu The Edit menu has the standard delete function as well as a few functions specific to Analysis Studio that are covered below.

Page 10 of 37

Undo and Redo

The Undo function can be used after an analysis function that modifies the data to recover the original data. The Redo function reapplies the modification function. These functions do not recover deleted or unsaved data channels.

Insert

In a nanoTA document, the Insert function inserts either a folder into a document or a cursor into a ramp plot. Select Edit/Insert/Folder to add a new folder to the bottom of the ramp list. This can be helpful for organizing your experiment data. Data channels can be copied and pasted into other folders, including folders in other nanoTA documents. Use the copy and paste functions (in Edit menu or right-click functions) or click and drag channels from one folder to another in the list.

To insert a cursor into a ramp plot, highlight a single data channel in the ramp list. Then select Edit/Insert/Cursor. Once inserted, the cursor can be moved to another plot by dragging the word “cursor” to another data channel in the list. The Insert folder or cursor options can also be accessed by right-clicking on a ramp in the list.

1.4 Setup Menu The Setup menu has functions that ready the system for use and configure the desired measurement mode. Following is a list of the functions and a description of their use.

Initialize/Deinitialize The Initialize operation verifies communication between all the components and readies the hardware and software for use. When initialization is complete, the bottom status bar changes from “Not Initialized” to “Idle” and the command name changes to “Deinitialize”. Initializing may take a couple of minute). The deinitialize command can be used if the hardware will be turned off but the software will be left on. Alternatively, when the user exits the software it will automatically deinitialize the communications. There is an Initialize/Deinitialize button in the toolbar as a shortcut to these operations.

Initialize Stage This operation initializes the X, Y, and Z axes of the stage. The initialization starts with the Z motor finding a home pulse and moving the head to the top of its range. Then the X and Y motors drive to the edge of their ranges. If the “Return to previous X, Y position” is enabled, the stage will go back to the x and y coordinates it had before initialization.

Figure 1-13: The Stage Initialization window. The nanoIR2 system also has Optics in the Initialization for the motorized focus.

Page 11 of 37

Hardware This menu selects the system being used, either a NanoTA2, VESTA, afm+, nanoIR, or nanoIR2 system. For a nanoIR/2 system, this menu also sets the communication parameters between the computer and the controller. The only setting which may need to be different than those shown is the com port for the power meter on a nanoIR/2 system. The correct com port should be set during the installation but if the computer is changed the user can look in the Windows Device Manager function to see the ports and which com port the SXI-D power meter is assigned.

Figure 1-14: The Hardware Configuration panel for a nanoIR/2 (left) and afm+ (right) system.

Engage Settings The Engage Settings menu contains the parameters that control the computer-controlled approach of the probe to the sample, called the engage. This section gives a description of the engage process followed by descriptions of the available parameters.

The motion of bringing the tip toward the sample is done by two mechanisms, the Z motor and the Z Piezo. The probe is mounted on the end of the Z Piezo which provides very fine motion of the probe over a small range (~7 um). The Z motor provides coarse motion of the probe and Z Piezo together over a large vertical range. Contact Mode Engage:

When Engage is selected, the height feedback turns on. The initial Deflection is less than the Setpoint so the Z Piezo extends the probe toward the sample. The Z motor steps the probe and Z Piezo together toward the sample until the probe contacts the sample and the probe deflects upward. The Z Piezo retracts as needed to bring the probe’s Deflection to

Page 12 of 37

the Setpoint value. The Z motor continues to step toward the surface until the Z Piezo reaches the desired place in its range, at which point the engage process is complete.

Figure 1-15: The Engage Settings in Contact mode (advanced options shown). Contact Engage Force - The Setpoint for the height feedback used during the engage is equal to the Deflection when Engage is selected plus the Contact Engage Force. Setpoint = Initial Deflection + Contact Engage Force A smaller value is less force; a larger value is more force. Free Air Deflection Target - the target value for the deflection when the detector is being aligned during setup. The Target Deflection is the center value of the Deflection light bar on the AFM Probe panel where the light turns green. Sewing Engage – a gentler but slower engage process. The Z Piezo and Z motor are moved alternately to ensure the probe contacts the surface when only the Z Piezo is moving. This better limits the initial force between the tip and sample when they first contact. Use this function if the tip is being dulled or the sample is being damaged with the normal engage. (For more details on Sewing Engage see the tapping engage description below) Unload Height – on a nanoIR2 instrument only, the amount the sample is lowered when Unload is selected. I & P Gains - the integral and proportional gains used in the height feedback during the engage. Step Size – the increment the Z motor moves during the engage. A smaller Step Size makes the engage gentler but slower. Withdraw Height - distance the Z motor moves the probe up away from the sample when Withdraw is selected.

Page 13 of 37

Z Piezo Target - the desired position of the Z Piezo in its range when the engage is completed. The Z Piezo’s range of motion corresponds to +/- 10 V. Positive voltage is extended toward the surface; negative voltage is retracted away from the surface. The engage is triggered to stop when the Z Piezo’s voltage is less than or equal to the Z Piezo Target. Force-Reset Withdraw Height – the height the Z piezo moves the probe up during a Force-Reset to measure the free-air deflection or amplitude. (Force-Reset is described in the AFM Scan Panel section of the Standard AFM Modes Manual.) Deflection Flattening – corrects for the Deflection changes that result from the Z Piezo’s motion (rather than from the probe’s bending). Performed automatically at the very start of each Engage when the probe is off the surface, the Z Piezo runs through its full range and the variance in the Deflection signal is recorded. For all subsequent Deflection data, that variance is subtracted out (as a function of the Z Piezo voltage). Tapping Mode Engage:

In Tapping mode, the Sewing Engage is always used. In this mode the Z Piezo and Z motor are moved alternately to ensure the probe contacts the surface when only the Z Piezo is moving. When Engage is selected, the probe is moved down some distance by the Z Piezo with feedback on to look for the sample. If the sample is not detected, then feedback is disabled and the Z Piezo is retracted to pull the probe up out of the way. Then the Z Motor is clear to take one step down without bringing the probe into contact with the surface.

This cycle repeats until during one of the Z Piezo’s excursions, the Amplitude falls below the initial Setpoint. Then an engage-test is performed to determine whether the probe has really contacted the sample (or if the amplitude has just been decreased due to air damping or static from getting near to the sample). If the test passes the engage process is complete. If the test fails, then the Setpoint is further reduced and the cycle continues until the engage is completed.

Page 14 of 37

Figure 1-16: The Engage Settings in Tapping mode (advanced options shown).

Most of the engage parameters are the same between Contact and Tapping modes. The parameters that are specific to Tapping mode are covered below. Tapping Engage Force - The Initial Setpoint for the height feedback used during the engage is equal to the Amplitude when Engage is selected multiplied by the Tapping Engage Force.

Initial Set Point = (initial Amplitude)(Tapping Engage Force) A larger percentage is less force; a smaller percentage is more force. False-Engage Test Threshold - An engage test is performed whenever the amplitude Setpoint is reached to determine whether the probe has really contacted the sample. This test looks at the ratio of how much the Z Piezo must change position to change the Setpoint by a certain

amount, ΔZ/ΔAmplitude. If the probe is on the surface the Z Piezo will not have to move

much. If the ratio is smaller than the False-Engage Test Threshold the engage test passes.

Tapping Force Delta – If the engage test fails, then the Setpoint is reduced by the Tapping Force Delta percentage and the engage process continues. Tapping Force Limit – sets the minimum Setpoint allowed during the engage process.

Minimum Setpoint = (initial Amplitude)(Tapping Force Limit)

Page 15 of 37

Video Settings

Figure 1-17: The Video settings panel. Video Settings opens the Gain and Exposure controls for the camera. The Gain is a multiplier applied to the intensity of each pixel. The Exposure adjusts the shutter speed (integration time) of the camera.

Edit Data Channels This menu allows various properties of the Data Signals to be edited: the label (display name), units, gain, offset, and default color.

For the nanoTA related signals the gain and offset are set by the Sensitivity and SensitivityOffset. For all other signals the gain and offset are set by the Scale and Offset.

Figure 1-18: The Data Channels Editor.

Control Panels The Control Panels menu allows the user to select what mode the system is in - nanoIR (on nanoIR/2 systems), nanoTA, Sweep, Force Curves, nuDMA, or AFM Only. The corresponding control panel will be displayed in the bottom portion of the Controls window.

Page 16 of 37

1.5 Tools Menu The general tools that are not specific to a certain technique are covered in this

section. Other tools that are specific to nanoTA, nanoIR, and Tapping Mode are covered elsewhere: nanoTA Calibration nanoTA manual, Tools chapter

Clean Probe nanoTA manual, Tools chapter Cantilever Tune Standard AFM Modes manual, AFM Scan Panel sect. IR Background Calibration nanoIR/2 System manual

Thermal Tune This tool measures the resonant frequency (and higher harmonics) of the probe. The un-driven motion (or “thermal noise”) of the probe is monitored. Select “Acquire” and an FFT of the probe’s deflection is plotted. The FFT continuously averages until the “Stop” button is selected. Click and drag the vertical green cursor to measure the frequency of a peak. In the figure below the fundamental resonant frequency of the probe is ~23 kHz. Use the slider control near the bottom right of the window to zoom along the Frequency axis. Use the horizontal scroll bar to pan.

Figure 1-19: The Thermal Tune window.

Video Capture This tool saves a jpeg or bitmap of the current video image.

1.6 Help Menu The Help/About command displays the version of software and a link to email Anasys

Instruments’ support.

Page 17 of 37

Figure 1-20: The Help/About window.

Page 18 of 37

Chapter 2

Ramp and Spectrum Analysis There are various analysis functions that modify or measure nanoTA and nanoIR

data. To access these functions first select the data to be analyzed by clicking on it in the Ramp or Spectra list at the left of the document. Below is a summary of how each feature works.

2.1 Process Functions

Arithmetic This function performs basic arithmetic operations (addition, subtraction,

multiplication, and division) to the selected data sets. Add and Multiply can be performed on two or more sets of data. Subtract and Divide work only with two data sets at a time. The data sets must be the same signal type to perform any of the arithmetic functions. If the data does not cover the same voltage/temperature range the output will be truncated to the common range of data.

Figure 2-1: The Arithmetic/Subtract View Shown above is the subtract view as an example. The Add, Multiply and Divide views are similar in terms of their layout and functionality. For the subtract function, the user can select whether to subtract the first set of data from the second or the inverse by clicking on the top or bottom button in the lower left corner of the view. The user can also select the color of the output in the upper right and the name of the output in the lower middle. Once the output is correct, the user can click on the Accept button to return to the main view and add the output to the current document. The Reset and Preview buttons can be used to remove and recalculate the output plots if desired for scaling issues.

Page 19 of 37

Average

This function allows averaging of a number of plots within a document. The user selects the plots to be averaged by highlighting the plots in the Ramp or Spectra list at the left of the document and then selects Analysis/Average. The following view will appear allowing selection of the output color and name.

Figure 2-2: The Average View

Gain

This modify function can be used to multiply one or a number of plots by a constant value. The user needs to input the gain value, output name, and output color. Additionally the user can decide to overwrite the original data or make a new plot of the data with the gain applied by checking the “Make a copy” checkbox.

Normalize

There are two choices for Normalize – Constant and Converge. Normalize/Constant is used to take one or a number of data sets and scale and offset them such that the minimum value in the plot is set to 0 and the maximum value in the plot is set to a value determined by the user. For nanoTA, this allows a more direct comparison of the transition temperatures of data taken at different rates or with different offsets. As with the above modify function, the user needs to set a value that the data will be normalized to, the output name and the color, and then choose whether to overwrite the data or make a copy.

Normalize/Converge is very similar except that the user selects a position along the x axis, and the plots are scaled so that their corresponding y values are equal at that position. The x position is selecting by dragging a vertical cursor to the desired location. For nanoIR, normalizing may be used in some cases to compensate for effects on the amplitude due to

Page 20 of 37

variations in sample thickness or mechanical properties. It is generally most useful to normalize spectra at a specific wavenumber, so Converge is the appropriate choice.

Offset

The offset function has three capabilities. It can be used to offset one or more data sets by a constant value by using the Offset/Constant selection. All of the plots will be offset by the same amount. The user can select Offset/Cascade to vertically shift each of a number of plots by a fixed amount at a selected horizontal value. Cascade is generally used for display purposes, to make multiple data sets easier to view and qualitatively compare. The figure below shows the Offset/Cascade function. This function allows multiple curves to be offset vertically. The offset stride value in the lower left is the value that each curve will be offset by relative to the previous curve. The cursor is used to select the horizontal value that will be used to offset each curve. For nanoTA, a point close to the start voltage/temperature is usually selected.

Figure 2-3: The Offset/Cascade View Finally, the Offset/Converge function can be used to shift two or more plots to the same value by positioning a cursor at a horizontal location of the plots and then the software will shift all the plots such that the vertical value at that horizontal value is the same. In nanoTA, this is typically used when you have taken multiple data sets and due to drift or parameter changes within the AFM the vertical offset has shifted between the different plots.

Smooth

This function applies a user-defined level of smoothing to the selected data set or sets. As before, the user must first select the plots to operate on in the Ramp or Spectra list at the left of the document. Then the output name, output color, intensity of smoothing and whether to overwrite or make a copy is set in the Smooth view. The intensity of smoothing defines the number of pixels that will be averaged to generate the output data.

Page 21 of 37

FFT

Fast Fourier Transform is used to process modulating channels.

Filter These functions employ a low or high pass filter of user defined frequency and slope

to a selected data channel(s).

Derivative

This function calculates the derivative of a data channel. The user specifies an averaging width.

Integral This function calculates the integral of a data channel.

Savitzky-Golay

This function applies a Savitzky-Golay filter to one or more spectra or ramps for the purpose of smoothing the data. This is the recommended smoothing filter to use on IR Spectra because it is easier to preserve peak positions with Savitzky-Golay than it is with the Smooth Analysis.

A least squares polynomial fit is made for each successive data point using its adjacent data points. The Polynomial Order and the number of adjacent Side Points used in the fits are specified by the user. Good starting values to smooth out small noise without shifting IR absorption peaks are Polynomial Order = 7 and Side Points = 5.

Figure 2-4: The Savitzy-Golay smoothing function.

Page 22 of 37

2.2 Analyze Functions

Slope

This analysis function allows the user to measure the slope of one or a number of plots from a document by positioning two cursors on the plots. The x values of the two cursors are displayed as the “Min” and “Max” of the Range. The software then does a 1st order fit to the data between the two cursors for each plot and displays the slope values in a text box on the lower right side of the view. It also calculates the average and standard deviation of the slope values for all the plots.

Figure 2-5: The Slope analysis function.

Onset Temperature This analysis function calculates the onset temperature from nanoTA plots. Select

one or a number of plots for analysis and then select Analysis/Onset Temperature from the main menu. The dialog displays the data and two sets of cursors - one red set and one blue set. For each cursor pair, a straight line fit to the data between the two points defined by the cursors is extrapolated and the voltage/temperature (x-axis) value at the point these extrapolated lines cross is taken to be the onset temperature. A screen shot of the view is shown in the figure below.

Page 23 of 37

Figure 2-6: The Onset Temperature analysis function

In order to calculate the onset temperature, the user must first select an input plot; the default input is the first plot. Then the cursors are positioned so that one pair of cursors is on the portion of the plot that is slopping upwards and the second is on the portion that is sloping downwards. Once the cursors are the correct position, the user can add the output to the output list by clicking on the Add Output button. The user can then select the next input plot and if needed reposition the cursors and add that output to the list. If needed, an output can be removed from the list by selecting it with the mouse and clicking on the Remove Output button. To exit from the dialog, click on the Close button.

Peak Find Peak Find can be used on nanoTA data to automatically analyze one or a number of

temperature ramps to find the peak in the ramp corresponding to a transition temperature. The function works by moving a fit window along the data looking for a peak in the data. This window size can be adjusted by changing the Peak fit width parameter. Typically the analysis will find a number of peaks within any data set. The specific peak desired can be selected by using a number of criteria including the peak with the largest or smallest Y value or the peak with the largest or smallest X value. Alternatively all peaks detected can be displayed. Additionally a range can be selected such that only peaks above or below a limit will be selected. This is useful if the temperature ramp contains a peak both from a Tg as well as an onset of the melting. The typical settings are to use the full range and select the peak with the largest Y value as shown in the example below.

Page 24 of 37

Figure 2-7: The Peak Find analysis function

Show All Peaks

If a data channel contains multiple peaks this function will calculate the peaks in the same method as peak find however multiple peaks will be identified and labeled in the plot. This is useful for identifying absorption peaks in nanoIR spectra as shown below.

Figure 2-8: The Show All Peaks window.

Intersect This function returns the y value from multiple nanoTA or nanoIR data sets at a user

selected x position. A vertical line cursor is positioned to define an x position (a voltage,

Page 25 of 37

temperature, or wavenumber) and the corresponding y value is determined from each data set.

Figure 2-9: The Intersect window.

Snap-In

The Snap-In function was developed to measure the Adhesion (Snap-Off in Deflection) and the SThM Snap-In of Force Curves.

Figure 2-10: Adhesion and SThM Snap-In are the typical measurements made with Snap-In analysis on Force Curves.

The Snap-In function first takes a derivative of the data (for example, “Deflection Up” data if Adhesion is the desired measurement). The Z position with the largest slope (highest peak in the derivative) is determined to be the step location. On both sides of the step, a best fit line is fitted to the data. The step height is the determined by the intersection of a vertical line at the step position with the 2 best-fits.

Page 26 of 37

Figure 2-11: The Snap-In analysis. Averaging Width – number of points in a sliding average done on the data before the derivative is taken to determine the step position. Exclusion Width – Z distance from the step that is not included in the data used for the best-fit lines. Often there is some roll-off or transient behavior after a step that is useful to exclude in the line fits. Slope Fit Width – Z length of the best-fit lines.

Page 27 of 37

Chapter 3

AFM Image Analysis

There are various analysis functions that modify or examine AFM images. To access these functions first select the image to be analyzed by clicking on it in the AFM Map images list. Below is a summary of how each feature works.

3.1 Process Functions

Flatten The flatten function performs a fit separately to each line of data in the image. It is

typically used to remove line artifacts from the image.

Figure 3-1: Flatten - the top image is the original data; bottom is flattened data.

Line artifacts are common in AFM imaging. As the probe scans the sample surface, small bits of loose material can stick to the end of the probe erroneously changing the effective height of the sample. When the debris scrapes back off, another artifact is generated. Line artifacts can also be due to low frequency mechanical noise (ex. floor motion) that is too low to be effectively damped by the vibration isolation being used. This is generally only a problem on very smooth samples where the surface roughness is small in comparison with the artifacts.

Line

Artifacts Original

Flattened

Page 28 of 37

Figure 3-2: The Flatten window.

The type of fit, Line (1st order polynomial) or Offset (0th order polynomial), is chosen from the Flatten Method drop-down list. The “Show original” and “Show modified” buttons allow the user to switch between viewing the original image and viewing the image resulting from the fitted data. To overwrite the original image with the flattened image, select the “Accept” button. The change will be reflected in the image displayed in the AFM Map. To create a new image with the flattened data (and preserve the original image unchanged), select the “Make a copy” option and then select the “Accept” button. The new flattened image will appear in the “AFM Map Images” list directly above the original image. To leave the Flatten function without making any changes, select the “Cancel” button. It can be useful to exclude areas of the image from the fit calculation. In the image above, there is step edge along the right side that would be appropriate to exclude. Select

the exclusion box icon on the toolbar and use the cursor to draw one or more boxes around the area to be excluded. The fit will be calculated without using the data in those areas. An exclusion box can be removed by selecting it (clicking on one of its sides) and then hitting the Delete key on the keyboard.

Plane Fit The Plane Fit function performs a single fit to the entire image. It is used to remove

offset or tilt from images.

Page 29 of 37

Figure 3-3: Plane Fit: The left image is the original data; right is the plane-fitted data (1st order in X and Y).

Figure 3-4: The Plane Fit window.

The type of plane fit, Linear (1st order) or Offset (0th order), is chosen from the Fit Order drop-down list. Whether to fit both axes or only X or Y is chosen via the radio buttons. The “Show original” and “Show modified” buttons allow the user to switch between viewing the original image and viewing the fitted image. To overwrite the original image with the fitted image, select the “Accept” button. The change will be reflected in the image displayed in the AFM Map. To create a new image with the fitted data (and preserve the original image unchanged), select the “Make a copy” option and then select the “Accept” button. The new fitted image will appear in the “AFM Map Images” list directly above the original image. To leave the Plane Fit function without making any changes, select the “Cancel” button. It can be useful to exclude areas of the image from the plane fit calculation. Select

the exclusion box icon on the toolbar and use the cursor to draw one or more boxes around the area to be excluded. The plane fit will be calculated without using the data in those areas. An exclusion box can be removed by selecting it (clicking on one of its sides) and then hitting the Delete key on the keyboard.

Resolution The Resolution function interpolates between pixels to offer enhanced image

resolution. It is designed for TTM (Transition Temperature Microscopy) images where the

Page 30 of 37

pixel size to image size ratio is generally quite large. The Resolution function is only used to generate a graphic image; the enhanced data cannot be saved into the document as an image.

3.2 Analyze Functions

RGB Overlay

RGB Overlay superimposes 2 images of the same size. The RGB (red, green, blue) color components can be manipulated independently for each image. This is typically done with a height image and another image such as phase or IR Peak that was collected simultaneously.

Figure 3-5: Top: Height image in green (left), IR Peak image in red (right).

Bottom: The resulting RGB Overlay image.

Page 31 of 37

Histogram This function generates a histogram of the image data. The histogram is a plot of the

number of points in the image that fall within consecutive bins of the overall range of the data.

Figure 3-6: The Histogram window. In the figure above, a height image is being analyzed. The user specifies the Number of bins to be used in the plot. By default, the width of each bin is the range of the image data (Rmax) divided by the number of bins. For a height image, the histogram’s x axis represents height and each bin spans a subset of the overall range of heights. The histogram’s y axis is the number of points in the image that have a height value within the range spanned by each bin. The Max/Min Control defaults to Automatic which sets the upper and lower limits of the x axis equal to the limits of the image’s data range. The limits of the x axis can be adjusted manually by disabling the Automatic option. Note that this will directly affect the width of the bins (bin width = plot width/# of bins). The histogram plot can be saved as a graphics file via the “Save Image” button. It can be useful to exclude areas of the image from the histogram and statistics. Click the Select Regions button on the Histogram toolbar. Then click and drag on the image to create one or more exclusion boxes. The data inside these boxes will not be included in the histogram plot or the related statistics. To remove an exclusion box select it (click on one of its sides) and then click the Clear button. To remove all exclusion boxes, click Clear All.

Various statistics from the image data are reported as described below. RMS – Root Mean Square of the image data. This will be the same as the Standard Deviation unless the Mean is non-zero. Rmax – Range of the image data (Zmax – Zmin). SD – Standard Deviation. Rsk – Skew. Mean – Average value of the image data. Ra – Mean Absolute Deviation. Rku – Kurtosis.

Page 32 of 37

The histogram data can be exported to a CSV file or the plot can be saved as a graphics file via buttons on the toolbar.

Profile Analysis This function allows the user to examine one or more profiles through the image data.

Figure 3-7: The Profile Analysis window.

The location of a profile is specified by drawing a line on the image. For a profile at any angle, click and drag on the image to define the line. Shift-click on the image to draw a horizontal line. Control-click for a vertical line. Each profile plot has two cursors (gray crosses) from which measurements are made. The corresponding locations of the cursors in the image are represented by two hash marks on the line. To change the location of a cursor, click and drag the gray cross to the desired point on the profile. To remove all profile lines select the “Clear” button.

Measurements are displayed for whichever profile is currently selected. A profile is selected by clicking on its plot; the plot will become bold. In-plane distance – Distance between the two cursor positions in the x-y plane. Vertical distance – Distance between the two cursor positions in the vertical direction (z axis). Surface distance – Length of the profile following the surface contours between the two cursors.

Image Ratio

This function divides 2 images of the same data type to create an image of their ratio. This is typically used on two IR images done at the same location with different wave numbers. To be suitable for this analysis, images must be saved with Capture Fit = None.

Page 33 of 37

Figure 3-8: Starting height (left) and IR (right) images for Image Ratio analysis.

With any image selected in the image list, open the Image Ratio analysis. All the open documents and their images are listed. Drag the names of 2 images from the list into the Ratio Map 1 and 2 fields. Map 1 will be the numerator, Map 2 the denominator. Note that the IR images shown above were Plane fit but their corresponding raw images are selected for analysis.

Figure 3-9: Selecting Files for Image Ratio analysis. Select the 2 corresponding height images and drag them from the list into the Correlation height Map 1 and 2 fields. Click Continue.

Page 34 of 37

Cross-correlate Inputs – compares 2 images (usually Height) to determine the lateral shift between them from thermal drift. The offset is corrected so the ratio images are better aligned.

Figure 3-10: Image Ratio result. The resulting image can be saved as a graphics file or exported to CSV. Scale – multiplies the numerator by this factor.

Calculate Drift

This function calculates the nominal thermal drift by determining the lateral shift between two images at the same x,y location taken some time apart. The drift results can be entered into the Drift Correction section of the AFM Scan panel to apply the vector to the XY sample stage in real-time. Drift Correction is only effective if the thermal drift is constant in both rate and direction.

Page 35 of 37

Figure 3-11: Example height images for Calculate Drift analysis.

Capture two height images with identical scan parameters some time apart on an area with distinct topographical features. With any image selected, open the Calculate Drift analysis. All the open documents and their images are listed. Drag the names of the 2 images from the list into the Map 1 and Map 2 fields. Map 1 should be the image that was collected first.

Figure 3-12: Calculate Drift analysis correlation result.

The shift between the images is determined using a correlation function. The resulting image shows the correlation in the overlapping area of the images after the second image is shifted. Offset – lateral shift between the images.

Page 36 of 37

Bearing – direction of the drift (angle of the Drift Vector).

Figure 3-13: Bearing angle. Drift Velocity – rate of the drift in nm/minute (magnitude of the Drift Vector).

3D View

This function displays an image in a 3D view. The Z information of the image (whatever the data type - height, IR amplitude, phase, etc.) is used to create contours as well as the color scale.

Figure 3-14: 3D View of height image.

The 3 primary controls of the 3D View can be changed via the slider bars, entering a value, or moving the mouse.

Spin – rotates the image in xy around the center point (click and hold, move mouse left/right). Pitch – tilts the image from side view to top view (click and hold, move mouse up/down) Zoom – resizes the displayed image (mouse scroll wheel).

There are separate controls for the Z Ranges of the contours and the color scale.

Height Z Range – sets the scale of the Z contours (a smaller Range makes taller contours). Z Range – sets the range of the color palette.

Page 37 of 37

Figure 3-15: 3D View with height image alone (top) and with 2 images: phase color superimposed on height contours (bottom).

The 3D View can also combine together 2 images of the same size, using the Z data from one image for the contours and the Z data from the other image for the color. This is typically done with a height image and another image such as phase or IR Peak that was collected simultaneously.